Starting phenix.real_space_refine on Sat Feb 17 16:49:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqh_21350/02_2024/6vqh_21350.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqh_21350/02_2024/6vqh_21350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqh_21350/02_2024/6vqh_21350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqh_21350/02_2024/6vqh_21350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqh_21350/02_2024/6vqh_21350.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqh_21350/02_2024/6vqh_21350.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 109 5.16 5 C 12438 2.51 5 N 3246 2.21 5 O 3545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 139": "OE1" <-> "OE2" Residue "g TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 139": "OE1" <-> "OE2" Residue "i TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 139": "OE1" <-> "OE2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 139": "OE1" <-> "OE2" Residue "k TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 139": "OE1" <-> "OE2" Residue "n PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 139": "OE1" <-> "OE2" Residue "o TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19338 Number of models: 1 Model: "" Number of chains: 18 Chain: "H" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 803 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 1, 'TRANS': 102} Chain: "L" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "a" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 2173 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 386} Link IDs: {'PTRANS': 18, 'TRANS': 422} Chain breaks: 2 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1513 Unresolved non-hydrogen angles: 1961 Unresolved non-hydrogen dihedrals: 1323 Unresolved non-hydrogen chiralities: 140 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 7, 'TYR:plan': 19, 'ASN:plan1': 21, 'TRP:plan': 9, 'HIS:plan': 15, 'PHE:plan': 45, 'GLU:plan': 17, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 816 Chain: "b" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1503 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "c" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 337 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "d" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2833 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain: "e" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 384 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 137 Chain: "f" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 412 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 337 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 141 Chain: "g" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "h" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "i" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "j" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "p" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 406 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 10.22, per 1000 atoms: 0.53 Number of scatterers: 19338 At special positions: 0 Unit cell: (120.84, 119.78, 162.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 109 16.00 O 3545 8.00 N 3246 7.00 C 12438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.99 Conformation dependent library (CDL) restraints added in 3.7 seconds 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5030 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 3 sheets defined 81.5% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'H' and resid 50 through 77 Processing helix chain 'H' and resid 79 through 86 Processing helix chain 'H' and resid 127 through 153 removed outlier: 3.622A pdb=" N THR H 153 " --> pdb=" O ALA H 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 23 Processing helix chain 'L' and resid 44 through 57 Processing helix chain 'L' and resid 68 through 74 Processing helix chain 'L' and resid 74 through 81 removed outlier: 3.804A pdb=" N LEU L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS L 81 " --> pdb=" O ALA L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 109 Processing helix chain 'a' and resid 370 through 380 removed outlier: 4.462A pdb=" N PHE a 374 " --> pdb=" O PHE a 370 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 407 removed outlier: 4.686A pdb=" N ILE a 397 " --> pdb=" O PRO a 393 " (cutoff:3.500A) Proline residue: a 400 - end of helix Processing helix chain 'a' and resid 409 through 426 Processing helix chain 'a' and resid 426 through 432 Processing helix chain 'a' and resid 437 through 446 Processing helix chain 'a' and resid 446 through 465 Processing helix chain 'a' and resid 481 through 488 removed outlier: 3.631A pdb=" N ILE a 487 " --> pdb=" O PRO a 483 " (cutoff:3.500A) Processing helix chain 'a' and resid 492 through 497 removed outlier: 4.320A pdb=" N LEU a 496 " --> pdb=" O GLU a 492 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 500 No H-bonds generated for 'chain 'a' and resid 498 through 500' Processing helix chain 'a' and resid 520 through 526 Processing helix chain 'a' and resid 528 through 563 removed outlier: 4.577A pdb=" N ASN a 534 " --> pdb=" O LEU a 530 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER a 556 " --> pdb=" O GLY a 552 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU a 557 " --> pdb=" O VAL a 553 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE a 558 " --> pdb=" O SER a 554 " (cutoff:3.500A) Processing helix chain 'a' and resid 565 through 571 removed outlier: 3.812A pdb=" N ILE a 569 " --> pdb=" O LYS a 565 " (cutoff:3.500A) Processing helix chain 'a' and resid 572 through 598 removed outlier: 4.228A pdb=" N TYR a 586 " --> pdb=" O SER a 582 " (cutoff:3.500A) Processing helix chain 'a' and resid 599 through 603 Processing helix chain 'a' and resid 608 through 619 Processing helix chain 'a' and resid 632 through 647 Processing helix chain 'a' and resid 647 through 667 removed outlier: 3.560A pdb=" N MET a 651 " --> pdb=" O CYS a 647 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LYS a 655 " --> pdb=" O MET a 651 " (cutoff:3.500A) Proline residue: a 656 - end of helix Processing helix chain 'a' and resid 713 through 739 removed outlier: 3.572A pdb=" N ILE a 733 " --> pdb=" O CYS a 729 " (cutoff:3.500A) Processing helix chain 'a' and resid 739 through 759 removed outlier: 4.259A pdb=" N TRP a 743 " --> pdb=" O TYR a 739 " (cutoff:3.500A) Processing helix chain 'a' and resid 761 through 765 Processing helix chain 'a' and resid 768 through 791 Processing helix chain 'a' and resid 793 through 810 Processing helix chain 'a' and resid 811 through 815 Processing helix chain 'b' and resid 3 through 29 Processing helix chain 'b' and resid 36 through 44 Processing helix chain 'b' and resid 45 through 80 removed outlier: 3.602A pdb=" N TRP b 49 " --> pdb=" O SER b 45 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER b 75 " --> pdb=" O ILE b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 81 through 82 No H-bonds generated for 'chain 'b' and resid 81 through 82' Processing helix chain 'b' and resid 83 through 84 No H-bonds generated for 'chain 'b' and resid 83 through 84' Processing helix chain 'b' and resid 85 through 90 removed outlier: 4.085A pdb=" N LYS b 89 " --> pdb=" O ARG b 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 113 Processing helix chain 'b' and resid 127 through 169 removed outlier: 3.928A pdb=" N GLN b 168 " --> pdb=" O LEU b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 172 through 198 removed outlier: 4.197A pdb=" N ILE b 178 " --> pdb=" O VAL b 174 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL b 179 " --> pdb=" O LYS b 175 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU b 180 " --> pdb=" O ILE b 176 " (cutoff:3.500A) Processing helix chain 'c' and resid 416 through 442 Processing helix chain 'd' and resid 8 through 25 removed outlier: 4.126A pdb=" N ASP d 12 " --> pdb=" O TYR d 8 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR d 15 " --> pdb=" O VAL d 11 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU d 16 " --> pdb=" O ASP d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 38 Processing helix chain 'd' and resid 41 through 50 Processing helix chain 'd' and resid 66 through 88 Processing helix chain 'd' and resid 90 through 116 removed outlier: 4.899A pdb=" N PHE d 96 " --> pdb=" O PRO d 92 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE d 100 " --> pdb=" O PHE d 96 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR d 114 " --> pdb=" O ILE d 110 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY d 115 " --> pdb=" O LEU d 111 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 126 Processing helix chain 'd' and resid 127 through 129 No H-bonds generated for 'chain 'd' and resid 127 through 129' Processing helix chain 'd' and resid 146 through 157 Processing helix chain 'd' and resid 158 through 167 removed outlier: 4.100A pdb=" N ALA d 162 " --> pdb=" O PRO d 159 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP d 166 " --> pdb=" O PHE d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 170 through 176 Processing helix chain 'd' and resid 177 through 200 Processing helix chain 'd' and resid 202 through 227 Proline residue: d 210 - end of helix Processing helix chain 'd' and resid 228 through 230 No H-bonds generated for 'chain 'd' and resid 228 through 230' Processing helix chain 'd' and resid 233 through 240 removed outlier: 3.636A pdb=" N LEU d 240 " --> pdb=" O ASP d 236 " (cutoff:3.500A) Processing helix chain 'd' and resid 251 through 258 Processing helix chain 'd' and resid 260 through 269 Processing helix chain 'd' and resid 271 through 281 removed outlier: 4.438A pdb=" N LEU d 277 " --> pdb=" O GLU d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 305 Processing helix chain 'd' and resid 306 through 308 No H-bonds generated for 'chain 'd' and resid 306 through 308' Processing helix chain 'd' and resid 312 through 338 removed outlier: 3.708A pdb=" N TYR d 316 " --> pdb=" O PHE d 312 " (cutoff:3.500A) Processing helix chain 'd' and resid 340 through 344 Processing helix chain 'e' and resid 6 through 23 Processing helix chain 'e' and resid 24 through 27 Processing helix chain 'e' and resid 33 through 58 Processing helix chain 'e' and resid 69 through 78 removed outlier: 3.575A pdb=" N ARG e 77 " --> pdb=" O ILE e 73 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE e 78 " --> pdb=" O TRP e 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 36 Processing helix chain 'f' and resid 54 through 90 removed outlier: 3.967A pdb=" N ILE f 58 " --> pdb=" O GLY f 54 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 46 removed outlier: 3.614A pdb=" N PHE g 14 " --> pdb=" O TYR g 10 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET g 23 " --> pdb=" O ALA g 19 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER g 26 " --> pdb=" O ALA g 22 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL g 46 " --> pdb=" O ALA g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 52 Processing helix chain 'g' and resid 53 through 55 No H-bonds generated for 'chain 'g' and resid 53 through 55' Processing helix chain 'g' and resid 56 through 78 Processing helix chain 'g' and resid 86 through 124 Processing helix chain 'g' and resid 127 through 153 removed outlier: 3.838A pdb=" N SER g 153 " --> pdb=" O ALA g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 46 removed outlier: 4.421A pdb=" N GLY h 15 " --> pdb=" O SER h 11 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL h 46 " --> pdb=" O ALA h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 52 Processing helix chain 'h' and resid 56 through 78 Processing helix chain 'h' and resid 86 through 124 Processing helix chain 'h' and resid 126 through 154 removed outlier: 4.454A pdb=" N GLY h 130 " --> pdb=" O ARG h 126 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY h 145 " --> pdb=" O LEU h 141 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR h 154 " --> pdb=" O LEU h 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 10 through 48 removed outlier: 4.083A pdb=" N PHE i 14 " --> pdb=" O TYR i 10 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY i 15 " --> pdb=" O SER i 11 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET i 23 " --> pdb=" O ALA i 19 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER i 26 " --> pdb=" O ALA i 22 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 52 Processing helix chain 'i' and resid 56 through 78 Processing helix chain 'i' and resid 86 through 124 removed outlier: 3.900A pdb=" N GLN i 123 " --> pdb=" O ARG i 119 " (cutoff:3.500A) Processing helix chain 'i' and resid 126 through 154 removed outlier: 4.604A pdb=" N GLY i 130 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY i 145 " --> pdb=" O LEU i 141 " (cutoff:3.500A) Processing helix chain 'j' and resid 11 through 48 removed outlier: 4.302A pdb=" N GLY j 15 " --> pdb=" O SER j 11 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET j 23 " --> pdb=" O ALA j 19 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL j 46 " --> pdb=" O ALA j 42 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N MET j 47 " --> pdb=" O ALA j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 49 through 52 Processing helix chain 'j' and resid 53 through 55 No H-bonds generated for 'chain 'j' and resid 53 through 55' Processing helix chain 'j' and resid 56 through 78 removed outlier: 3.614A pdb=" N ILE j 64 " --> pdb=" O VAL j 60 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE j 65 " --> pdb=" O MET j 61 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA j 66 " --> pdb=" O ALA j 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 86 through 124 Processing helix chain 'j' and resid 126 through 154 removed outlier: 4.483A pdb=" N GLY j 130 " --> pdb=" O ARG j 126 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY j 145 " --> pdb=" O LEU j 141 " (cutoff:3.500A) Processing helix chain 'k' and resid 10 through 48 removed outlier: 3.898A pdb=" N PHE k 14 " --> pdb=" O TYR k 10 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY k 15 " --> pdb=" O SER k 11 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET k 23 " --> pdb=" O ALA k 19 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL k 46 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET k 47 " --> pdb=" O ALA k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 52 Processing helix chain 'k' and resid 53 through 55 No H-bonds generated for 'chain 'k' and resid 53 through 55' Processing helix chain 'k' and resid 56 through 80 Processing helix chain 'k' and resid 86 through 124 Processing helix chain 'k' and resid 127 through 154 Processing helix chain 'l' and resid 11 through 48 removed outlier: 4.417A pdb=" N GLY l 15 " --> pdb=" O SER l 11 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA l 43 " --> pdb=" O THR l 39 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL l 46 " --> pdb=" O ALA l 42 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 52 Processing helix chain 'l' and resid 53 through 55 No H-bonds generated for 'chain 'l' and resid 53 through 55' Processing helix chain 'l' and resid 56 through 80 Processing helix chain 'l' and resid 86 through 124 removed outlier: 3.737A pdb=" N GLN l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 126 through 155 removed outlier: 4.390A pdb=" N GLY l 130 " --> pdb=" O ARG l 126 " (cutoff:3.500A) Processing helix chain 'm' and resid 10 through 45 removed outlier: 3.641A pdb=" N SER m 26 " --> pdb=" O ALA m 22 " (cutoff:3.500A) Processing helix chain 'm' and resid 46 through 47 No H-bonds generated for 'chain 'm' and resid 46 through 47' Processing helix chain 'm' and resid 48 through 55 removed outlier: 4.732A pdb=" N MET m 53 " --> pdb=" O GLU m 50 " (cutoff:3.500A) Processing helix chain 'm' and resid 56 through 80 Processing helix chain 'm' and resid 86 through 124 removed outlier: 3.989A pdb=" N GLN m 123 " --> pdb=" O ARG m 119 " (cutoff:3.500A) Processing helix chain 'm' and resid 126 through 154 removed outlier: 4.365A pdb=" N GLY m 130 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY m 145 " --> pdb=" O LEU m 141 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR m 154 " --> pdb=" O LEU m 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 46 removed outlier: 4.512A pdb=" N GLY n 15 " --> pdb=" O SER n 11 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET n 23 " --> pdb=" O ALA n 19 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL n 46 " --> pdb=" O ALA n 42 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 52 Processing helix chain 'n' and resid 56 through 79 removed outlier: 3.567A pdb=" N SER n 79 " --> pdb=" O LEU n 75 " (cutoff:3.500A) Processing helix chain 'n' and resid 86 through 124 removed outlier: 3.590A pdb=" N ARG n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 126 through 154 removed outlier: 4.631A pdb=" N GLY n 130 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY n 145 " --> pdb=" O LEU n 141 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR n 154 " --> pdb=" O LEU n 150 " (cutoff:3.500A) Processing helix chain 'o' and resid 10 through 48 removed outlier: 4.311A pdb=" N PHE o 14 " --> pdb=" O TYR o 10 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY o 15 " --> pdb=" O SER o 11 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET o 47 " --> pdb=" O ALA o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 52 Processing helix chain 'o' and resid 53 through 55 No H-bonds generated for 'chain 'o' and resid 53 through 55' Processing helix chain 'o' and resid 56 through 80 removed outlier: 3.527A pdb=" N VAL o 60 " --> pdb=" O ILE o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 86 through 124 Processing helix chain 'o' and resid 127 through 154 removed outlier: 3.662A pdb=" N THR o 154 " --> pdb=" O LEU o 150 " (cutoff:3.500A) Processing helix chain 'p' and resid 302 through 330 Processing helix chain 'p' and resid 338 through 343 Processing sheet with id=AA1, first strand: chain 'H' and resid 93 through 99 Processing sheet with id=AA2, first strand: chain 'L' and resid 36 through 38 removed outlier: 8.550A pdb=" N LEU L 37 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL L 10 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA L 9 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ASN L 67 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ILE L 11 " --> pdb=" O ASN L 67 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE L 64 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE L 91 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE L 66 " --> pdb=" O ILE L 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'a' and resid 362 through 363 1741 hydrogen bonds defined for protein. 5118 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.49 Time building geometry restraints manager: 8.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3210 1.30 - 1.43: 4702 1.43 - 1.56: 11493 1.56 - 1.68: 0 1.68 - 1.81: 205 Bond restraints: 19610 Sorted by residual: bond pdb=" C PRO H 107 " pdb=" O PRO H 107 " ideal model delta sigma weight residual 1.233 1.171 0.062 1.13e-02 7.83e+03 3.06e+01 bond pdb=" N PRO c 417 " pdb=" CD PRO c 417 " ideal model delta sigma weight residual 1.473 1.543 -0.070 1.40e-02 5.10e+03 2.52e+01 bond pdb=" N PRO L 86 " pdb=" CD PRO L 86 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.87e+01 bond pdb=" CA ALA L 109 " pdb=" CB ALA L 109 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.38e-02 5.25e+03 1.67e+01 bond pdb=" N GLN h 124 " pdb=" CA GLN h 124 " ideal model delta sigma weight residual 1.462 1.419 0.043 1.06e-02 8.90e+03 1.63e+01 ... (remaining 19605 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.39: 435 106.39 - 113.24: 10874 113.24 - 120.08: 7409 120.08 - 126.93: 7831 126.93 - 133.77: 98 Bond angle restraints: 26647 Sorted by residual: angle pdb=" C ILE L 91 " pdb=" N PRO L 92 " pdb=" CA PRO L 92 " ideal model delta sigma weight residual 119.76 127.74 -7.98 1.00e+00 1.00e+00 6.37e+01 angle pdb=" C ARG L 108 " pdb=" N ALA L 109 " pdb=" CA ALA L 109 " ideal model delta sigma weight residual 123.05 112.32 10.73 1.40e+00 5.10e-01 5.88e+01 angle pdb=" N SER L 104 " pdb=" CA SER L 104 " pdb=" C SER L 104 " ideal model delta sigma weight residual 111.82 103.06 8.76 1.16e+00 7.43e-01 5.70e+01 angle pdb=" C ASN m 7 " pdb=" N PRO m 8 " pdb=" CA PRO m 8 " ideal model delta sigma weight residual 119.76 127.31 -7.55 1.03e+00 9.43e-01 5.37e+01 angle pdb=" N GLN d 171 " pdb=" CA GLN d 171 " pdb=" C GLN d 171 " ideal model delta sigma weight residual 111.33 102.55 8.78 1.21e+00 6.83e-01 5.26e+01 ... (remaining 26642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11062 17.93 - 35.87: 285 35.87 - 53.80: 87 53.80 - 71.73: 18 71.73 - 89.67: 23 Dihedral angle restraints: 11475 sinusoidal: 3573 harmonic: 7902 Sorted by residual: dihedral pdb=" CA ILE a 793 " pdb=" C ILE a 793 " pdb=" N MET a 794 " pdb=" CA MET a 794 " ideal model delta harmonic sigma weight residual 180.00 -160.57 -19.43 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PRO p 292 " pdb=" C PRO p 292 " pdb=" N TYR p 293 " pdb=" CA TYR p 293 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA GLN d 119 " pdb=" C GLN d 119 " pdb=" N ARG d 120 " pdb=" CA ARG d 120 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 11472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2210 0.063 - 0.125: 878 0.125 - 0.188: 99 0.188 - 0.250: 75 0.250 - 0.313: 6 Chirality restraints: 3268 Sorted by residual: chirality pdb=" CA TYR o 68 " pdb=" N TYR o 68 " pdb=" C TYR o 68 " pdb=" CB TYR o 68 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA TYR l 68 " pdb=" N TYR l 68 " pdb=" C TYR l 68 " pdb=" CB TYR l 68 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA TYR m 68 " pdb=" N TYR m 68 " pdb=" C TYR m 68 " pdb=" CB TYR m 68 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 3265 not shown) Planarity restraints: 3401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU o 86 " -0.023 2.00e-02 2.50e+03 4.59e-02 2.10e+01 pdb=" C LEU o 86 " 0.079 2.00e-02 2.50e+03 pdb=" O LEU o 86 " -0.030 2.00e-02 2.50e+03 pdb=" N TYR o 87 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN k 7 " -0.022 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C ASN k 7 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN k 7 " -0.028 2.00e-02 2.50e+03 pdb=" N PRO k 8 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU d 160 " 0.019 2.00e-02 2.50e+03 3.99e-02 1.60e+01 pdb=" C LEU d 160 " -0.069 2.00e-02 2.50e+03 pdb=" O LEU d 160 " 0.026 2.00e-02 2.50e+03 pdb=" N ALA d 161 " 0.023 2.00e-02 2.50e+03 ... (remaining 3398 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 7273 2.85 - 3.36: 21816 3.36 - 3.87: 32693 3.87 - 4.39: 38695 4.39 - 4.90: 61389 Nonbonded interactions: 161866 Sorted by model distance: nonbonded pdb=" NZ LYS H 55 " pdb=" OD2 ASP L 99 " model vdw 2.336 2.520 nonbonded pdb=" OD1 ASP d 12 " pdb=" NZ LYS g 36 " model vdw 2.341 2.520 nonbonded pdb=" O LEU n 86 " pdb=" OG SER n 89 " model vdw 2.354 2.440 nonbonded pdb=" O PRO d 249 " pdb=" NE2 GLN m 123 " model vdw 2.355 2.520 nonbonded pdb=" O PRO i 8 " pdb=" OG SER i 11 " model vdw 2.357 2.440 ... (remaining 161861 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.350 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 51.260 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 19610 Z= 0.540 Angle : 1.001 10.860 26647 Z= 0.763 Chirality : 0.068 0.313 3268 Planarity : 0.005 0.046 3401 Dihedral : 11.127 89.669 6445 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.60 % Favored : 97.19 % Rotamer: Outliers : 2.06 % Allowed : 1.18 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 2771 helix: 0.86 (0.10), residues: 2122 sheet: -0.93 (0.97), residues: 18 loop : -0.78 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP c 420 HIS 0.001 0.000 HIS L 96 PHE 0.010 0.000 PHE d 96 TYR 0.011 0.000 TYR d 33 ARG 0.001 0.000 ARG l 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1294 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1259 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 52 ILE cc_start: 0.9510 (tp) cc_final: 0.9101 (tp) REVERT: H 55 LYS cc_start: 0.9579 (tttp) cc_final: 0.9166 (tmtt) REVERT: H 56 MET cc_start: 0.8992 (mmp) cc_final: 0.8748 (mmm) REVERT: H 60 GLU cc_start: 0.9371 (mm-30) cc_final: 0.8840 (mp0) REVERT: H 64 GLU cc_start: 0.9401 (tp30) cc_final: 0.8567 (tm-30) REVERT: H 81 THR cc_start: 0.9562 (m) cc_final: 0.9333 (p) REVERT: H 85 GLN cc_start: 0.9340 (mm-40) cc_final: 0.9078 (mm-40) REVERT: H 143 GLU cc_start: 0.9468 (mt-10) cc_final: 0.9074 (mm-30) REVERT: H 147 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8639 (mt-10) REVERT: H 153 THR cc_start: 0.6258 (m) cc_final: 0.5824 (m) REVERT: L 11 ILE cc_start: 0.9595 (mt) cc_final: 0.9349 (mp) REVERT: L 15 ASP cc_start: 0.9095 (m-30) cc_final: 0.8694 (m-30) REVERT: L 31 ASN cc_start: 0.8771 (m-40) cc_final: 0.8549 (m-40) REVERT: L 46 ASN cc_start: 0.9452 (m-40) cc_final: 0.8903 (t0) REVERT: L 53 ARG cc_start: 0.8595 (ttp-110) cc_final: 0.8264 (ttp-110) REVERT: L 61 ILE cc_start: 0.8898 (mm) cc_final: 0.8674 (mm) REVERT: L 67 ASN cc_start: 0.9043 (m110) cc_final: 0.8295 (m110) REVERT: L 70 ILE cc_start: 0.9747 (mt) cc_final: 0.9414 (mt) REVERT: L 73 MET cc_start: 0.8630 (mtp) cc_final: 0.8425 (mtt) REVERT: L 78 LEU cc_start: 0.9212 (mp) cc_final: 0.8917 (tt) REVERT: L 94 LYS cc_start: 0.9236 (ttpt) cc_final: 0.8644 (tptt) REVERT: L 98 TYR cc_start: 0.6897 (t80) cc_final: 0.6394 (t80) REVERT: L 106 LEU cc_start: 0.9527 (mt) cc_final: 0.9079 (mm) REVERT: b 5 GLU cc_start: 0.9123 (mp0) cc_final: 0.8853 (pt0) REVERT: b 8 TYR cc_start: 0.8823 (m-80) cc_final: 0.8540 (m-80) REVERT: b 43 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8072 (mm-30) REVERT: b 48 MET cc_start: 0.8901 (tmm) cc_final: 0.8634 (tmm) REVERT: b 51 ASN cc_start: 0.9483 (m-40) cc_final: 0.9108 (t0) REVERT: b 74 SER cc_start: 0.9870 (m) cc_final: 0.9640 (p) REVERT: b 75 SER cc_start: 0.9704 (m) cc_final: 0.9471 (p) REVERT: b 90 ASN cc_start: 0.9039 (m110) cc_final: 0.8776 (m110) REVERT: b 103 TYR cc_start: 0.8615 (m-10) cc_final: 0.8351 (m-10) REVERT: b 107 MET cc_start: 0.9327 (mmm) cc_final: 0.9064 (mmm) REVERT: b 114 MET cc_start: 0.8505 (mmm) cc_final: 0.8038 (mmm) REVERT: b 116 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7309 (mp0) REVERT: b 135 TYR cc_start: 0.9130 (m-80) cc_final: 0.8876 (m-80) REVERT: b 137 MET cc_start: 0.9194 (mtp) cc_final: 0.8627 (mtp) REVERT: b 164 LEU cc_start: 0.9597 (mt) cc_final: 0.9164 (mp) REVERT: b 169 ASN cc_start: 0.9087 (t0) cc_final: 0.8677 (t0) REVERT: b 172 LEU cc_start: 0.9245 (mt) cc_final: 0.8587 (mt) REVERT: b 186 ILE cc_start: 0.9635 (mt) cc_final: 0.9236 (mt) REVERT: b 189 PHE cc_start: 0.8175 (m-10) cc_final: 0.7850 (m-80) REVERT: b 193 VAL cc_start: 0.9649 (t) cc_final: 0.9418 (t) REVERT: b 202 LYS cc_start: 0.8601 (tttt) cc_final: 0.8378 (tmmt) REVERT: c 421 MET cc_start: 0.9068 (mtm) cc_final: 0.8749 (mtp) REVERT: c 442 SER cc_start: 0.9276 (m) cc_final: 0.8860 (p) REVERT: d 7 LEU cc_start: 0.9492 (mt) cc_final: 0.8867 (mp) REVERT: d 34 LEU cc_start: 0.9474 (mt) cc_final: 0.9241 (mt) REVERT: d 39 CYS cc_start: 0.3445 (m) cc_final: 0.2943 (m) REVERT: d 40 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7480 (mm-30) REVERT: d 63 SER cc_start: 0.9046 (m) cc_final: 0.8804 (p) REVERT: d 76 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8711 (mt-10) REVERT: d 97 LEU cc_start: 0.9521 (mt) cc_final: 0.9281 (mt) REVERT: d 105 MET cc_start: 0.9039 (mtt) cc_final: 0.8815 (mmm) REVERT: d 135 PHE cc_start: 0.8626 (m-80) cc_final: 0.8070 (m-80) REVERT: d 170 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8627 (mt-10) REVERT: d 197 CYS cc_start: 0.9579 (m) cc_final: 0.9315 (m) REVERT: d 208 MET cc_start: 0.9058 (tpt) cc_final: 0.8773 (tpt) REVERT: d 226 ASN cc_start: 0.8965 (m-40) cc_final: 0.8583 (m-40) REVERT: d 241 PHE cc_start: 0.9034 (m-10) cc_final: 0.8656 (m-10) REVERT: d 262 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8412 (tm-30) REVERT: d 276 LEU cc_start: 0.9339 (mt) cc_final: 0.9060 (tt) REVERT: d 315 PHE cc_start: 0.9470 (m-80) cc_final: 0.9115 (m-80) REVERT: d 324 GLN cc_start: 0.8741 (tp40) cc_final: 0.7981 (tp40) REVERT: d 339 ARG cc_start: 0.9155 (mmm160) cc_final: 0.8400 (mmp-170) REVERT: d 348 ILE cc_start: 0.8826 (mm) cc_final: 0.8408 (mp) REVERT: g 8 PRO cc_start: 0.8768 (Cg_exo) cc_final: 0.8309 (Cg_endo) REVERT: g 28 MET cc_start: 0.9585 (mtp) cc_final: 0.9334 (mtp) REVERT: g 32 TYR cc_start: 0.8811 (t80) cc_final: 0.8364 (t80) REVERT: g 53 MET cc_start: 0.8621 (mtm) cc_final: 0.8344 (ttp) REVERT: g 57 ILE cc_start: 0.9609 (mt) cc_final: 0.9233 (mt) REVERT: g 108 PHE cc_start: 0.8308 (m-10) cc_final: 0.7932 (m-10) REVERT: g 118 VAL cc_start: 0.9695 (t) cc_final: 0.9387 (p) REVERT: g 124 GLN cc_start: 0.8399 (tp-100) cc_final: 0.7735 (tm-30) REVERT: g 136 ILE cc_start: 0.9813 (OUTLIER) cc_final: 0.9561 (mt) REVERT: g 143 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8619 (tp) REVERT: g 144 TYR cc_start: 0.9278 (m-80) cc_final: 0.8827 (m-80) REVERT: h 8 PRO cc_start: 0.8196 (Cg_exo) cc_final: 0.7855 (Cg_endo) REVERT: h 28 MET cc_start: 0.8937 (mtp) cc_final: 0.8580 (mtm) REVERT: h 45 SER cc_start: 0.7970 (m) cc_final: 0.7765 (p) REVERT: h 52 ILE cc_start: 0.8686 (tt) cc_final: 0.8391 (pt) REVERT: h 54 LYS cc_start: 0.7853 (mttt) cc_final: 0.7370 (mttt) REVERT: h 57 ILE cc_start: 0.9794 (mt) cc_final: 0.9529 (mt) REVERT: h 88 ARG cc_start: 0.8128 (mtp-110) cc_final: 0.7831 (mmm-85) REVERT: h 112 ILE cc_start: 0.9458 (mm) cc_final: 0.9009 (tp) REVERT: h 128 PHE cc_start: 0.8879 (t80) cc_final: 0.8622 (t80) REVERT: h 137 PHE cc_start: 0.9287 (m-80) cc_final: 0.8789 (m-80) REVERT: h 139 GLU cc_start: 0.9348 (OUTLIER) cc_final: 0.9105 (tp30) REVERT: h 144 TYR cc_start: 0.9664 (m-10) cc_final: 0.9282 (m-10) REVERT: i 16 VAL cc_start: 0.9593 (t) cc_final: 0.9386 (t) REVERT: i 17 MET cc_start: 0.9332 (mmp) cc_final: 0.8839 (mmm) REVERT: i 65 ILE cc_start: 0.9687 (OUTLIER) cc_final: 0.9393 (mm) REVERT: i 68 TYR cc_start: 0.9551 (m-10) cc_final: 0.8903 (m-80) REVERT: i 82 ASP cc_start: 0.9064 (p0) cc_final: 0.8753 (p0) REVERT: i 90 PHE cc_start: 0.9271 (m-80) cc_final: 0.8862 (m-10) REVERT: i 124 GLN cc_start: 0.8524 (tp-100) cc_final: 0.8195 (tm-30) REVERT: i 127 LEU cc_start: 0.7538 (tp) cc_final: 0.7251 (tp) REVERT: i 131 MET cc_start: 0.9075 (ttp) cc_final: 0.8701 (ttt) REVERT: i 152 LEU cc_start: 0.9728 (mt) cc_final: 0.9487 (mt) REVERT: j 28 MET cc_start: 0.9037 (mtp) cc_final: 0.8553 (mmt) REVERT: j 84 ILE cc_start: 0.7365 (mt) cc_final: 0.7000 (mt) REVERT: j 101 LEU cc_start: 0.9310 (mt) cc_final: 0.9019 (mt) REVERT: j 108 PHE cc_start: 0.9246 (m-80) cc_final: 0.8743 (m-80) REVERT: j 121 THR cc_start: 0.8949 (m) cc_final: 0.8748 (p) REVERT: j 124 GLN cc_start: 0.7864 (tp-100) cc_final: 0.7160 (tm-30) REVERT: j 127 LEU cc_start: 0.9330 (tp) cc_final: 0.8779 (tp) REVERT: j 140 VAL cc_start: 0.9417 (OUTLIER) cc_final: 0.8955 (t) REVERT: j 141 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9014 (mt) REVERT: j 144 TYR cc_start: 0.9428 (m-10) cc_final: 0.9218 (m-80) REVERT: j 152 LEU cc_start: 0.9421 (tp) cc_final: 0.9156 (tp) REVERT: k 6 ASN cc_start: 0.8804 (m-40) cc_final: 0.8550 (p0) REVERT: k 17 MET cc_start: 0.8981 (mtm) cc_final: 0.8695 (mtm) REVERT: k 23 MET cc_start: 0.9047 (tpt) cc_final: 0.8831 (mmm) REVERT: k 28 MET cc_start: 0.9018 (mtp) cc_final: 0.8755 (mtt) REVERT: k 41 ILE cc_start: 0.9440 (mt) cc_final: 0.8999 (mm) REVERT: k 51 LEU cc_start: 0.8826 (mt) cc_final: 0.8602 (mt) REVERT: k 57 ILE cc_start: 0.9296 (mt) cc_final: 0.8855 (mm) REVERT: k 61 MET cc_start: 0.8291 (mmp) cc_final: 0.8077 (mmm) REVERT: k 91 LEU cc_start: 0.9308 (mt) cc_final: 0.8829 (mt) REVERT: k 118 VAL cc_start: 0.9502 (t) cc_final: 0.9195 (p) REVERT: k 121 THR cc_start: 0.8209 (m) cc_final: 0.7766 (p) REVERT: k 152 LEU cc_start: 0.9581 (mt) cc_final: 0.9349 (mt) REVERT: l 68 TYR cc_start: 0.8076 (m-10) cc_final: 0.7028 (m-80) REVERT: l 74 VAL cc_start: 0.9407 (t) cc_final: 0.8946 (t) REVERT: l 113 VAL cc_start: 0.9668 (t) cc_final: 0.9467 (p) REVERT: l 124 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7587 (tm-30) REVERT: l 131 MET cc_start: 0.9296 (ttp) cc_final: 0.8995 (ttm) REVERT: m 11 SER cc_start: 0.8224 (p) cc_final: 0.7698 (t) REVERT: m 21 SER cc_start: 0.9270 (m) cc_final: 0.8977 (p) REVERT: m 47 MET cc_start: 0.9111 (mmm) cc_final: 0.8479 (mmm) REVERT: m 53 MET cc_start: 0.8741 (mmm) cc_final: 0.7810 (tmm) REVERT: m 89 SER cc_start: 0.9387 (m) cc_final: 0.8731 (p) REVERT: m 92 GLN cc_start: 0.9161 (mt0) cc_final: 0.8856 (mt0) REVERT: m 118 VAL cc_start: 0.9297 (t) cc_final: 0.9034 (m) REVERT: n 13 PHE cc_start: 0.8986 (t80) cc_final: 0.8709 (t80) REVERT: n 23 MET cc_start: 0.9362 (tpt) cc_final: 0.8632 (tpp) REVERT: n 32 TYR cc_start: 0.7907 (t80) cc_final: 0.7705 (t80) REVERT: n 47 MET cc_start: 0.9257 (mmm) cc_final: 0.8996 (mmm) REVERT: n 64 ILE cc_start: 0.9143 (mt) cc_final: 0.8849 (mt) REVERT: n 68 TYR cc_start: 0.8374 (m-10) cc_final: 0.8158 (m-80) REVERT: n 70 LEU cc_start: 0.9123 (tp) cc_final: 0.8748 (tp) REVERT: n 72 VAL cc_start: 0.9505 (t) cc_final: 0.9282 (p) REVERT: n 99 VAL cc_start: 0.9736 (p) cc_final: 0.9424 (m) REVERT: n 119 ARG cc_start: 0.8532 (mtm-85) cc_final: 0.8325 (ptp90) REVERT: o 13 PHE cc_start: 0.9059 (t80) cc_final: 0.8445 (t80) REVERT: o 17 MET cc_start: 0.9340 (mmp) cc_final: 0.8906 (mmp) REVERT: o 21 SER cc_start: 0.9109 (m) cc_final: 0.8659 (p) REVERT: o 48 ARG cc_start: 0.8827 (ptm160) cc_final: 0.8519 (ptp-170) REVERT: o 51 LEU cc_start: 0.8960 (mt) cc_final: 0.8752 (mt) REVERT: o 64 ILE cc_start: 0.9337 (mt) cc_final: 0.9061 (mt) REVERT: o 68 TYR cc_start: 0.8631 (m-10) cc_final: 0.8392 (m-80) REVERT: o 82 ASP cc_start: 0.8543 (p0) cc_final: 0.8334 (m-30) REVERT: o 91 LEU cc_start: 0.9728 (mt) cc_final: 0.9493 (mp) REVERT: o 97 LEU cc_start: 0.9479 (mt) cc_final: 0.9250 (mt) REVERT: o 112 ILE cc_start: 0.9307 (mm) cc_final: 0.9080 (mm) REVERT: o 119 ARG cc_start: 0.9207 (mtm-85) cc_final: 0.8973 (mpp80) REVERT: o 132 ILE cc_start: 0.9254 (mm) cc_final: 0.8492 (mt) REVERT: o 135 LEU cc_start: 0.9813 (mt) cc_final: 0.9484 (mt) REVERT: o 144 TYR cc_start: 0.9146 (m-10) cc_final: 0.8840 (m-10) REVERT: p 303 TYR cc_start: 0.9001 (t80) cc_final: 0.8356 (t80) REVERT: p 328 ILE cc_start: 0.9633 (mt) cc_final: 0.9417 (tp) REVERT: p 338 ILE cc_start: 0.8323 (pt) cc_final: 0.7672 (pt) outliers start: 35 outliers final: 15 residues processed: 1265 average time/residue: 0.2852 time to fit residues: 556.2264 Evaluate side-chains 970 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 949 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 0.5980 chunk 211 optimal weight: 0.2980 chunk 117 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 218 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 253 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN L 96 HIS ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 92 GLN j 92 GLN ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 92 GLN ** n 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19610 Z= 0.234 Angle : 0.670 9.866 26647 Z= 0.362 Chirality : 0.042 0.210 3268 Planarity : 0.005 0.054 3401 Dihedral : 4.037 17.992 2941 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.29 % Allowed : 2.36 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.15), residues: 2771 helix: 2.15 (0.11), residues: 2075 sheet: -1.04 (1.00), residues: 18 loop : -0.39 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP b 67 HIS 0.008 0.001 HIS d 311 PHE 0.030 0.002 PHE k 90 TYR 0.027 0.002 TYR o 32 ARG 0.006 0.001 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1084 time to evaluate : 2.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 55 LYS cc_start: 0.9538 (tttp) cc_final: 0.9205 (tptp) REVERT: H 56 MET cc_start: 0.9082 (mmp) cc_final: 0.8857 (mmm) REVERT: H 60 GLU cc_start: 0.9346 (mm-30) cc_final: 0.9001 (mm-30) REVERT: H 64 GLU cc_start: 0.9482 (tp30) cc_final: 0.8834 (tm-30) REVERT: H 81 THR cc_start: 0.9610 (m) cc_final: 0.9403 (p) REVERT: H 84 ILE cc_start: 0.9445 (mt) cc_final: 0.9201 (mt) REVERT: H 85 GLN cc_start: 0.9288 (mm-40) cc_final: 0.9004 (mm-40) REVERT: H 119 TYR cc_start: 0.7241 (p90) cc_final: 0.6626 (p90) REVERT: H 138 TYR cc_start: 0.9189 (m-80) cc_final: 0.8979 (m-80) REVERT: H 143 GLU cc_start: 0.9477 (mt-10) cc_final: 0.9215 (mm-30) REVERT: H 144 LEU cc_start: 0.9484 (mm) cc_final: 0.9241 (mm) REVERT: H 147 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8634 (mt-10) REVERT: L 11 ILE cc_start: 0.9556 (mt) cc_final: 0.9277 (mt) REVERT: L 15 ASP cc_start: 0.8911 (m-30) cc_final: 0.8427 (m-30) REVERT: L 22 LEU cc_start: 0.9363 (mt) cc_final: 0.9113 (mt) REVERT: L 53 ARG cc_start: 0.8633 (ttp-110) cc_final: 0.8262 (ttp-110) REVERT: L 59 ASP cc_start: 0.8933 (p0) cc_final: 0.8613 (t0) REVERT: L 67 ASN cc_start: 0.9139 (m110) cc_final: 0.8342 (m110) REVERT: L 70 ILE cc_start: 0.9583 (mt) cc_final: 0.9206 (mt) REVERT: L 90 GLU cc_start: 0.9154 (mp0) cc_final: 0.8865 (mp0) REVERT: b 4 LEU cc_start: 0.9457 (mm) cc_final: 0.9084 (mm) REVERT: b 5 GLU cc_start: 0.9000 (mp0) cc_final: 0.8772 (pt0) REVERT: b 8 TYR cc_start: 0.8870 (m-80) cc_final: 0.8589 (m-80) REVERT: b 19 MET cc_start: 0.8708 (mtp) cc_final: 0.8357 (mtp) REVERT: b 43 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8157 (mm-30) REVERT: b 48 MET cc_start: 0.9154 (tmm) cc_final: 0.8588 (tmm) REVERT: b 51 ASN cc_start: 0.9321 (m-40) cc_final: 0.8877 (m110) REVERT: b 75 SER cc_start: 0.9592 (m) cc_final: 0.9380 (p) REVERT: b 90 ASN cc_start: 0.9081 (m110) cc_final: 0.8741 (m110) REVERT: b 91 LEU cc_start: 0.9554 (tp) cc_final: 0.9307 (tp) REVERT: b 102 ILE cc_start: 0.9729 (mm) cc_final: 0.9501 (mm) REVERT: b 103 TYR cc_start: 0.8562 (m-10) cc_final: 0.8202 (m-10) REVERT: b 114 MET cc_start: 0.8458 (mmm) cc_final: 0.7482 (mmm) REVERT: b 116 GLU cc_start: 0.7949 (mm-30) cc_final: 0.6923 (mp0) REVERT: b 126 ILE cc_start: 0.8522 (mm) cc_final: 0.8277 (mm) REVERT: b 131 TYR cc_start: 0.9324 (m-80) cc_final: 0.8304 (m-80) REVERT: b 135 TYR cc_start: 0.9027 (m-80) cc_final: 0.8318 (m-80) REVERT: b 137 MET cc_start: 0.9298 (mtp) cc_final: 0.9075 (mtp) REVERT: b 150 PHE cc_start: 0.9420 (m-80) cc_final: 0.8897 (m-80) REVERT: b 164 LEU cc_start: 0.9513 (mt) cc_final: 0.8973 (mm) REVERT: b 169 ASN cc_start: 0.8973 (t0) cc_final: 0.8567 (t0) REVERT: b 172 LEU cc_start: 0.9444 (mt) cc_final: 0.8726 (mt) REVERT: b 186 ILE cc_start: 0.9694 (mt) cc_final: 0.9295 (mt) REVERT: b 189 PHE cc_start: 0.8617 (m-10) cc_final: 0.8322 (m-80) REVERT: b 197 GLN cc_start: 0.8784 (mt0) cc_final: 0.8244 (mt0) REVERT: b 202 LYS cc_start: 0.8713 (tttt) cc_final: 0.8486 (tmmt) REVERT: b 203 MET cc_start: 0.8048 (mmm) cc_final: 0.7811 (ttm) REVERT: c 421 MET cc_start: 0.9105 (mtm) cc_final: 0.8807 (mtp) REVERT: c 430 LEU cc_start: 0.9752 (tp) cc_final: 0.9485 (tp) REVERT: c 442 SER cc_start: 0.9239 (m) cc_final: 0.8789 (p) REVERT: d 30 GLN cc_start: 0.9329 (tm-30) cc_final: 0.9015 (tm-30) REVERT: d 40 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8050 (mm-30) REVERT: d 76 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8776 (mt-10) REVERT: d 81 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8740 (tp30) REVERT: d 93 LEU cc_start: 0.9707 (tt) cc_final: 0.9312 (tt) REVERT: d 105 MET cc_start: 0.8803 (mtt) cc_final: 0.8363 (tpp) REVERT: d 132 LEU cc_start: 0.8924 (mp) cc_final: 0.8496 (mp) REVERT: d 135 PHE cc_start: 0.8720 (m-80) cc_final: 0.7811 (m-80) REVERT: d 158 THR cc_start: 0.8908 (m) cc_final: 0.8392 (p) REVERT: d 181 ILE cc_start: 0.9004 (mt) cc_final: 0.8801 (mt) REVERT: d 183 ASN cc_start: 0.9464 (t0) cc_final: 0.9192 (t0) REVERT: d 197 CYS cc_start: 0.9631 (m) cc_final: 0.9423 (m) REVERT: d 208 MET cc_start: 0.9120 (tpt) cc_final: 0.8672 (tpt) REVERT: d 215 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8906 (mm-30) REVERT: d 241 PHE cc_start: 0.8916 (m-10) cc_final: 0.8565 (m-10) REVERT: d 244 CYS cc_start: 0.8673 (m) cc_final: 0.7991 (m) REVERT: d 250 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8158 (tm-30) REVERT: d 262 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8301 (tm-30) REVERT: d 276 LEU cc_start: 0.9336 (mt) cc_final: 0.9131 (tt) REVERT: d 302 ASN cc_start: 0.9717 (m-40) cc_final: 0.9437 (m110) REVERT: d 312 PHE cc_start: 0.8569 (m-80) cc_final: 0.7966 (m-80) REVERT: d 315 PHE cc_start: 0.9751 (m-80) cc_final: 0.9191 (m-80) REVERT: d 325 GLU cc_start: 0.9323 (tt0) cc_final: 0.9031 (tm-30) REVERT: d 334 GLU cc_start: 0.9437 (tp30) cc_final: 0.9223 (mm-30) REVERT: d 338 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8740 (mm110) REVERT: d 339 ARG cc_start: 0.9198 (mmm160) cc_final: 0.8751 (mmm160) REVERT: d 348 ILE cc_start: 0.9053 (mm) cc_final: 0.8832 (mp) REVERT: g 8 PRO cc_start: 0.8946 (Cg_exo) cc_final: 0.8437 (Cg_endo) REVERT: g 32 TYR cc_start: 0.8892 (t80) cc_final: 0.8192 (t80) REVERT: g 47 MET cc_start: 0.9525 (tmm) cc_final: 0.9318 (tmm) REVERT: g 48 ARG cc_start: 0.8476 (mtp180) cc_final: 0.7850 (mtp180) REVERT: g 51 LEU cc_start: 0.8586 (mm) cc_final: 0.8142 (mm) REVERT: g 53 MET cc_start: 0.8638 (mtm) cc_final: 0.8108 (ttp) REVERT: g 54 LYS cc_start: 0.8332 (ptpt) cc_final: 0.8055 (pttt) REVERT: g 57 ILE cc_start: 0.9546 (mt) cc_final: 0.9249 (mt) REVERT: g 70 LEU cc_start: 0.9422 (tp) cc_final: 0.9067 (tp) REVERT: g 78 ASN cc_start: 0.8638 (p0) cc_final: 0.8408 (m-40) REVERT: g 112 ILE cc_start: 0.9580 (mm) cc_final: 0.9318 (mm) REVERT: g 124 GLN cc_start: 0.8525 (tp-100) cc_final: 0.8262 (tm-30) REVERT: g 140 VAL cc_start: 0.9339 (t) cc_final: 0.8764 (t) REVERT: g 141 LEU cc_start: 0.9529 (mt) cc_final: 0.9244 (mt) REVERT: g 144 TYR cc_start: 0.9066 (m-80) cc_final: 0.8763 (m-80) REVERT: h 8 PRO cc_start: 0.8435 (Cg_exo) cc_final: 0.8147 (Cg_endo) REVERT: h 11 SER cc_start: 0.8859 (p) cc_final: 0.8531 (m) REVERT: h 44 MET cc_start: 0.8153 (tmm) cc_final: 0.7911 (tmm) REVERT: h 45 SER cc_start: 0.8367 (m) cc_final: 0.7530 (m) REVERT: h 48 ARG cc_start: 0.7737 (ttm170) cc_final: 0.6993 (ttm-80) REVERT: h 51 LEU cc_start: 0.8722 (mt) cc_final: 0.8444 (mt) REVERT: h 54 LYS cc_start: 0.7506 (mttt) cc_final: 0.7108 (mttt) REVERT: h 112 ILE cc_start: 0.9476 (mm) cc_final: 0.9060 (tp) REVERT: h 115 ASP cc_start: 0.9384 (t70) cc_final: 0.9085 (p0) REVERT: h 127 LEU cc_start: 0.8728 (tt) cc_final: 0.8256 (tt) REVERT: h 128 PHE cc_start: 0.8849 (t80) cc_final: 0.8611 (t80) REVERT: h 135 LEU cc_start: 0.9643 (mp) cc_final: 0.9413 (mp) REVERT: h 137 PHE cc_start: 0.9305 (m-80) cc_final: 0.8916 (m-80) REVERT: h 144 TYR cc_start: 0.9672 (m-10) cc_final: 0.9180 (m-10) REVERT: h 152 LEU cc_start: 0.9685 (mt) cc_final: 0.9460 (mt) REVERT: i 13 PHE cc_start: 0.8686 (t80) cc_final: 0.8032 (t80) REVERT: i 23 MET cc_start: 0.8896 (tpt) cc_final: 0.8685 (tpp) REVERT: i 32 TYR cc_start: 0.8726 (t80) cc_final: 0.8472 (t80) REVERT: i 127 LEU cc_start: 0.7999 (tp) cc_final: 0.7779 (tp) REVERT: i 131 MET cc_start: 0.9061 (ttp) cc_final: 0.8674 (ttt) REVERT: i 135 LEU cc_start: 0.9583 (mm) cc_final: 0.9249 (mm) REVERT: i 152 LEU cc_start: 0.9707 (mt) cc_final: 0.9477 (mt) REVERT: j 17 MET cc_start: 0.9181 (mtm) cc_final: 0.8659 (mtp) REVERT: j 28 MET cc_start: 0.9008 (mtp) cc_final: 0.8428 (mmt) REVERT: j 90 PHE cc_start: 0.8931 (m-10) cc_final: 0.8643 (m-10) REVERT: j 91 LEU cc_start: 0.9198 (mt) cc_final: 0.8917 (mt) REVERT: j 108 PHE cc_start: 0.9160 (m-80) cc_final: 0.8774 (m-80) REVERT: j 121 THR cc_start: 0.8815 (m) cc_final: 0.8272 (m) REVERT: j 124 GLN cc_start: 0.8243 (tp-100) cc_final: 0.7394 (tm-30) REVERT: j 127 LEU cc_start: 0.9129 (tp) cc_final: 0.8308 (tp) REVERT: j 141 LEU cc_start: 0.9336 (mt) cc_final: 0.9035 (mt) REVERT: j 143 LEU cc_start: 0.9372 (tp) cc_final: 0.9131 (tp) REVERT: j 152 LEU cc_start: 0.9368 (tp) cc_final: 0.9018 (tp) REVERT: k 44 MET cc_start: 0.8954 (ppp) cc_final: 0.8503 (ppp) REVERT: k 53 MET cc_start: 0.8800 (tmm) cc_final: 0.8061 (mtt) REVERT: k 57 ILE cc_start: 0.9061 (mt) cc_final: 0.8605 (mm) REVERT: k 59 VAL cc_start: 0.9321 (t) cc_final: 0.8986 (t) REVERT: k 64 ILE cc_start: 0.8840 (mm) cc_final: 0.8620 (mm) REVERT: k 65 ILE cc_start: 0.9617 (mm) cc_final: 0.9201 (mm) REVERT: k 68 TYR cc_start: 0.7640 (m-10) cc_final: 0.7088 (m-80) REVERT: k 91 LEU cc_start: 0.9180 (mt) cc_final: 0.8783 (mt) REVERT: k 92 GLN cc_start: 0.9394 (mm-40) cc_final: 0.9184 (mm-40) REVERT: k 131 MET cc_start: 0.8352 (mtm) cc_final: 0.8092 (mtp) REVERT: l 13 PHE cc_start: 0.9196 (t80) cc_final: 0.8568 (t80) REVERT: l 17 MET cc_start: 0.9358 (mmp) cc_final: 0.8623 (mmt) REVERT: l 24 VAL cc_start: 0.9371 (t) cc_final: 0.9039 (t) REVERT: l 28 MET cc_start: 0.8719 (mtp) cc_final: 0.8477 (mtp) REVERT: l 53 MET cc_start: 0.7875 (mtp) cc_final: 0.7461 (ttp) REVERT: l 68 TYR cc_start: 0.8370 (m-10) cc_final: 0.7591 (m-80) REVERT: l 97 LEU cc_start: 0.9304 (mt) cc_final: 0.9095 (mm) REVERT: l 124 GLN cc_start: 0.8374 (tp-100) cc_final: 0.7841 (tm-30) REVERT: l 127 LEU cc_start: 0.7260 (tp) cc_final: 0.6732 (tp) REVERT: l 131 MET cc_start: 0.9333 (ttp) cc_final: 0.9041 (ttm) REVERT: l 135 LEU cc_start: 0.9278 (mt) cc_final: 0.8914 (pp) REVERT: l 137 PHE cc_start: 0.8663 (m-80) cc_final: 0.8441 (m-10) REVERT: l 152 LEU cc_start: 0.9730 (mt) cc_final: 0.9527 (mt) REVERT: m 10 TYR cc_start: 0.4690 (m-80) cc_final: 0.4432 (m-80) REVERT: m 11 SER cc_start: 0.7979 (p) cc_final: 0.7556 (t) REVERT: m 14 PHE cc_start: 0.9192 (m-80) cc_final: 0.8922 (m-80) REVERT: m 21 SER cc_start: 0.9360 (m) cc_final: 0.9071 (p) REVERT: m 47 MET cc_start: 0.9238 (mmm) cc_final: 0.8865 (mmm) REVERT: m 48 ARG cc_start: 0.8735 (mmm160) cc_final: 0.8409 (mmm160) REVERT: m 51 LEU cc_start: 0.8529 (mt) cc_final: 0.8293 (mt) REVERT: m 53 MET cc_start: 0.8921 (mmm) cc_final: 0.7995 (tmm) REVERT: m 61 MET cc_start: 0.8989 (mtt) cc_final: 0.8740 (mmm) REVERT: m 70 LEU cc_start: 0.8946 (mt) cc_final: 0.8709 (mt) REVERT: m 86 LEU cc_start: 0.9501 (tp) cc_final: 0.9300 (tp) REVERT: m 89 SER cc_start: 0.9219 (m) cc_final: 0.8995 (p) REVERT: m 92 GLN cc_start: 0.9286 (mt0) cc_final: 0.8995 (mt0) REVERT: m 97 LEU cc_start: 0.8953 (mt) cc_final: 0.8721 (mt) REVERT: m 139 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8425 (mm-30) REVERT: m 144 TYR cc_start: 0.9411 (m-10) cc_final: 0.9085 (m-10) REVERT: n 13 PHE cc_start: 0.9033 (t80) cc_final: 0.8678 (t80) REVERT: n 17 MET cc_start: 0.9302 (mmt) cc_final: 0.9075 (mmm) REVERT: n 23 MET cc_start: 0.9145 (tpt) cc_final: 0.8608 (tpp) REVERT: n 47 MET cc_start: 0.9378 (mmm) cc_final: 0.8993 (mmm) REVERT: n 61 MET cc_start: 0.9101 (mmp) cc_final: 0.8391 (mmm) REVERT: n 68 TYR cc_start: 0.8681 (m-10) cc_final: 0.8307 (m-10) REVERT: n 70 LEU cc_start: 0.9158 (tp) cc_final: 0.8597 (tp) REVERT: n 121 THR cc_start: 0.7104 (p) cc_final: 0.6773 (p) REVERT: n 124 GLN cc_start: 0.8519 (tp-100) cc_final: 0.8143 (tm-30) REVERT: n 152 LEU cc_start: 0.9249 (mt) cc_final: 0.9033 (tp) REVERT: o 7 ASN cc_start: 0.7659 (m-40) cc_final: 0.7424 (t0) REVERT: o 13 PHE cc_start: 0.9070 (t80) cc_final: 0.8394 (t80) REVERT: o 17 MET cc_start: 0.9237 (mmp) cc_final: 0.8798 (mmt) REVERT: o 21 SER cc_start: 0.8922 (m) cc_final: 0.8688 (p) REVERT: o 47 MET cc_start: 0.8736 (tmm) cc_final: 0.8167 (tmm) REVERT: o 48 ARG cc_start: 0.9078 (ptm160) cc_final: 0.8583 (ptp-170) REVERT: o 51 LEU cc_start: 0.8810 (mt) cc_final: 0.8550 (mt) REVERT: o 57 ILE cc_start: 0.9162 (mt) cc_final: 0.8655 (tt) REVERT: o 64 ILE cc_start: 0.9310 (mt) cc_final: 0.8950 (mt) REVERT: o 68 TYR cc_start: 0.8936 (m-10) cc_final: 0.8426 (m-80) REVERT: o 90 PHE cc_start: 0.9279 (m-80) cc_final: 0.8969 (m-80) REVERT: o 112 ILE cc_start: 0.9358 (mm) cc_final: 0.8921 (mm) REVERT: o 128 PHE cc_start: 0.8492 (t80) cc_final: 0.7974 (t80) REVERT: o 132 ILE cc_start: 0.8999 (mm) cc_final: 0.8565 (tp) REVERT: o 144 TYR cc_start: 0.9201 (m-10) cc_final: 0.8838 (m-10) REVERT: p 303 TYR cc_start: 0.8654 (t80) cc_final: 0.8081 (t80) REVERT: p 314 MET cc_start: 0.8847 (mtt) cc_final: 0.8415 (tmm) REVERT: p 330 ASN cc_start: 0.8979 (t0) cc_final: 0.8683 (t0) outliers start: 5 outliers final: 0 residues processed: 1085 average time/residue: 0.2700 time to fit residues: 462.3617 Evaluate side-chains 913 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 913 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 chunk 210 optimal weight: 0.5980 chunk 172 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 253 optimal weight: 7.9990 chunk 274 optimal weight: 0.8980 chunk 226 optimal weight: 2.9990 chunk 251 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 137 ASN ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 GLN L 82 GLN L 96 HIS ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 88 HIS d 340 HIS d 346 ASN ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 92 GLN ** n 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 300 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19610 Z= 0.232 Angle : 0.629 9.188 26647 Z= 0.337 Chirality : 0.041 0.191 3268 Planarity : 0.004 0.033 3401 Dihedral : 3.967 23.224 2941 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.47 % Allowed : 2.00 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.16), residues: 2771 helix: 2.18 (0.11), residues: 2073 sheet: -1.72 (0.95), residues: 18 loop : -0.43 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP p 312 HIS 0.005 0.001 HIS b 128 PHE 0.035 0.002 PHE j 13 TYR 0.031 0.002 TYR g 68 ARG 0.011 0.001 ARG H 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1059 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 55 LYS cc_start: 0.9380 (tttp) cc_final: 0.9066 (tptp) REVERT: H 56 MET cc_start: 0.9014 (mmp) cc_final: 0.8811 (mmm) REVERT: H 60 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8908 (mm-30) REVERT: H 64 GLU cc_start: 0.9398 (tp30) cc_final: 0.8867 (tp30) REVERT: H 81 THR cc_start: 0.9607 (m) cc_final: 0.9405 (p) REVERT: H 85 GLN cc_start: 0.9267 (mm-40) cc_final: 0.8858 (mm-40) REVERT: H 119 TYR cc_start: 0.7496 (p90) cc_final: 0.6986 (p90) REVERT: H 143 GLU cc_start: 0.9501 (mt-10) cc_final: 0.9255 (mm-30) REVERT: H 144 LEU cc_start: 0.9516 (mm) cc_final: 0.9279 (mm) REVERT: H 147 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8620 (mt-10) REVERT: L 22 LEU cc_start: 0.9360 (mt) cc_final: 0.9138 (mt) REVERT: L 53 ARG cc_start: 0.8578 (ttp-110) cc_final: 0.8101 (ttp-110) REVERT: L 59 ASP cc_start: 0.8929 (p0) cc_final: 0.8481 (t0) REVERT: L 67 ASN cc_start: 0.9160 (m110) cc_final: 0.8626 (m110) REVERT: L 72 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8439 (mm-30) REVERT: L 79 ASP cc_start: 0.9333 (m-30) cc_final: 0.9035 (m-30) REVERT: b 4 LEU cc_start: 0.9523 (mm) cc_final: 0.9152 (mm) REVERT: b 5 GLU cc_start: 0.8998 (mp0) cc_final: 0.8786 (pt0) REVERT: b 8 TYR cc_start: 0.8877 (m-80) cc_final: 0.8572 (m-80) REVERT: b 19 MET cc_start: 0.8833 (mtp) cc_final: 0.8306 (mtp) REVERT: b 48 MET cc_start: 0.9203 (tmm) cc_final: 0.8645 (tmm) REVERT: b 90 ASN cc_start: 0.9104 (m110) cc_final: 0.8758 (m110) REVERT: b 91 LEU cc_start: 0.9562 (tp) cc_final: 0.9272 (tp) REVERT: b 102 ILE cc_start: 0.9741 (mm) cc_final: 0.9500 (mm) REVERT: b 103 TYR cc_start: 0.8615 (m-10) cc_final: 0.8155 (m-10) REVERT: b 114 MET cc_start: 0.8560 (mmm) cc_final: 0.7668 (mmm) REVERT: b 116 GLU cc_start: 0.7994 (mm-30) cc_final: 0.6932 (mp0) REVERT: b 126 ILE cc_start: 0.8428 (mm) cc_final: 0.8194 (mm) REVERT: b 131 TYR cc_start: 0.9378 (m-80) cc_final: 0.8357 (m-80) REVERT: b 135 TYR cc_start: 0.9035 (m-80) cc_final: 0.8239 (m-80) REVERT: b 164 LEU cc_start: 0.9574 (mt) cc_final: 0.9240 (mp) REVERT: b 168 GLN cc_start: 0.8998 (mp10) cc_final: 0.8762 (mp10) REVERT: b 169 ASN cc_start: 0.8806 (t0) cc_final: 0.8347 (t0) REVERT: b 172 LEU cc_start: 0.9423 (mt) cc_final: 0.8675 (mt) REVERT: b 186 ILE cc_start: 0.9702 (mt) cc_final: 0.9276 (mt) REVERT: b 189 PHE cc_start: 0.8671 (m-10) cc_final: 0.8276 (m-80) REVERT: b 197 GLN cc_start: 0.8961 (mt0) cc_final: 0.8537 (mt0) REVERT: b 202 LYS cc_start: 0.8873 (tttt) cc_final: 0.8594 (tmmt) REVERT: c 425 THR cc_start: 0.9795 (p) cc_final: 0.9459 (p) REVERT: c 442 SER cc_start: 0.9185 (m) cc_final: 0.8716 (p) REVERT: d 30 GLN cc_start: 0.9296 (tm-30) cc_final: 0.9040 (tm-30) REVERT: d 35 ASN cc_start: 0.9323 (m-40) cc_final: 0.9102 (t0) REVERT: d 40 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8099 (mm-30) REVERT: d 44 ASP cc_start: 0.9094 (m-30) cc_final: 0.8867 (m-30) REVERT: d 48 HIS cc_start: 0.8980 (m90) cc_final: 0.8471 (m90) REVERT: d 57 PHE cc_start: 0.8602 (p90) cc_final: 0.8274 (m-80) REVERT: d 76 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8724 (mt-10) REVERT: d 81 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8735 (tp30) REVERT: d 128 LYS cc_start: 0.9277 (mmtt) cc_final: 0.8858 (mmmt) REVERT: d 135 PHE cc_start: 0.8707 (m-80) cc_final: 0.8133 (m-80) REVERT: d 158 THR cc_start: 0.8895 (m) cc_final: 0.8449 (p) REVERT: d 181 ILE cc_start: 0.9013 (mt) cc_final: 0.8813 (mt) REVERT: d 183 ASN cc_start: 0.9440 (t0) cc_final: 0.9162 (t0) REVERT: d 208 MET cc_start: 0.9116 (tpt) cc_final: 0.8725 (tpt) REVERT: d 215 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8959 (mm-30) REVERT: d 233 SER cc_start: 0.8968 (p) cc_final: 0.8655 (p) REVERT: d 235 GLU cc_start: 0.9155 (mp0) cc_final: 0.8827 (pp20) REVERT: d 250 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8118 (tm-30) REVERT: d 262 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8279 (tm-30) REVERT: d 276 LEU cc_start: 0.9291 (mt) cc_final: 0.9075 (tt) REVERT: d 315 PHE cc_start: 0.9781 (m-80) cc_final: 0.9261 (m-80) REVERT: d 325 GLU cc_start: 0.9363 (tt0) cc_final: 0.9008 (tm-30) REVERT: d 338 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8781 (mm110) REVERT: d 348 ILE cc_start: 0.9138 (mm) cc_final: 0.8812 (mp) REVERT: g 8 PRO cc_start: 0.8769 (Cg_exo) cc_final: 0.8480 (Cg_endo) REVERT: g 13 PHE cc_start: 0.8671 (t80) cc_final: 0.8407 (t80) REVERT: g 28 MET cc_start: 0.9820 (mtm) cc_final: 0.9439 (mtm) REVERT: g 32 TYR cc_start: 0.8970 (t80) cc_final: 0.8224 (t80) REVERT: g 47 MET cc_start: 0.9558 (tmm) cc_final: 0.9275 (tmm) REVERT: g 51 LEU cc_start: 0.8708 (mm) cc_final: 0.8385 (mm) REVERT: g 53 MET cc_start: 0.8626 (mtm) cc_final: 0.8113 (ttp) REVERT: g 54 LYS cc_start: 0.8779 (ptpp) cc_final: 0.8550 (pttm) REVERT: g 70 LEU cc_start: 0.9487 (tp) cc_final: 0.9122 (tp) REVERT: g 93 LEU cc_start: 0.9307 (pp) cc_final: 0.8996 (pp) REVERT: g 112 ILE cc_start: 0.9527 (mm) cc_final: 0.9238 (mm) REVERT: g 118 VAL cc_start: 0.9339 (p) cc_final: 0.9094 (p) REVERT: g 135 LEU cc_start: 0.9756 (mt) cc_final: 0.9546 (mt) REVERT: g 141 LEU cc_start: 0.9471 (mt) cc_final: 0.9115 (mt) REVERT: g 144 TYR cc_start: 0.9019 (m-80) cc_final: 0.8649 (m-80) REVERT: h 11 SER cc_start: 0.8923 (p) cc_final: 0.8651 (m) REVERT: h 13 PHE cc_start: 0.9332 (t80) cc_final: 0.9109 (t80) REVERT: h 32 TYR cc_start: 0.8576 (t80) cc_final: 0.7780 (t80) REVERT: h 44 MET cc_start: 0.8164 (tmm) cc_final: 0.7838 (tmm) REVERT: h 45 SER cc_start: 0.8427 (m) cc_final: 0.7767 (m) REVERT: h 48 ARG cc_start: 0.7951 (ttm170) cc_final: 0.7134 (ttm170) REVERT: h 51 LEU cc_start: 0.8626 (mt) cc_final: 0.8292 (mt) REVERT: h 54 LYS cc_start: 0.7288 (mttt) cc_final: 0.6935 (mttt) REVERT: h 57 ILE cc_start: 0.9736 (mt) cc_final: 0.9507 (mt) REVERT: h 86 LEU cc_start: 0.9295 (tt) cc_final: 0.9060 (tt) REVERT: h 90 PHE cc_start: 0.9034 (m-10) cc_final: 0.8365 (m-80) REVERT: h 112 ILE cc_start: 0.9474 (mm) cc_final: 0.9078 (tp) REVERT: h 115 ASP cc_start: 0.9339 (t70) cc_final: 0.9058 (p0) REVERT: h 137 PHE cc_start: 0.9240 (m-80) cc_final: 0.8828 (m-80) REVERT: h 144 TYR cc_start: 0.9663 (m-10) cc_final: 0.9119 (m-10) REVERT: h 152 LEU cc_start: 0.9643 (mt) cc_final: 0.9405 (mt) REVERT: i 13 PHE cc_start: 0.9046 (t80) cc_final: 0.8227 (t80) REVERT: i 17 MET cc_start: 0.9545 (mmt) cc_final: 0.9243 (mmt) REVERT: i 131 MET cc_start: 0.9041 (ttp) cc_final: 0.8654 (ttt) REVERT: i 135 LEU cc_start: 0.9600 (mm) cc_final: 0.9249 (mm) REVERT: i 152 LEU cc_start: 0.9691 (mt) cc_final: 0.9452 (mt) REVERT: j 28 MET cc_start: 0.8975 (mtp) cc_final: 0.8402 (mmt) REVERT: j 84 ILE cc_start: 0.8259 (mm) cc_final: 0.7623 (pt) REVERT: j 86 LEU cc_start: 0.9002 (tt) cc_final: 0.8510 (tt) REVERT: j 90 PHE cc_start: 0.9038 (m-10) cc_final: 0.8708 (m-10) REVERT: j 91 LEU cc_start: 0.9096 (mt) cc_final: 0.8664 (pp) REVERT: j 108 PHE cc_start: 0.9047 (m-80) cc_final: 0.8690 (m-80) REVERT: j 121 THR cc_start: 0.8798 (m) cc_final: 0.8179 (m) REVERT: j 124 GLN cc_start: 0.8443 (tp-100) cc_final: 0.7565 (tm-30) REVERT: j 127 LEU cc_start: 0.9277 (tp) cc_final: 0.8489 (tp) REVERT: j 131 MET cc_start: 0.8319 (ttp) cc_final: 0.8057 (ttp) REVERT: j 137 PHE cc_start: 0.9408 (m-80) cc_final: 0.9190 (m-80) REVERT: j 140 VAL cc_start: 0.9404 (t) cc_final: 0.9197 (t) REVERT: j 141 LEU cc_start: 0.9266 (mt) cc_final: 0.8793 (mt) REVERT: j 144 TYR cc_start: 0.9145 (m-10) cc_final: 0.8869 (m-80) REVERT: j 152 LEU cc_start: 0.9347 (tp) cc_final: 0.8999 (tp) REVERT: k 7 ASN cc_start: 0.5065 (p0) cc_final: 0.4747 (p0) REVERT: k 44 MET cc_start: 0.9021 (ppp) cc_final: 0.8559 (ppp) REVERT: k 53 MET cc_start: 0.8641 (tmm) cc_final: 0.7980 (mtt) REVERT: k 59 VAL cc_start: 0.9335 (t) cc_final: 0.9048 (t) REVERT: k 65 ILE cc_start: 0.9615 (mm) cc_final: 0.9136 (mm) REVERT: k 67 ILE cc_start: 0.8612 (mt) cc_final: 0.8321 (mt) REVERT: k 68 TYR cc_start: 0.7889 (m-10) cc_final: 0.7287 (m-80) REVERT: k 70 LEU cc_start: 0.9144 (tp) cc_final: 0.8724 (pp) REVERT: k 91 LEU cc_start: 0.9058 (mt) cc_final: 0.8701 (mt) REVERT: k 119 ARG cc_start: 0.8762 (tpt90) cc_final: 0.8425 (tpt90) REVERT: k 124 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8670 (tm-30) REVERT: k 131 MET cc_start: 0.8309 (mtm) cc_final: 0.8018 (mtp) REVERT: l 13 PHE cc_start: 0.9213 (t80) cc_final: 0.8630 (t80) REVERT: l 17 MET cc_start: 0.9360 (mmp) cc_final: 0.8931 (mmp) REVERT: l 24 VAL cc_start: 0.9408 (t) cc_final: 0.9136 (t) REVERT: l 28 MET cc_start: 0.8783 (mtp) cc_final: 0.8519 (mtp) REVERT: l 32 TYR cc_start: 0.7985 (t80) cc_final: 0.7535 (t80) REVERT: l 48 ARG cc_start: 0.8715 (mtt90) cc_final: 0.8478 (mtt-85) REVERT: l 53 MET cc_start: 0.7929 (mtp) cc_final: 0.7489 (ttp) REVERT: l 68 TYR cc_start: 0.8610 (m-10) cc_final: 0.7978 (m-80) REVERT: l 97 LEU cc_start: 0.9326 (mt) cc_final: 0.9125 (mm) REVERT: l 113 VAL cc_start: 0.9694 (p) cc_final: 0.9462 (p) REVERT: l 124 GLN cc_start: 0.8465 (tp-100) cc_final: 0.8083 (tm-30) REVERT: l 127 LEU cc_start: 0.7270 (tp) cc_final: 0.6978 (tp) REVERT: l 131 MET cc_start: 0.9339 (ttp) cc_final: 0.9013 (ttm) REVERT: l 137 PHE cc_start: 0.8710 (m-80) cc_final: 0.8482 (m-10) REVERT: l 143 LEU cc_start: 0.9496 (mm) cc_final: 0.9167 (mm) REVERT: l 146 LEU cc_start: 0.8810 (tt) cc_final: 0.8393 (pp) REVERT: m 11 SER cc_start: 0.8187 (p) cc_final: 0.7849 (t) REVERT: m 21 SER cc_start: 0.9287 (m) cc_final: 0.9029 (p) REVERT: m 47 MET cc_start: 0.9137 (mmm) cc_final: 0.8757 (mmm) REVERT: m 48 ARG cc_start: 0.8733 (mmm160) cc_final: 0.8387 (mmm160) REVERT: m 51 LEU cc_start: 0.8517 (mt) cc_final: 0.8190 (mt) REVERT: m 52 ILE cc_start: 0.9635 (mt) cc_final: 0.9392 (mt) REVERT: m 53 MET cc_start: 0.8815 (mmm) cc_final: 0.8130 (tmm) REVERT: m 61 MET cc_start: 0.9018 (mtt) cc_final: 0.8801 (mmm) REVERT: m 86 LEU cc_start: 0.9501 (tp) cc_final: 0.8918 (tp) REVERT: m 89 SER cc_start: 0.9451 (m) cc_final: 0.8953 (p) REVERT: m 90 PHE cc_start: 0.9062 (m-10) cc_final: 0.8704 (m-80) REVERT: m 92 GLN cc_start: 0.9322 (mt0) cc_final: 0.8973 (mt0) REVERT: m 139 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8408 (mm-30) REVERT: m 144 TYR cc_start: 0.9440 (m-10) cc_final: 0.9065 (m-10) REVERT: m 152 LEU cc_start: 0.9247 (mt) cc_final: 0.9043 (mt) REVERT: n 13 PHE cc_start: 0.9071 (t80) cc_final: 0.8627 (t80) REVERT: n 17 MET cc_start: 0.9267 (mmt) cc_final: 0.8948 (mmm) REVERT: n 47 MET cc_start: 0.9384 (mmm) cc_final: 0.8932 (mmm) REVERT: n 61 MET cc_start: 0.9182 (mmp) cc_final: 0.8438 (mmm) REVERT: n 68 TYR cc_start: 0.8866 (m-10) cc_final: 0.8438 (m-10) REVERT: n 90 PHE cc_start: 0.9214 (m-80) cc_final: 0.8759 (m-80) REVERT: n 121 THR cc_start: 0.7094 (p) cc_final: 0.6769 (p) REVERT: n 124 GLN cc_start: 0.8601 (tp-100) cc_final: 0.8146 (tm-30) REVERT: n 133 LEU cc_start: 0.9396 (mt) cc_final: 0.9192 (mt) REVERT: n 152 LEU cc_start: 0.9287 (mt) cc_final: 0.9049 (tp) REVERT: o 13 PHE cc_start: 0.9038 (t80) cc_final: 0.8471 (t80) REVERT: o 17 MET cc_start: 0.9194 (mmp) cc_final: 0.8795 (mmt) REVERT: o 47 MET cc_start: 0.8749 (tmm) cc_final: 0.8120 (tmm) REVERT: o 48 ARG cc_start: 0.9084 (ptm160) cc_final: 0.8605 (ptp-170) REVERT: o 51 LEU cc_start: 0.8737 (mt) cc_final: 0.8479 (mt) REVERT: o 57 ILE cc_start: 0.9123 (mt) cc_final: 0.8820 (mm) REVERT: o 64 ILE cc_start: 0.9318 (mt) cc_final: 0.8904 (mt) REVERT: o 65 ILE cc_start: 0.9441 (mp) cc_final: 0.9219 (mp) REVERT: o 68 TYR cc_start: 0.9133 (m-10) cc_final: 0.8487 (m-80) REVERT: o 70 LEU cc_start: 0.9240 (tp) cc_final: 0.8924 (tp) REVERT: o 91 LEU cc_start: 0.9768 (mm) cc_final: 0.9500 (mp) REVERT: o 128 PHE cc_start: 0.8337 (t80) cc_final: 0.7899 (t80) REVERT: o 144 TYR cc_start: 0.9174 (m-10) cc_final: 0.8772 (m-10) REVERT: o 152 LEU cc_start: 0.9435 (mt) cc_final: 0.8955 (mt) REVERT: p 303 TYR cc_start: 0.8795 (t80) cc_final: 0.8294 (t80) REVERT: p 314 MET cc_start: 0.8872 (mtt) cc_final: 0.8416 (tmm) REVERT: p 330 ASN cc_start: 0.8880 (t0) cc_final: 0.8600 (t0) outliers start: 8 outliers final: 0 residues processed: 1060 average time/residue: 0.2696 time to fit residues: 455.1072 Evaluate side-chains 921 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 921 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 250 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 131 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 254 optimal weight: 5.9990 chunk 269 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 137 ASN ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 88 HIS ** g 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 92 GLN ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 92 GLN ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 300 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19610 Z= 0.219 Angle : 0.611 7.686 26647 Z= 0.325 Chirality : 0.041 0.194 3268 Planarity : 0.004 0.060 3401 Dihedral : 3.936 20.350 2941 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.18 % Allowed : 1.53 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.16), residues: 2771 helix: 2.12 (0.11), residues: 2104 sheet: -1.96 (0.94), residues: 18 loop : -0.69 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP p 312 HIS 0.005 0.001 HIS b 128 PHE 0.027 0.002 PHE c 431 TYR 0.036 0.002 TYR H 138 ARG 0.006 0.000 ARG j 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1042 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 55 LYS cc_start: 0.9395 (tttp) cc_final: 0.9139 (tptp) REVERT: H 60 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8945 (mm-30) REVERT: H 64 GLU cc_start: 0.9373 (tp30) cc_final: 0.8823 (tm-30) REVERT: H 81 THR cc_start: 0.9608 (m) cc_final: 0.9403 (p) REVERT: H 85 GLN cc_start: 0.9283 (mm-40) cc_final: 0.8860 (mm-40) REVERT: H 119 TYR cc_start: 0.7534 (p90) cc_final: 0.7049 (p90) REVERT: H 143 GLU cc_start: 0.9510 (mt-10) cc_final: 0.9031 (mm-30) REVERT: H 147 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8623 (mt-10) REVERT: L 11 ILE cc_start: 0.9637 (mp) cc_final: 0.9182 (mm) REVERT: L 14 GLU cc_start: 0.9087 (pm20) cc_final: 0.8848 (pm20) REVERT: L 15 ASP cc_start: 0.8968 (m-30) cc_final: 0.8467 (m-30) REVERT: L 43 THR cc_start: 0.8143 (p) cc_final: 0.7750 (p) REVERT: L 47 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8861 (mt-10) REVERT: L 53 ARG cc_start: 0.8597 (ttp-110) cc_final: 0.8118 (ttp-110) REVERT: L 67 ASN cc_start: 0.9081 (m110) cc_final: 0.8229 (m110) REVERT: L 70 ILE cc_start: 0.9453 (mt) cc_final: 0.9188 (mt) REVERT: L 72 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8388 (mm-30) REVERT: L 73 MET cc_start: 0.8524 (mtt) cc_final: 0.8274 (mtt) REVERT: L 79 ASP cc_start: 0.9349 (m-30) cc_final: 0.9061 (m-30) REVERT: L 89 LEU cc_start: 0.8337 (mt) cc_final: 0.7905 (mt) REVERT: L 90 GLU cc_start: 0.8680 (mp0) cc_final: 0.8167 (tt0) REVERT: L 99 ASP cc_start: 0.8788 (t0) cc_final: 0.7061 (t0) REVERT: L 108 ARG cc_start: 0.8072 (mmm-85) cc_final: 0.7823 (mmm-85) REVERT: b 4 LEU cc_start: 0.9539 (mm) cc_final: 0.9288 (mm) REVERT: b 8 TYR cc_start: 0.8866 (m-80) cc_final: 0.8552 (m-80) REVERT: b 19 MET cc_start: 0.8757 (mtp) cc_final: 0.8377 (mtp) REVERT: b 42 THR cc_start: 0.8961 (t) cc_final: 0.8720 (t) REVERT: b 43 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7737 (mm-30) REVERT: b 48 MET cc_start: 0.9234 (tmm) cc_final: 0.8723 (tmm) REVERT: b 90 ASN cc_start: 0.9146 (m110) cc_final: 0.8800 (m110) REVERT: b 91 LEU cc_start: 0.9549 (tp) cc_final: 0.9241 (tp) REVERT: b 102 ILE cc_start: 0.9718 (mm) cc_final: 0.9502 (mm) REVERT: b 103 TYR cc_start: 0.8715 (m-10) cc_final: 0.8227 (m-10) REVERT: b 116 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7473 (mm-30) REVERT: b 137 MET cc_start: 0.9516 (mtm) cc_final: 0.9232 (mtm) REVERT: b 164 LEU cc_start: 0.9583 (mt) cc_final: 0.9212 (mp) REVERT: b 169 ASN cc_start: 0.8660 (t0) cc_final: 0.8144 (t0) REVERT: b 172 LEU cc_start: 0.9400 (mt) cc_final: 0.8908 (mt) REVERT: b 186 ILE cc_start: 0.9706 (mt) cc_final: 0.9280 (mt) REVERT: b 189 PHE cc_start: 0.8806 (m-10) cc_final: 0.8321 (m-80) REVERT: b 197 GLN cc_start: 0.8979 (mt0) cc_final: 0.8628 (mt0) REVERT: b 202 LYS cc_start: 0.8894 (tttt) cc_final: 0.8575 (mptt) REVERT: d 40 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8171 (mm-30) REVERT: d 48 HIS cc_start: 0.8985 (m90) cc_final: 0.8503 (m-70) REVERT: d 76 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8809 (mt-10) REVERT: d 81 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8770 (tp30) REVERT: d 105 MET cc_start: 0.8934 (mmm) cc_final: 0.8357 (tpt) REVERT: d 125 LEU cc_start: 0.9177 (mt) cc_final: 0.8790 (mt) REVERT: d 128 LYS cc_start: 0.9326 (mmtt) cc_final: 0.8944 (mmmt) REVERT: d 181 ILE cc_start: 0.9030 (mt) cc_final: 0.8826 (mt) REVERT: d 183 ASN cc_start: 0.9384 (t0) cc_final: 0.9104 (t0) REVERT: d 215 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8865 (mm-30) REVERT: d 224 THR cc_start: 0.9516 (m) cc_final: 0.9246 (p) REVERT: d 233 SER cc_start: 0.8984 (p) cc_final: 0.8664 (p) REVERT: d 235 GLU cc_start: 0.9151 (mp0) cc_final: 0.8855 (pp20) REVERT: d 241 PHE cc_start: 0.9067 (m-10) cc_final: 0.8705 (m-10) REVERT: d 262 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8332 (tm-30) REVERT: d 302 ASN cc_start: 0.9792 (m-40) cc_final: 0.9573 (m110) REVERT: d 315 PHE cc_start: 0.9778 (m-80) cc_final: 0.9329 (m-80) REVERT: d 325 GLU cc_start: 0.9325 (tt0) cc_final: 0.8911 (tm-30) REVERT: d 348 ILE cc_start: 0.9225 (mm) cc_final: 0.8985 (mp) REVERT: g 8 PRO cc_start: 0.8832 (Cg_exo) cc_final: 0.8547 (Cg_endo) REVERT: g 28 MET cc_start: 0.9838 (mtm) cc_final: 0.9419 (mtm) REVERT: g 32 TYR cc_start: 0.8964 (t80) cc_final: 0.8227 (t80) REVERT: g 47 MET cc_start: 0.9571 (tmm) cc_final: 0.9227 (tmm) REVERT: g 51 LEU cc_start: 0.8879 (mm) cc_final: 0.8560 (mm) REVERT: g 53 MET cc_start: 0.8686 (mtm) cc_final: 0.8138 (ttp) REVERT: g 54 LYS cc_start: 0.8744 (ptpp) cc_final: 0.8496 (pttt) REVERT: g 64 ILE cc_start: 0.9528 (mt) cc_final: 0.9282 (mt) REVERT: g 68 TYR cc_start: 0.9472 (m-80) cc_final: 0.9225 (m-80) REVERT: g 70 LEU cc_start: 0.9490 (tp) cc_final: 0.9135 (tp) REVERT: g 112 ILE cc_start: 0.9516 (mm) cc_final: 0.9178 (mm) REVERT: g 118 VAL cc_start: 0.9351 (p) cc_final: 0.9119 (p) REVERT: g 131 MET cc_start: 0.9549 (ttm) cc_final: 0.9332 (ttm) REVERT: g 140 VAL cc_start: 0.9310 (t) cc_final: 0.8759 (t) REVERT: g 141 LEU cc_start: 0.9450 (mt) cc_final: 0.9153 (mt) REVERT: g 144 TYR cc_start: 0.8992 (m-80) cc_final: 0.8675 (m-80) REVERT: h 11 SER cc_start: 0.9186 (p) cc_final: 0.8750 (m) REVERT: h 44 MET cc_start: 0.8319 (tmm) cc_final: 0.7929 (tmm) REVERT: h 45 SER cc_start: 0.8467 (m) cc_final: 0.7814 (m) REVERT: h 48 ARG cc_start: 0.8149 (ttm170) cc_final: 0.7267 (ttm170) REVERT: h 51 LEU cc_start: 0.8711 (mt) cc_final: 0.8337 (mt) REVERT: h 54 LYS cc_start: 0.7279 (mttt) cc_final: 0.6883 (tttt) REVERT: h 57 ILE cc_start: 0.9696 (mt) cc_final: 0.9316 (mt) REVERT: h 112 ILE cc_start: 0.9529 (mm) cc_final: 0.9108 (tp) REVERT: h 137 PHE cc_start: 0.9218 (m-80) cc_final: 0.8774 (m-80) REVERT: h 144 TYR cc_start: 0.9630 (m-10) cc_final: 0.9081 (m-10) REVERT: h 152 LEU cc_start: 0.9613 (mt) cc_final: 0.9386 (mt) REVERT: i 13 PHE cc_start: 0.9157 (t80) cc_final: 0.8137 (t80) REVERT: i 17 MET cc_start: 0.9607 (mmt) cc_final: 0.9155 (mmt) REVERT: i 23 MET cc_start: 0.9086 (tpp) cc_final: 0.8829 (tpp) REVERT: i 32 TYR cc_start: 0.8708 (t80) cc_final: 0.8410 (t80) REVERT: i 61 MET cc_start: 0.9289 (mtp) cc_final: 0.8937 (mtp) REVERT: i 68 TYR cc_start: 0.9460 (m-80) cc_final: 0.9252 (m-80) REVERT: i 76 ILE cc_start: 0.9477 (mt) cc_final: 0.9202 (mt) REVERT: i 131 MET cc_start: 0.9066 (ttp) cc_final: 0.8651 (ttt) REVERT: i 135 LEU cc_start: 0.9569 (mm) cc_final: 0.9171 (mm) REVERT: i 152 LEU cc_start: 0.9671 (mt) cc_final: 0.9449 (mt) REVERT: j 17 MET cc_start: 0.9048 (mtt) cc_final: 0.8281 (mtm) REVERT: j 23 MET cc_start: 0.9592 (tpp) cc_final: 0.9295 (ttt) REVERT: j 28 MET cc_start: 0.8945 (mtp) cc_final: 0.8640 (mtt) REVERT: j 84 ILE cc_start: 0.8276 (mm) cc_final: 0.7618 (pt) REVERT: j 86 LEU cc_start: 0.9013 (tt) cc_final: 0.8545 (tt) REVERT: j 90 PHE cc_start: 0.9077 (m-10) cc_final: 0.8766 (m-10) REVERT: j 91 LEU cc_start: 0.9157 (mt) cc_final: 0.8722 (pp) REVERT: j 97 LEU cc_start: 0.9140 (tt) cc_final: 0.8869 (pp) REVERT: j 121 THR cc_start: 0.8781 (m) cc_final: 0.8174 (m) REVERT: j 124 GLN cc_start: 0.8425 (tp-100) cc_final: 0.7533 (tm-30) REVERT: j 127 LEU cc_start: 0.9294 (tp) cc_final: 0.8408 (tp) REVERT: j 131 MET cc_start: 0.8317 (ttp) cc_final: 0.7977 (ttp) REVERT: j 137 PHE cc_start: 0.9396 (m-80) cc_final: 0.9143 (m-80) REVERT: j 140 VAL cc_start: 0.9383 (t) cc_final: 0.9131 (t) REVERT: j 141 LEU cc_start: 0.9193 (mt) cc_final: 0.8669 (mt) REVERT: j 144 TYR cc_start: 0.9208 (m-10) cc_final: 0.8895 (m-80) REVERT: j 152 LEU cc_start: 0.9386 (tp) cc_final: 0.9083 (tp) REVERT: k 7 ASN cc_start: 0.5373 (p0) cc_final: 0.4442 (p0) REVERT: k 17 MET cc_start: 0.8954 (mtm) cc_final: 0.8609 (mtm) REVERT: k 53 MET cc_start: 0.8658 (tmm) cc_final: 0.8000 (mtt) REVERT: k 59 VAL cc_start: 0.9309 (t) cc_final: 0.8988 (t) REVERT: k 84 ILE cc_start: 0.8286 (tp) cc_final: 0.8020 (tp) REVERT: k 86 LEU cc_start: 0.8331 (tp) cc_final: 0.7707 (mp) REVERT: k 90 PHE cc_start: 0.9051 (m-10) cc_final: 0.8644 (m-10) REVERT: k 91 LEU cc_start: 0.9014 (mt) cc_final: 0.8739 (mt) REVERT: k 121 THR cc_start: 0.8474 (p) cc_final: 0.8144 (p) REVERT: k 124 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8638 (tm-30) REVERT: k 131 MET cc_start: 0.8240 (mtm) cc_final: 0.7900 (mtp) REVERT: l 13 PHE cc_start: 0.9239 (t80) cc_final: 0.8689 (t80) REVERT: l 17 MET cc_start: 0.9363 (mmp) cc_final: 0.8964 (mmp) REVERT: l 24 VAL cc_start: 0.9443 (t) cc_final: 0.9132 (t) REVERT: l 28 MET cc_start: 0.8790 (mtp) cc_final: 0.8507 (mtp) REVERT: l 32 TYR cc_start: 0.7976 (t80) cc_final: 0.7470 (t80) REVERT: l 53 MET cc_start: 0.7971 (mtp) cc_final: 0.7544 (ttp) REVERT: l 68 TYR cc_start: 0.8801 (m-10) cc_final: 0.8356 (m-80) REVERT: l 97 LEU cc_start: 0.9324 (mt) cc_final: 0.9123 (mm) REVERT: l 113 VAL cc_start: 0.9666 (p) cc_final: 0.9339 (p) REVERT: l 124 GLN cc_start: 0.8543 (tp-100) cc_final: 0.8213 (tm-30) REVERT: l 127 LEU cc_start: 0.7439 (tp) cc_final: 0.7162 (tp) REVERT: l 131 MET cc_start: 0.9393 (ttp) cc_final: 0.8967 (ttm) REVERT: l 143 LEU cc_start: 0.9440 (mm) cc_final: 0.9119 (mm) REVERT: l 146 LEU cc_start: 0.8906 (tt) cc_final: 0.8507 (pp) REVERT: m 11 SER cc_start: 0.8333 (p) cc_final: 0.7597 (t) REVERT: m 14 PHE cc_start: 0.9409 (m-80) cc_final: 0.9161 (m-80) REVERT: m 17 MET cc_start: 0.9183 (mtp) cc_final: 0.8967 (mtp) REVERT: m 21 SER cc_start: 0.9158 (m) cc_final: 0.8925 (p) REVERT: m 48 ARG cc_start: 0.8715 (mmm160) cc_final: 0.8457 (mmm160) REVERT: m 51 LEU cc_start: 0.8555 (mt) cc_final: 0.8209 (mt) REVERT: m 52 ILE cc_start: 0.9647 (mt) cc_final: 0.9435 (mt) REVERT: m 53 MET cc_start: 0.8845 (mmm) cc_final: 0.8115 (tmm) REVERT: m 86 LEU cc_start: 0.9483 (tp) cc_final: 0.9007 (tp) REVERT: m 89 SER cc_start: 0.9448 (m) cc_final: 0.8573 (t) REVERT: m 90 PHE cc_start: 0.9007 (m-10) cc_final: 0.8659 (m-80) REVERT: m 92 GLN cc_start: 0.9336 (mt0) cc_final: 0.8920 (mt0) REVERT: m 124 GLN cc_start: 0.8703 (tp-100) cc_final: 0.8006 (tm-30) REVERT: m 144 TYR cc_start: 0.9457 (m-10) cc_final: 0.9031 (m-10) REVERT: m 152 LEU cc_start: 0.9222 (mt) cc_final: 0.8972 (mt) REVERT: n 47 MET cc_start: 0.9306 (mmm) cc_final: 0.8901 (mmm) REVERT: n 61 MET cc_start: 0.9231 (mmp) cc_final: 0.8516 (mmm) REVERT: n 68 TYR cc_start: 0.8995 (m-10) cc_final: 0.8658 (m-10) REVERT: n 70 LEU cc_start: 0.9444 (tp) cc_final: 0.9079 (tp) REVERT: n 90 PHE cc_start: 0.9214 (m-80) cc_final: 0.8731 (m-80) REVERT: n 121 THR cc_start: 0.7066 (p) cc_final: 0.6748 (p) REVERT: n 124 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8226 (tm-30) REVERT: n 135 LEU cc_start: 0.9588 (mt) cc_final: 0.9367 (mt) REVERT: n 146 LEU cc_start: 0.9021 (mt) cc_final: 0.8813 (mt) REVERT: o 13 PHE cc_start: 0.9027 (t80) cc_final: 0.8511 (t80) REVERT: o 17 MET cc_start: 0.9194 (mmp) cc_final: 0.8869 (mmt) REVERT: o 47 MET cc_start: 0.8717 (tmm) cc_final: 0.8268 (tmm) REVERT: o 48 ARG cc_start: 0.9085 (ptm160) cc_final: 0.8553 (ptp-170) REVERT: o 51 LEU cc_start: 0.8667 (mt) cc_final: 0.8419 (mt) REVERT: o 57 ILE cc_start: 0.9056 (mt) cc_final: 0.8751 (mm) REVERT: o 64 ILE cc_start: 0.9313 (mt) cc_final: 0.8973 (mt) REVERT: o 65 ILE cc_start: 0.9520 (mp) cc_final: 0.9226 (mp) REVERT: o 68 TYR cc_start: 0.9244 (m-10) cc_final: 0.8571 (m-80) REVERT: o 70 LEU cc_start: 0.9238 (tp) cc_final: 0.8874 (tp) REVERT: o 91 LEU cc_start: 0.9782 (mm) cc_final: 0.9492 (mp) REVERT: o 128 PHE cc_start: 0.8277 (t80) cc_final: 0.7857 (t80) REVERT: o 144 TYR cc_start: 0.9185 (m-10) cc_final: 0.8834 (m-10) REVERT: o 152 LEU cc_start: 0.9361 (mt) cc_final: 0.8966 (mt) REVERT: p 303 TYR cc_start: 0.8805 (t80) cc_final: 0.8252 (t80) REVERT: p 313 ILE cc_start: 0.9746 (pt) cc_final: 0.9525 (pt) REVERT: p 314 MET cc_start: 0.9001 (mtt) cc_final: 0.8762 (mmt) REVERT: p 330 ASN cc_start: 0.8849 (t0) cc_final: 0.8568 (t0) outliers start: 3 outliers final: 0 residues processed: 1043 average time/residue: 0.2789 time to fit residues: 469.0737 Evaluate side-chains 887 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 887 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 224 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 242 optimal weight: 0.5980 chunk 68 optimal weight: 0.0040 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 308 ASN d 338 GLN ** g 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 92 GLN ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 19610 Z= 0.203 Angle : 0.630 13.291 26647 Z= 0.329 Chirality : 0.041 0.182 3268 Planarity : 0.004 0.037 3401 Dihedral : 3.950 20.738 2941 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.12 % Allowed : 1.36 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.16), residues: 2771 helix: 1.97 (0.11), residues: 2136 sheet: -2.04 (0.86), residues: 18 loop : -0.88 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP p 312 HIS 0.006 0.001 HIS d 48 PHE 0.052 0.002 PHE b 118 TYR 0.023 0.002 TYR b 135 ARG 0.004 0.000 ARG h 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1021 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 52 ILE cc_start: 0.9292 (tp) cc_final: 0.9062 (tp) REVERT: H 55 LYS cc_start: 0.9423 (tttp) cc_final: 0.9120 (tptp) REVERT: H 56 MET cc_start: 0.9046 (mmp) cc_final: 0.8794 (mmm) REVERT: H 60 GLU cc_start: 0.9347 (mm-30) cc_final: 0.8903 (mm-30) REVERT: H 81 THR cc_start: 0.9599 (m) cc_final: 0.9388 (p) REVERT: H 85 GLN cc_start: 0.9267 (mm-40) cc_final: 0.8845 (mm-40) REVERT: H 144 LEU cc_start: 0.9462 (mm) cc_final: 0.9187 (mm) REVERT: H 147 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8473 (mt-10) REVERT: L 11 ILE cc_start: 0.9639 (mp) cc_final: 0.9163 (mm) REVERT: L 14 GLU cc_start: 0.9075 (pm20) cc_final: 0.8822 (pm20) REVERT: L 15 ASP cc_start: 0.8977 (m-30) cc_final: 0.8453 (m-30) REVERT: L 43 THR cc_start: 0.8538 (p) cc_final: 0.8060 (p) REVERT: L 47 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8840 (mt-10) REVERT: L 53 ARG cc_start: 0.8483 (ttp-110) cc_final: 0.8057 (ttp-110) REVERT: L 67 ASN cc_start: 0.8942 (m110) cc_final: 0.8315 (m110) REVERT: L 70 ILE cc_start: 0.9439 (mt) cc_final: 0.9125 (mt) REVERT: L 72 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8532 (mm-30) REVERT: L 73 MET cc_start: 0.8552 (mtt) cc_final: 0.8299 (mtt) REVERT: L 79 ASP cc_start: 0.9343 (m-30) cc_final: 0.9055 (m-30) REVERT: L 90 GLU cc_start: 0.8959 (mp0) cc_final: 0.8125 (tt0) REVERT: L 99 ASP cc_start: 0.8800 (t0) cc_final: 0.6712 (t0) REVERT: L 108 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7839 (mmm-85) REVERT: b 4 LEU cc_start: 0.9394 (mm) cc_final: 0.9008 (mm) REVERT: b 8 TYR cc_start: 0.8965 (m-80) cc_final: 0.8639 (m-80) REVERT: b 19 MET cc_start: 0.8736 (mtp) cc_final: 0.8324 (mtp) REVERT: b 42 THR cc_start: 0.8960 (t) cc_final: 0.8706 (t) REVERT: b 43 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7622 (mm-30) REVERT: b 48 MET cc_start: 0.9228 (tmm) cc_final: 0.8592 (tmm) REVERT: b 90 ASN cc_start: 0.9148 (m110) cc_final: 0.8814 (m110) REVERT: b 102 ILE cc_start: 0.9698 (mm) cc_final: 0.9490 (mm) REVERT: b 103 TYR cc_start: 0.8735 (m-10) cc_final: 0.8206 (m-10) REVERT: b 116 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7638 (mm-30) REVERT: b 137 MET cc_start: 0.9487 (mtm) cc_final: 0.9248 (mtm) REVERT: b 169 ASN cc_start: 0.8450 (t0) cc_final: 0.7914 (t0) REVERT: b 172 LEU cc_start: 0.9383 (mt) cc_final: 0.8772 (mt) REVERT: b 186 ILE cc_start: 0.9671 (mt) cc_final: 0.9280 (mt) REVERT: b 197 GLN cc_start: 0.8881 (mt0) cc_final: 0.8549 (mt0) REVERT: b 202 LYS cc_start: 0.8706 (tttt) cc_final: 0.8318 (tmmt) REVERT: d 28 LEU cc_start: 0.9131 (mt) cc_final: 0.8750 (mm) REVERT: d 40 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8405 (mm-30) REVERT: d 44 ASP cc_start: 0.9086 (m-30) cc_final: 0.8864 (m-30) REVERT: d 48 HIS cc_start: 0.8866 (m90) cc_final: 0.8416 (m90) REVERT: d 76 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8858 (mt-10) REVERT: d 81 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8755 (tp30) REVERT: d 105 MET cc_start: 0.8930 (mmm) cc_final: 0.8256 (tpt) REVERT: d 125 LEU cc_start: 0.9146 (mt) cc_final: 0.8768 (mt) REVERT: d 128 LYS cc_start: 0.9362 (mmtt) cc_final: 0.8962 (mmmt) REVERT: d 129 CYS cc_start: 0.8287 (m) cc_final: 0.7698 (m) REVERT: d 181 ILE cc_start: 0.9004 (mt) cc_final: 0.8663 (mt) REVERT: d 183 ASN cc_start: 0.9355 (t0) cc_final: 0.9096 (t0) REVERT: d 233 SER cc_start: 0.8976 (p) cc_final: 0.8636 (p) REVERT: d 235 GLU cc_start: 0.9148 (mp0) cc_final: 0.8821 (pp20) REVERT: d 250 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8081 (tm-30) REVERT: d 262 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8325 (tm-30) REVERT: d 302 ASN cc_start: 0.9785 (m-40) cc_final: 0.9564 (m110) REVERT: d 315 PHE cc_start: 0.9769 (m-80) cc_final: 0.9334 (m-80) REVERT: d 325 GLU cc_start: 0.9484 (tt0) cc_final: 0.9001 (tm-30) REVERT: d 338 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8473 (mm110) REVERT: d 348 ILE cc_start: 0.9387 (mm) cc_final: 0.9062 (mp) REVERT: g 8 PRO cc_start: 0.8781 (Cg_exo) cc_final: 0.8503 (Cg_endo) REVERT: g 28 MET cc_start: 0.9834 (mtm) cc_final: 0.9456 (mtm) REVERT: g 32 TYR cc_start: 0.8957 (t80) cc_final: 0.8248 (t80) REVERT: g 47 MET cc_start: 0.9583 (tmm) cc_final: 0.9297 (tmm) REVERT: g 51 LEU cc_start: 0.8837 (mm) cc_final: 0.8610 (mm) REVERT: g 53 MET cc_start: 0.8614 (mtm) cc_final: 0.8370 (ttm) REVERT: g 57 ILE cc_start: 0.9555 (mt) cc_final: 0.9254 (mt) REVERT: g 64 ILE cc_start: 0.9507 (mt) cc_final: 0.9264 (mt) REVERT: g 70 LEU cc_start: 0.9507 (tp) cc_final: 0.9229 (tp) REVERT: g 118 VAL cc_start: 0.9458 (p) cc_final: 0.9202 (p) REVERT: g 131 MET cc_start: 0.9563 (ttm) cc_final: 0.9340 (ttm) REVERT: g 140 VAL cc_start: 0.9254 (t) cc_final: 0.8646 (t) REVERT: g 141 LEU cc_start: 0.9411 (mt) cc_final: 0.9123 (mt) REVERT: g 144 TYR cc_start: 0.8929 (m-80) cc_final: 0.8660 (m-80) REVERT: h 16 VAL cc_start: 0.9541 (t) cc_final: 0.9331 (t) REVERT: h 17 MET cc_start: 0.9367 (mtt) cc_final: 0.8992 (mmm) REVERT: h 24 VAL cc_start: 0.9557 (p) cc_final: 0.9282 (p) REVERT: h 28 MET cc_start: 0.8856 (mtp) cc_final: 0.8499 (mtm) REVERT: h 32 TYR cc_start: 0.8589 (t80) cc_final: 0.8312 (t80) REVERT: h 44 MET cc_start: 0.8306 (tmm) cc_final: 0.7832 (tmm) REVERT: h 48 ARG cc_start: 0.8171 (ttm170) cc_final: 0.7263 (ttm170) REVERT: h 51 LEU cc_start: 0.8685 (mt) cc_final: 0.8288 (mt) REVERT: h 57 ILE cc_start: 0.9680 (mt) cc_final: 0.9359 (mt) REVERT: h 60 VAL cc_start: 0.9252 (p) cc_final: 0.9048 (m) REVERT: h 121 THR cc_start: 0.8797 (p) cc_final: 0.8559 (p) REVERT: h 137 PHE cc_start: 0.9136 (m-80) cc_final: 0.8649 (m-80) REVERT: h 144 TYR cc_start: 0.9607 (m-10) cc_final: 0.9137 (m-10) REVERT: h 152 LEU cc_start: 0.9595 (mt) cc_final: 0.9358 (mt) REVERT: i 17 MET cc_start: 0.9544 (mmt) cc_final: 0.9025 (mmm) REVERT: i 23 MET cc_start: 0.9070 (tpp) cc_final: 0.8865 (tpp) REVERT: i 32 TYR cc_start: 0.8583 (t80) cc_final: 0.8286 (t80) REVERT: i 45 SER cc_start: 0.8450 (m) cc_final: 0.8148 (m) REVERT: i 61 MET cc_start: 0.9256 (mtp) cc_final: 0.8962 (mtp) REVERT: i 101 LEU cc_start: 0.9327 (mt) cc_final: 0.9110 (mt) REVERT: i 131 MET cc_start: 0.9020 (ttp) cc_final: 0.8641 (ttt) REVERT: i 135 LEU cc_start: 0.9546 (mm) cc_final: 0.9145 (mm) REVERT: i 152 LEU cc_start: 0.9651 (mt) cc_final: 0.9428 (mt) REVERT: j 10 TYR cc_start: 0.9039 (p90) cc_final: 0.8606 (p90) REVERT: j 13 PHE cc_start: 0.8391 (m-80) cc_final: 0.8048 (m-80) REVERT: j 17 MET cc_start: 0.8828 (mtt) cc_final: 0.8192 (mtt) REVERT: j 28 MET cc_start: 0.8991 (mtp) cc_final: 0.8665 (mtt) REVERT: j 61 MET cc_start: 0.8989 (mtp) cc_final: 0.8542 (ttm) REVERT: j 91 LEU cc_start: 0.9164 (mt) cc_final: 0.8745 (pp) REVERT: j 97 LEU cc_start: 0.9138 (tt) cc_final: 0.8865 (pp) REVERT: j 108 PHE cc_start: 0.9158 (m-80) cc_final: 0.8800 (m-80) REVERT: j 121 THR cc_start: 0.8742 (m) cc_final: 0.8149 (m) REVERT: j 124 GLN cc_start: 0.8455 (tp-100) cc_final: 0.7630 (tm-30) REVERT: j 127 LEU cc_start: 0.9049 (tp) cc_final: 0.8244 (tp) REVERT: j 131 MET cc_start: 0.8128 (ttp) cc_final: 0.7821 (ttp) REVERT: j 141 LEU cc_start: 0.9153 (mt) cc_final: 0.8603 (mt) REVERT: j 144 TYR cc_start: 0.9200 (m-10) cc_final: 0.8926 (m-80) REVERT: j 152 LEU cc_start: 0.9356 (tp) cc_final: 0.9035 (tp) REVERT: k 13 PHE cc_start: 0.9448 (t80) cc_final: 0.9204 (t80) REVERT: k 23 MET cc_start: 0.9099 (mmm) cc_final: 0.8578 (mmm) REVERT: k 44 MET cc_start: 0.9036 (ppp) cc_final: 0.8604 (ppp) REVERT: k 45 SER cc_start: 0.9232 (p) cc_final: 0.8983 (p) REVERT: k 53 MET cc_start: 0.8656 (tmm) cc_final: 0.8003 (mtt) REVERT: k 91 LEU cc_start: 0.9053 (mt) cc_final: 0.8770 (mt) REVERT: k 124 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8688 (tm-30) REVERT: l 13 PHE cc_start: 0.9232 (t80) cc_final: 0.8686 (t80) REVERT: l 17 MET cc_start: 0.9345 (mmp) cc_final: 0.8944 (mmp) REVERT: l 24 VAL cc_start: 0.9454 (t) cc_final: 0.8909 (t) REVERT: l 32 TYR cc_start: 0.7972 (t80) cc_final: 0.7439 (t80) REVERT: l 48 ARG cc_start: 0.8646 (mtt90) cc_final: 0.8438 (ttt180) REVERT: l 51 LEU cc_start: 0.8782 (mt) cc_final: 0.8340 (mt) REVERT: l 68 TYR cc_start: 0.8854 (m-10) cc_final: 0.8434 (m-80) REVERT: l 113 VAL cc_start: 0.9648 (p) cc_final: 0.9327 (p) REVERT: l 124 GLN cc_start: 0.8630 (tp-100) cc_final: 0.8401 (tm-30) REVERT: l 131 MET cc_start: 0.9393 (ttp) cc_final: 0.8991 (ttm) REVERT: l 143 LEU cc_start: 0.9416 (mm) cc_final: 0.9104 (mm) REVERT: l 146 LEU cc_start: 0.8962 (tt) cc_final: 0.8531 (pp) REVERT: m 11 SER cc_start: 0.8471 (p) cc_final: 0.7807 (t) REVERT: m 14 PHE cc_start: 0.9453 (m-80) cc_final: 0.9146 (m-80) REVERT: m 17 MET cc_start: 0.9148 (mtp) cc_final: 0.8887 (mmm) REVERT: m 21 SER cc_start: 0.9081 (m) cc_final: 0.8830 (p) REVERT: m 47 MET cc_start: 0.8931 (mmm) cc_final: 0.8110 (mmm) REVERT: m 48 ARG cc_start: 0.8693 (mmm160) cc_final: 0.8428 (mmm160) REVERT: m 51 LEU cc_start: 0.8562 (mt) cc_final: 0.8223 (mt) REVERT: m 52 ILE cc_start: 0.9651 (mt) cc_final: 0.9443 (mt) REVERT: m 53 MET cc_start: 0.8808 (mmm) cc_final: 0.8084 (tmm) REVERT: m 61 MET cc_start: 0.9140 (tpt) cc_final: 0.8674 (mmm) REVERT: m 86 LEU cc_start: 0.9467 (tp) cc_final: 0.8940 (tp) REVERT: m 89 SER cc_start: 0.9414 (m) cc_final: 0.8558 (t) REVERT: m 90 PHE cc_start: 0.8997 (m-10) cc_final: 0.8690 (m-80) REVERT: m 92 GLN cc_start: 0.9333 (mt0) cc_final: 0.8925 (mt0) REVERT: m 133 LEU cc_start: 0.8820 (tp) cc_final: 0.8401 (tp) REVERT: m 135 LEU cc_start: 0.9377 (mt) cc_final: 0.9148 (mt) REVERT: m 137 PHE cc_start: 0.9004 (m-80) cc_final: 0.8734 (m-80) REVERT: m 144 TYR cc_start: 0.9456 (m-10) cc_final: 0.8999 (m-10) REVERT: m 152 LEU cc_start: 0.9238 (mt) cc_final: 0.9001 (mt) REVERT: n 47 MET cc_start: 0.9287 (mmm) cc_final: 0.8891 (mmm) REVERT: n 61 MET cc_start: 0.9261 (mmp) cc_final: 0.8267 (mmm) REVERT: n 68 TYR cc_start: 0.9069 (m-10) cc_final: 0.8666 (m-10) REVERT: n 70 LEU cc_start: 0.9483 (tp) cc_final: 0.9273 (tp) REVERT: n 72 VAL cc_start: 0.9381 (t) cc_final: 0.9139 (p) REVERT: n 90 PHE cc_start: 0.9141 (m-80) cc_final: 0.8639 (m-80) REVERT: n 146 LEU cc_start: 0.9028 (mt) cc_final: 0.8707 (mt) REVERT: o 13 PHE cc_start: 0.8976 (t80) cc_final: 0.8449 (t80) REVERT: o 17 MET cc_start: 0.9156 (mmp) cc_final: 0.8840 (mmt) REVERT: o 47 MET cc_start: 0.8739 (tmm) cc_final: 0.8470 (tmm) REVERT: o 48 ARG cc_start: 0.9048 (ptm160) cc_final: 0.8656 (ptp-170) REVERT: o 51 LEU cc_start: 0.8646 (mt) cc_final: 0.8264 (mt) REVERT: o 61 MET cc_start: 0.9358 (mmp) cc_final: 0.9153 (mmm) REVERT: o 64 ILE cc_start: 0.9303 (mt) cc_final: 0.9013 (mt) REVERT: o 65 ILE cc_start: 0.9547 (mp) cc_final: 0.9237 (mp) REVERT: o 68 TYR cc_start: 0.9305 (m-10) cc_final: 0.8673 (m-80) REVERT: o 70 LEU cc_start: 0.9275 (tp) cc_final: 0.9041 (tp) REVERT: o 80 LEU cc_start: 0.9003 (mm) cc_final: 0.8775 (mm) REVERT: o 91 LEU cc_start: 0.9761 (mm) cc_final: 0.9492 (mp) REVERT: o 128 PHE cc_start: 0.8272 (t80) cc_final: 0.7845 (t80) REVERT: o 131 MET cc_start: 0.8627 (ppp) cc_final: 0.8389 (ppp) REVERT: o 144 TYR cc_start: 0.9060 (m-10) cc_final: 0.8733 (m-10) REVERT: o 152 LEU cc_start: 0.9394 (mt) cc_final: 0.9033 (mt) REVERT: p 303 TYR cc_start: 0.8735 (t80) cc_final: 0.8241 (t80) REVERT: p 313 ILE cc_start: 0.9720 (pt) cc_final: 0.9359 (pt) outliers start: 2 outliers final: 2 residues processed: 1022 average time/residue: 0.2830 time to fit residues: 464.2388 Evaluate side-chains 888 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 886 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 90 optimal weight: 0.9980 chunk 242 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 158 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 269 optimal weight: 8.9990 chunk 224 optimal weight: 0.6980 chunk 124 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 HIS H 113 HIS H 137 ASN H 152 GLN L 82 GLN ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 92 GLN ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19610 Z= 0.213 Angle : 0.657 18.335 26647 Z= 0.340 Chirality : 0.041 0.220 3268 Planarity : 0.004 0.035 3401 Dihedral : 3.954 23.009 2941 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.12 % Allowed : 2.12 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.16), residues: 2771 helix: 1.86 (0.11), residues: 2159 sheet: -2.41 (0.82), residues: 18 loop : -1.01 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP p 312 HIS 0.009 0.001 HIS b 128 PHE 0.029 0.002 PHE b 118 TYR 0.035 0.002 TYR b 135 ARG 0.006 0.000 ARG j 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 990 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 52 ILE cc_start: 0.9307 (tp) cc_final: 0.9080 (tp) REVERT: H 55 LYS cc_start: 0.9426 (tttp) cc_final: 0.9119 (tptp) REVERT: H 60 GLU cc_start: 0.9325 (mm-30) cc_final: 0.8943 (mm-30) REVERT: H 81 THR cc_start: 0.9619 (m) cc_final: 0.9409 (p) REVERT: H 85 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8830 (mm-40) REVERT: H 144 LEU cc_start: 0.9497 (mm) cc_final: 0.9222 (mm) REVERT: H 147 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8453 (mt-10) REVERT: L 11 ILE cc_start: 0.9666 (mp) cc_final: 0.9201 (mm) REVERT: L 14 GLU cc_start: 0.9099 (pm20) cc_final: 0.8864 (pm20) REVERT: L 15 ASP cc_start: 0.8959 (m-30) cc_final: 0.8518 (m-30) REVERT: L 47 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8857 (mt-10) REVERT: L 53 ARG cc_start: 0.8414 (ttp-110) cc_final: 0.8131 (ttp-110) REVERT: L 67 ASN cc_start: 0.8964 (m110) cc_final: 0.8360 (m110) REVERT: L 69 TYR cc_start: 0.8246 (p90) cc_final: 0.8021 (p90) REVERT: L 70 ILE cc_start: 0.9418 (mt) cc_final: 0.9077 (mt) REVERT: L 72 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8574 (mm-30) REVERT: L 73 MET cc_start: 0.8579 (mtt) cc_final: 0.8352 (mtt) REVERT: L 79 ASP cc_start: 0.9354 (m-30) cc_final: 0.9051 (m-30) REVERT: L 90 GLU cc_start: 0.8974 (mp0) cc_final: 0.8012 (tt0) REVERT: L 99 ASP cc_start: 0.8797 (t0) cc_final: 0.6306 (t0) REVERT: b 4 LEU cc_start: 0.9430 (mm) cc_final: 0.9053 (mm) REVERT: b 8 TYR cc_start: 0.8908 (m-80) cc_final: 0.8592 (m-80) REVERT: b 19 MET cc_start: 0.8746 (mtp) cc_final: 0.8325 (mtp) REVERT: b 41 LEU cc_start: 0.9382 (mm) cc_final: 0.9130 (mm) REVERT: b 48 MET cc_start: 0.8979 (tmm) cc_final: 0.8666 (tmm) REVERT: b 51 ASN cc_start: 0.8748 (p0) cc_final: 0.8202 (p0) REVERT: b 90 ASN cc_start: 0.9171 (m110) cc_final: 0.8651 (m110) REVERT: b 91 LEU cc_start: 0.9495 (tp) cc_final: 0.9234 (tp) REVERT: b 102 ILE cc_start: 0.9692 (mm) cc_final: 0.9477 (mm) REVERT: b 103 TYR cc_start: 0.8770 (m-10) cc_final: 0.8251 (m-10) REVERT: b 116 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7614 (mm-30) REVERT: b 126 ILE cc_start: 0.8205 (mm) cc_final: 0.7995 (mm) REVERT: b 130 ASN cc_start: 0.9164 (m-40) cc_final: 0.8927 (m-40) REVERT: b 131 TYR cc_start: 0.9237 (m-80) cc_final: 0.8391 (m-80) REVERT: b 164 LEU cc_start: 0.9541 (mp) cc_final: 0.9337 (mm) REVERT: b 169 ASN cc_start: 0.8422 (t0) cc_final: 0.7869 (t0) REVERT: b 172 LEU cc_start: 0.9375 (mt) cc_final: 0.8772 (mt) REVERT: b 186 ILE cc_start: 0.9644 (mt) cc_final: 0.9217 (mt) REVERT: b 189 PHE cc_start: 0.9025 (m-10) cc_final: 0.8742 (m-80) REVERT: b 197 GLN cc_start: 0.8881 (mt0) cc_final: 0.8625 (mt0) REVERT: c 425 THR cc_start: 0.9838 (p) cc_final: 0.9560 (p) REVERT: c 429 MET cc_start: 0.9546 (ptp) cc_final: 0.8911 (ptp) REVERT: d 28 LEU cc_start: 0.9179 (mt) cc_final: 0.8712 (mm) REVERT: d 40 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8585 (mm-30) REVERT: d 44 ASP cc_start: 0.9084 (m-30) cc_final: 0.8849 (m-30) REVERT: d 48 HIS cc_start: 0.8885 (m90) cc_final: 0.8420 (m90) REVERT: d 76 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8801 (mt-10) REVERT: d 81 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8808 (tp30) REVERT: d 105 MET cc_start: 0.8953 (mmm) cc_final: 0.8278 (tpt) REVERT: d 125 LEU cc_start: 0.9142 (mt) cc_final: 0.8773 (mt) REVERT: d 128 LYS cc_start: 0.9388 (mmtt) cc_final: 0.8966 (mmmt) REVERT: d 129 CYS cc_start: 0.8338 (m) cc_final: 0.7786 (m) REVERT: d 181 ILE cc_start: 0.9019 (mt) cc_final: 0.8776 (mt) REVERT: d 183 ASN cc_start: 0.9402 (t0) cc_final: 0.9129 (t0) REVERT: d 213 GLU cc_start: 0.8431 (pp20) cc_final: 0.7652 (tt0) REVERT: d 233 SER cc_start: 0.8960 (p) cc_final: 0.8412 (p) REVERT: d 235 GLU cc_start: 0.9149 (mp0) cc_final: 0.8814 (pm20) REVERT: d 262 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8302 (tm-30) REVERT: d 291 GLU cc_start: 0.9649 (mm-30) cc_final: 0.9418 (mm-30) REVERT: d 315 PHE cc_start: 0.9761 (m-80) cc_final: 0.9381 (m-80) REVERT: d 322 LYS cc_start: 0.9538 (mtpp) cc_final: 0.9155 (mtmm) REVERT: d 325 GLU cc_start: 0.9530 (tt0) cc_final: 0.8948 (tm-30) REVERT: d 348 ILE cc_start: 0.9449 (mm) cc_final: 0.9143 (mp) REVERT: g 8 PRO cc_start: 0.8804 (Cg_exo) cc_final: 0.8520 (Cg_endo) REVERT: g 28 MET cc_start: 0.9843 (mtm) cc_final: 0.9440 (mtm) REVERT: g 32 TYR cc_start: 0.8950 (t80) cc_final: 0.8180 (t80) REVERT: g 47 MET cc_start: 0.9593 (tmm) cc_final: 0.9291 (tmm) REVERT: g 48 ARG cc_start: 0.8602 (mtp180) cc_final: 0.7889 (mtp180) REVERT: g 51 LEU cc_start: 0.8418 (mm) cc_final: 0.7961 (mm) REVERT: g 53 MET cc_start: 0.8563 (mtm) cc_final: 0.8242 (ttm) REVERT: g 64 ILE cc_start: 0.9441 (mt) cc_final: 0.9164 (mt) REVERT: g 68 TYR cc_start: 0.9633 (m-80) cc_final: 0.9227 (m-80) REVERT: g 70 LEU cc_start: 0.9504 (tp) cc_final: 0.9250 (tp) REVERT: g 90 PHE cc_start: 0.8995 (m-80) cc_final: 0.8745 (m-80) REVERT: g 112 ILE cc_start: 0.9416 (mm) cc_final: 0.9091 (mm) REVERT: g 140 VAL cc_start: 0.9277 (t) cc_final: 0.8708 (t) REVERT: g 141 LEU cc_start: 0.9404 (mt) cc_final: 0.9101 (mt) REVERT: g 144 TYR cc_start: 0.8910 (m-80) cc_final: 0.8672 (m-80) REVERT: g 146 LEU cc_start: 0.9801 (tp) cc_final: 0.9480 (tp) REVERT: g 151 ILE cc_start: 0.9476 (mt) cc_final: 0.9167 (mt) REVERT: h 13 PHE cc_start: 0.9449 (t80) cc_final: 0.8718 (t80) REVERT: h 17 MET cc_start: 0.9404 (mtt) cc_final: 0.8906 (mtt) REVERT: h 24 VAL cc_start: 0.9556 (p) cc_final: 0.9326 (p) REVERT: h 28 MET cc_start: 0.8838 (mtp) cc_final: 0.8040 (tpt) REVERT: h 32 TYR cc_start: 0.8651 (t80) cc_final: 0.8332 (t80) REVERT: h 44 MET cc_start: 0.8356 (tmm) cc_final: 0.7864 (tmm) REVERT: h 48 ARG cc_start: 0.8161 (ttm170) cc_final: 0.7258 (ttm170) REVERT: h 51 LEU cc_start: 0.8650 (mt) cc_final: 0.8287 (mt) REVERT: h 57 ILE cc_start: 0.9654 (mt) cc_final: 0.9316 (mt) REVERT: h 60 VAL cc_start: 0.9231 (p) cc_final: 0.9027 (m) REVERT: h 92 GLN cc_start: 0.9136 (mp10) cc_final: 0.8433 (mp10) REVERT: h 128 PHE cc_start: 0.9100 (t80) cc_final: 0.8649 (t80) REVERT: h 137 PHE cc_start: 0.9139 (m-80) cc_final: 0.8670 (m-80) REVERT: h 144 TYR cc_start: 0.9587 (m-10) cc_final: 0.9150 (m-10) REVERT: h 152 LEU cc_start: 0.9589 (mt) cc_final: 0.9355 (mt) REVERT: i 13 PHE cc_start: 0.8803 (t80) cc_final: 0.7920 (t80) REVERT: i 17 MET cc_start: 0.9600 (mmt) cc_final: 0.9258 (mmt) REVERT: i 32 TYR cc_start: 0.8465 (t80) cc_final: 0.8182 (t80) REVERT: i 61 MET cc_start: 0.9227 (mtp) cc_final: 0.8900 (mtp) REVERT: i 90 PHE cc_start: 0.8994 (m-10) cc_final: 0.8293 (m-80) REVERT: i 101 LEU cc_start: 0.9339 (mt) cc_final: 0.9114 (mt) REVERT: i 131 MET cc_start: 0.8947 (ttp) cc_final: 0.8501 (ttt) REVERT: i 135 LEU cc_start: 0.9514 (mm) cc_final: 0.9114 (mm) REVERT: i 152 LEU cc_start: 0.9655 (mt) cc_final: 0.9432 (mt) REVERT: j 10 TYR cc_start: 0.9061 (p90) cc_final: 0.8517 (p90) REVERT: j 13 PHE cc_start: 0.8372 (m-80) cc_final: 0.7958 (m-80) REVERT: j 17 MET cc_start: 0.8862 (mtt) cc_final: 0.8258 (mtt) REVERT: j 28 MET cc_start: 0.8995 (mtp) cc_final: 0.8652 (mtt) REVERT: j 52 ILE cc_start: 0.9487 (tt) cc_final: 0.9170 (mm) REVERT: j 61 MET cc_start: 0.8937 (mtp) cc_final: 0.8476 (ttm) REVERT: j 84 ILE cc_start: 0.8210 (mm) cc_final: 0.7615 (pt) REVERT: j 91 LEU cc_start: 0.9188 (mt) cc_final: 0.8892 (pp) REVERT: j 97 LEU cc_start: 0.9198 (tt) cc_final: 0.8872 (pp) REVERT: j 108 PHE cc_start: 0.8956 (m-80) cc_final: 0.8563 (m-80) REVERT: j 121 THR cc_start: 0.8712 (m) cc_final: 0.8187 (m) REVERT: j 124 GLN cc_start: 0.8553 (tp-100) cc_final: 0.7769 (tm-30) REVERT: j 127 LEU cc_start: 0.9056 (tp) cc_final: 0.8415 (tp) REVERT: j 131 MET cc_start: 0.8115 (ttp) cc_final: 0.7723 (ttp) REVERT: j 141 LEU cc_start: 0.9114 (mt) cc_final: 0.8571 (mt) REVERT: j 144 TYR cc_start: 0.9205 (m-10) cc_final: 0.8929 (m-80) REVERT: j 152 LEU cc_start: 0.9375 (tp) cc_final: 0.9022 (tp) REVERT: k 23 MET cc_start: 0.9082 (mmm) cc_final: 0.8536 (mmm) REVERT: k 32 TYR cc_start: 0.8158 (t80) cc_final: 0.7953 (t80) REVERT: k 53 MET cc_start: 0.8580 (tmm) cc_final: 0.7922 (mtt) REVERT: k 59 VAL cc_start: 0.9420 (t) cc_final: 0.9170 (t) REVERT: k 65 ILE cc_start: 0.9494 (mt) cc_final: 0.9204 (mt) REVERT: k 68 TYR cc_start: 0.8625 (m-10) cc_final: 0.8068 (m-80) REVERT: l 17 MET cc_start: 0.9343 (mmp) cc_final: 0.8932 (mmp) REVERT: l 23 MET cc_start: 0.9158 (mmp) cc_final: 0.8644 (mmm) REVERT: l 32 TYR cc_start: 0.7968 (t80) cc_final: 0.7364 (t80) REVERT: l 48 ARG cc_start: 0.8660 (mtt90) cc_final: 0.8354 (ttt180) REVERT: l 113 VAL cc_start: 0.9665 (p) cc_final: 0.9329 (p) REVERT: l 124 GLN cc_start: 0.8649 (tp-100) cc_final: 0.8403 (tm-30) REVERT: l 131 MET cc_start: 0.9447 (ttp) cc_final: 0.9020 (ttm) REVERT: m 11 SER cc_start: 0.8494 (p) cc_final: 0.7863 (t) REVERT: m 14 PHE cc_start: 0.9511 (m-80) cc_final: 0.9149 (m-80) REVERT: m 17 MET cc_start: 0.9116 (mtp) cc_final: 0.8839 (mmm) REVERT: m 21 SER cc_start: 0.9046 (m) cc_final: 0.8788 (p) REVERT: m 48 ARG cc_start: 0.8657 (mmm160) cc_final: 0.8257 (mmm160) REVERT: m 51 LEU cc_start: 0.8577 (mt) cc_final: 0.8336 (mt) REVERT: m 53 MET cc_start: 0.8809 (mmm) cc_final: 0.8089 (tmm) REVERT: m 61 MET cc_start: 0.9375 (tpt) cc_final: 0.8831 (tpt) REVERT: m 86 LEU cc_start: 0.9456 (tp) cc_final: 0.8926 (tp) REVERT: m 89 SER cc_start: 0.9429 (m) cc_final: 0.8596 (t) REVERT: m 90 PHE cc_start: 0.8991 (m-10) cc_final: 0.8667 (m-80) REVERT: m 92 GLN cc_start: 0.9360 (mt0) cc_final: 0.8945 (mt0) REVERT: m 133 LEU cc_start: 0.8754 (tp) cc_final: 0.8435 (tt) REVERT: m 135 LEU cc_start: 0.9377 (mt) cc_final: 0.9070 (mt) REVERT: m 137 PHE cc_start: 0.8972 (m-80) cc_final: 0.8757 (m-80) REVERT: m 144 TYR cc_start: 0.9664 (m-10) cc_final: 0.9180 (m-10) REVERT: m 152 LEU cc_start: 0.9255 (mt) cc_final: 0.9031 (mt) REVERT: n 13 PHE cc_start: 0.8943 (t80) cc_final: 0.8730 (t80) REVERT: n 25 PHE cc_start: 0.8936 (m-80) cc_final: 0.8658 (m-80) REVERT: n 47 MET cc_start: 0.9279 (mmm) cc_final: 0.8902 (mmm) REVERT: n 61 MET cc_start: 0.9297 (mmp) cc_final: 0.8315 (mmm) REVERT: n 68 TYR cc_start: 0.9178 (m-10) cc_final: 0.8776 (m-10) REVERT: n 72 VAL cc_start: 0.9385 (t) cc_final: 0.9147 (p) REVERT: n 90 PHE cc_start: 0.9070 (m-80) cc_final: 0.8541 (m-80) REVERT: n 146 LEU cc_start: 0.8945 (mt) cc_final: 0.8590 (mt) REVERT: o 13 PHE cc_start: 0.8892 (t80) cc_final: 0.8428 (t80) REVERT: o 17 MET cc_start: 0.9101 (mmp) cc_final: 0.8845 (mmt) REVERT: o 47 MET cc_start: 0.8722 (tmm) cc_final: 0.8439 (tmm) REVERT: o 48 ARG cc_start: 0.9040 (ptm160) cc_final: 0.8652 (ptp-170) REVERT: o 51 LEU cc_start: 0.8667 (mt) cc_final: 0.8314 (mt) REVERT: o 57 ILE cc_start: 0.9111 (mt) cc_final: 0.8702 (tt) REVERT: o 64 ILE cc_start: 0.9308 (mt) cc_final: 0.9035 (mt) REVERT: o 65 ILE cc_start: 0.9568 (mp) cc_final: 0.9253 (mp) REVERT: o 68 TYR cc_start: 0.9385 (m-10) cc_final: 0.8721 (m-80) REVERT: o 91 LEU cc_start: 0.9776 (mm) cc_final: 0.9531 (mm) REVERT: o 128 PHE cc_start: 0.8277 (t80) cc_final: 0.7683 (t80) REVERT: o 131 MET cc_start: 0.8647 (ppp) cc_final: 0.8272 (ppp) REVERT: o 132 ILE cc_start: 0.8646 (mm) cc_final: 0.8085 (mm) REVERT: o 144 TYR cc_start: 0.9071 (m-10) cc_final: 0.8794 (m-10) REVERT: o 152 LEU cc_start: 0.9410 (mt) cc_final: 0.9021 (mt) REVERT: p 303 TYR cc_start: 0.8843 (t80) cc_final: 0.8338 (t80) REVERT: p 313 ILE cc_start: 0.9683 (pt) cc_final: 0.9433 (pt) outliers start: 2 outliers final: 1 residues processed: 990 average time/residue: 0.2696 time to fit residues: 427.1280 Evaluate side-chains 899 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 898 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 260 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 227 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 268 optimal weight: 10.0000 chunk 168 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 HIS ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 168 GLN ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 92 GLN ** k 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 19610 Z= 0.303 Angle : 0.692 15.308 26647 Z= 0.372 Chirality : 0.042 0.264 3268 Planarity : 0.004 0.035 3401 Dihedral : 4.128 22.450 2941 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.06 % Allowed : 1.77 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.16), residues: 2771 helix: 1.72 (0.11), residues: 2142 sheet: -3.03 (0.80), residues: 18 loop : -0.85 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP c 420 HIS 0.010 0.002 HIS b 128 PHE 0.026 0.002 PHE b 118 TYR 0.046 0.002 TYR l 68 ARG 0.004 0.001 ARG d 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 989 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 52 ILE cc_start: 0.9363 (tp) cc_final: 0.9066 (tp) REVERT: H 56 MET cc_start: 0.9107 (mmp) cc_final: 0.8859 (mmm) REVERT: H 60 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8944 (mm-30) REVERT: H 63 ARG cc_start: 0.8890 (ptp-170) cc_final: 0.8507 (ptp-170) REVERT: H 64 GLU cc_start: 0.9337 (tp30) cc_final: 0.8550 (tm-30) REVERT: H 84 ILE cc_start: 0.9418 (mt) cc_final: 0.9149 (mt) REVERT: H 85 GLN cc_start: 0.9346 (mm-40) cc_final: 0.8963 (mm-40) REVERT: H 119 TYR cc_start: 0.7821 (p90) cc_final: 0.7611 (p90) REVERT: L 11 ILE cc_start: 0.9697 (mp) cc_final: 0.9264 (mm) REVERT: L 15 ASP cc_start: 0.9016 (m-30) cc_final: 0.8610 (m-30) REVERT: L 47 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8875 (mt-10) REVERT: L 53 ARG cc_start: 0.8432 (ttp-110) cc_final: 0.8187 (ttp-110) REVERT: L 54 GLN cc_start: 0.8661 (mt0) cc_final: 0.8269 (tp-100) REVERT: L 67 ASN cc_start: 0.9117 (m110) cc_final: 0.8506 (m110) REVERT: L 69 TYR cc_start: 0.8547 (p90) cc_final: 0.8117 (p90) REVERT: L 70 ILE cc_start: 0.9452 (mt) cc_final: 0.9112 (mt) REVERT: L 72 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8717 (mm-30) REVERT: L 73 MET cc_start: 0.8688 (mtt) cc_final: 0.8467 (mtt) REVERT: L 79 ASP cc_start: 0.9406 (m-30) cc_final: 0.9121 (m-30) REVERT: L 89 LEU cc_start: 0.8232 (mt) cc_final: 0.7977 (mt) REVERT: L 90 GLU cc_start: 0.9046 (mp0) cc_final: 0.8174 (tt0) REVERT: L 99 ASP cc_start: 0.8866 (t0) cc_final: 0.6650 (t0) REVERT: b 4 LEU cc_start: 0.9473 (mm) cc_final: 0.9170 (mm) REVERT: b 8 TYR cc_start: 0.8938 (m-80) cc_final: 0.8529 (m-80) REVERT: b 19 MET cc_start: 0.8764 (mtp) cc_final: 0.8372 (mtp) REVERT: b 41 LEU cc_start: 0.9265 (mm) cc_final: 0.9004 (mm) REVERT: b 51 ASN cc_start: 0.8654 (p0) cc_final: 0.8181 (p0) REVERT: b 90 ASN cc_start: 0.9148 (m110) cc_final: 0.8894 (m110) REVERT: b 91 LEU cc_start: 0.9509 (tp) cc_final: 0.9234 (tp) REVERT: b 102 ILE cc_start: 0.9742 (mm) cc_final: 0.9524 (mm) REVERT: b 103 TYR cc_start: 0.8844 (m-10) cc_final: 0.8411 (m-10) REVERT: b 111 ILE cc_start: 0.9555 (mm) cc_final: 0.9283 (mm) REVERT: b 116 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7578 (mm-30) REVERT: b 126 ILE cc_start: 0.8360 (mm) cc_final: 0.8123 (mm) REVERT: b 130 ASN cc_start: 0.9122 (m-40) cc_final: 0.8879 (m110) REVERT: b 131 TYR cc_start: 0.9250 (m-80) cc_final: 0.8433 (m-80) REVERT: b 137 MET cc_start: 0.9458 (mtm) cc_final: 0.9208 (mtm) REVERT: b 164 LEU cc_start: 0.9600 (mp) cc_final: 0.9284 (mm) REVERT: b 168 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8857 (mp10) REVERT: b 169 ASN cc_start: 0.8132 (t0) cc_final: 0.7521 (t0) REVERT: b 172 LEU cc_start: 0.9370 (mt) cc_final: 0.8754 (mt) REVERT: b 186 ILE cc_start: 0.9651 (mt) cc_final: 0.9253 (mt) REVERT: b 189 PHE cc_start: 0.9090 (m-10) cc_final: 0.8799 (m-80) REVERT: b 197 GLN cc_start: 0.9005 (mt0) cc_final: 0.8689 (mt0) REVERT: b 202 LYS cc_start: 0.8368 (tptp) cc_final: 0.7989 (mptt) REVERT: b 203 MET cc_start: 0.8774 (ptp) cc_final: 0.8330 (pmm) REVERT: d 40 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8810 (mm-30) REVERT: d 44 ASP cc_start: 0.9116 (m-30) cc_final: 0.8887 (m-30) REVERT: d 48 HIS cc_start: 0.8894 (m90) cc_final: 0.8462 (m90) REVERT: d 76 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8750 (mt-10) REVERT: d 81 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8885 (tp30) REVERT: d 105 MET cc_start: 0.9035 (mmm) cc_final: 0.8353 (tpt) REVERT: d 125 LEU cc_start: 0.9186 (mt) cc_final: 0.8841 (mt) REVERT: d 128 LYS cc_start: 0.9429 (mmtt) cc_final: 0.9023 (mmmt) REVERT: d 129 CYS cc_start: 0.8528 (m) cc_final: 0.7969 (m) REVERT: d 132 LEU cc_start: 0.8928 (mp) cc_final: 0.8682 (mp) REVERT: d 181 ILE cc_start: 0.9100 (mt) cc_final: 0.8860 (mt) REVERT: d 183 ASN cc_start: 0.9497 (t0) cc_final: 0.9221 (t0) REVERT: d 262 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8285 (tm-30) REVERT: d 291 GLU cc_start: 0.9691 (mm-30) cc_final: 0.9405 (mm-30) REVERT: d 315 PHE cc_start: 0.9751 (m-80) cc_final: 0.9363 (m-80) REVERT: d 322 LYS cc_start: 0.9609 (mtpp) cc_final: 0.9345 (mtpp) REVERT: d 325 GLU cc_start: 0.9568 (tt0) cc_final: 0.8866 (tm-30) REVERT: d 348 ILE cc_start: 0.9473 (mm) cc_final: 0.9180 (mp) REVERT: g 14 PHE cc_start: 0.9762 (m-10) cc_final: 0.9453 (m-10) REVERT: g 28 MET cc_start: 0.9829 (mtm) cc_final: 0.9448 (mtm) REVERT: g 32 TYR cc_start: 0.9073 (t80) cc_final: 0.8322 (t80) REVERT: g 53 MET cc_start: 0.8575 (mtm) cc_final: 0.8243 (ttm) REVERT: g 57 ILE cc_start: 0.9549 (mt) cc_final: 0.9115 (mt) REVERT: g 64 ILE cc_start: 0.9453 (mt) cc_final: 0.9162 (mt) REVERT: g 68 TYR cc_start: 0.9668 (m-80) cc_final: 0.9288 (m-80) REVERT: g 70 LEU cc_start: 0.9519 (tp) cc_final: 0.9276 (tp) REVERT: g 90 PHE cc_start: 0.9003 (m-80) cc_final: 0.8564 (m-80) REVERT: g 112 ILE cc_start: 0.9456 (mm) cc_final: 0.9089 (mm) REVERT: g 140 VAL cc_start: 0.9285 (t) cc_final: 0.8731 (t) REVERT: g 141 LEU cc_start: 0.9413 (mt) cc_final: 0.9112 (mt) REVERT: g 144 TYR cc_start: 0.9031 (m-80) cc_final: 0.8750 (m-80) REVERT: h 44 MET cc_start: 0.8534 (tmm) cc_final: 0.8032 (tmm) REVERT: h 48 ARG cc_start: 0.8240 (ttm170) cc_final: 0.7295 (ttm-80) REVERT: h 51 LEU cc_start: 0.8747 (mt) cc_final: 0.8348 (mt) REVERT: h 57 ILE cc_start: 0.9652 (mt) cc_final: 0.9301 (mt) REVERT: h 60 VAL cc_start: 0.9218 (p) cc_final: 0.9009 (m) REVERT: h 112 ILE cc_start: 0.9481 (mm) cc_final: 0.9198 (tp) REVERT: h 128 PHE cc_start: 0.9160 (t80) cc_final: 0.8741 (t80) REVERT: h 137 PHE cc_start: 0.9180 (m-80) cc_final: 0.8675 (m-80) REVERT: h 144 TYR cc_start: 0.9608 (m-10) cc_final: 0.9164 (m-10) REVERT: h 146 LEU cc_start: 0.9478 (tp) cc_final: 0.9236 (tp) REVERT: h 152 LEU cc_start: 0.9617 (mt) cc_final: 0.9411 (mt) REVERT: i 17 MET cc_start: 0.9643 (mmt) cc_final: 0.9237 (mmm) REVERT: i 61 MET cc_start: 0.9236 (mtp) cc_final: 0.8909 (mtp) REVERT: i 68 TYR cc_start: 0.9448 (m-80) cc_final: 0.9241 (m-80) REVERT: i 90 PHE cc_start: 0.9005 (m-10) cc_final: 0.8307 (m-80) REVERT: i 92 GLN cc_start: 0.9341 (mt0) cc_final: 0.9109 (mt0) REVERT: i 131 MET cc_start: 0.8949 (ttp) cc_final: 0.8525 (ttt) REVERT: i 135 LEU cc_start: 0.9523 (mm) cc_final: 0.9159 (mm) REVERT: i 152 LEU cc_start: 0.9683 (mt) cc_final: 0.9478 (mt) REVERT: j 28 MET cc_start: 0.8988 (mtp) cc_final: 0.8368 (mmm) REVERT: j 47 MET cc_start: 0.9023 (mmm) cc_final: 0.8460 (mmm) REVERT: j 97 LEU cc_start: 0.9188 (tt) cc_final: 0.8851 (pp) REVERT: j 108 PHE cc_start: 0.8912 (m-80) cc_final: 0.8558 (m-80) REVERT: j 121 THR cc_start: 0.8670 (m) cc_final: 0.8089 (m) REVERT: j 124 GLN cc_start: 0.8649 (tp-100) cc_final: 0.7764 (tm-30) REVERT: j 127 LEU cc_start: 0.9039 (tp) cc_final: 0.8313 (tp) REVERT: j 141 LEU cc_start: 0.9112 (mt) cc_final: 0.8592 (mt) REVERT: j 144 TYR cc_start: 0.9237 (m-10) cc_final: 0.9006 (m-80) REVERT: j 147 ILE cc_start: 0.9537 (mm) cc_final: 0.9329 (mm) REVERT: j 150 LEU cc_start: 0.9753 (mt) cc_final: 0.9546 (mt) REVERT: j 152 LEU cc_start: 0.9438 (tp) cc_final: 0.9156 (tp) REVERT: k 17 MET cc_start: 0.9083 (mtm) cc_final: 0.8858 (mtm) REVERT: k 23 MET cc_start: 0.9138 (mmm) cc_final: 0.8604 (mmm) REVERT: k 32 TYR cc_start: 0.8190 (t80) cc_final: 0.7911 (t80) REVERT: k 44 MET cc_start: 0.9195 (ppp) cc_final: 0.8886 (ppp) REVERT: k 53 MET cc_start: 0.8595 (tmm) cc_final: 0.7959 (mtt) REVERT: k 65 ILE cc_start: 0.9462 (mt) cc_final: 0.9170 (mt) REVERT: k 68 TYR cc_start: 0.8814 (m-10) cc_final: 0.8279 (m-80) REVERT: k 91 LEU cc_start: 0.9160 (mt) cc_final: 0.8842 (mt) REVERT: k 118 VAL cc_start: 0.9490 (t) cc_final: 0.9197 (t) REVERT: k 127 LEU cc_start: 0.8688 (mp) cc_final: 0.8418 (mp) REVERT: k 131 MET cc_start: 0.8349 (mtt) cc_final: 0.7796 (mtt) REVERT: l 17 MET cc_start: 0.9335 (mmp) cc_final: 0.8938 (mmp) REVERT: l 47 MET cc_start: 0.8647 (tpt) cc_final: 0.8248 (tpp) REVERT: l 48 ARG cc_start: 0.8556 (mtt90) cc_final: 0.7962 (mtt-85) REVERT: l 108 PHE cc_start: 0.8427 (t80) cc_final: 0.8199 (t80) REVERT: l 124 GLN cc_start: 0.8650 (tp-100) cc_final: 0.8347 (tm-30) REVERT: l 127 LEU cc_start: 0.8367 (tp) cc_final: 0.7916 (tp) REVERT: l 131 MET cc_start: 0.9469 (ttp) cc_final: 0.9096 (ttm) REVERT: l 155 LYS cc_start: 0.8709 (tptt) cc_final: 0.8488 (tptt) REVERT: m 11 SER cc_start: 0.8525 (p) cc_final: 0.8015 (t) REVERT: m 14 PHE cc_start: 0.9631 (m-80) cc_final: 0.9114 (m-80) REVERT: m 17 MET cc_start: 0.9173 (mtp) cc_final: 0.8903 (mmm) REVERT: m 21 SER cc_start: 0.9156 (m) cc_final: 0.8896 (p) REVERT: m 51 LEU cc_start: 0.8475 (mt) cc_final: 0.8231 (mt) REVERT: m 53 MET cc_start: 0.8873 (mmm) cc_final: 0.8126 (tmm) REVERT: m 61 MET cc_start: 0.9564 (mmm) cc_final: 0.9020 (tpt) REVERT: m 86 LEU cc_start: 0.9479 (tp) cc_final: 0.8848 (tp) REVERT: m 89 SER cc_start: 0.9488 (m) cc_final: 0.8868 (t) REVERT: m 90 PHE cc_start: 0.9005 (m-10) cc_final: 0.8661 (m-80) REVERT: m 92 GLN cc_start: 0.9381 (mt0) cc_final: 0.9020 (mt0) REVERT: m 144 TYR cc_start: 0.9669 (m-10) cc_final: 0.9213 (m-10) REVERT: n 25 PHE cc_start: 0.8902 (m-80) cc_final: 0.8584 (m-80) REVERT: n 47 MET cc_start: 0.9303 (mmm) cc_final: 0.8831 (mmm) REVERT: n 61 MET cc_start: 0.9355 (mmp) cc_final: 0.8436 (mmm) REVERT: n 68 TYR cc_start: 0.9257 (m-10) cc_final: 0.8914 (m-10) REVERT: n 90 PHE cc_start: 0.9071 (m-80) cc_final: 0.8538 (m-80) REVERT: n 121 THR cc_start: 0.7072 (p) cc_final: 0.6784 (p) REVERT: n 124 GLN cc_start: 0.8719 (tp-100) cc_final: 0.8236 (tm-30) REVERT: n 146 LEU cc_start: 0.8883 (mt) cc_final: 0.8505 (mt) REVERT: o 13 PHE cc_start: 0.8899 (t80) cc_final: 0.8472 (t80) REVERT: o 17 MET cc_start: 0.9101 (mmp) cc_final: 0.8845 (mmt) REVERT: o 51 LEU cc_start: 0.8718 (mt) cc_final: 0.8441 (mt) REVERT: o 57 ILE cc_start: 0.9117 (mt) cc_final: 0.8445 (tt) REVERT: o 61 MET cc_start: 0.9468 (mmp) cc_final: 0.9161 (mmm) REVERT: o 64 ILE cc_start: 0.9306 (mt) cc_final: 0.9056 (mt) REVERT: o 65 ILE cc_start: 0.9635 (mp) cc_final: 0.9276 (mp) REVERT: o 68 TYR cc_start: 0.9356 (m-10) cc_final: 0.8653 (m-80) REVERT: o 91 LEU cc_start: 0.9774 (mm) cc_final: 0.9394 (pp) REVERT: o 128 PHE cc_start: 0.8254 (t80) cc_final: 0.7758 (t80) REVERT: o 131 MET cc_start: 0.8652 (ppp) cc_final: 0.8336 (ppp) REVERT: o 152 LEU cc_start: 0.9432 (mt) cc_final: 0.9035 (mt) REVERT: p 303 TYR cc_start: 0.8814 (t80) cc_final: 0.8260 (t80) REVERT: p 313 ILE cc_start: 0.9761 (pt) cc_final: 0.9474 (pt) REVERT: p 330 ASN cc_start: 0.8783 (t0) cc_final: 0.8524 (t0) outliers start: 1 outliers final: 0 residues processed: 989 average time/residue: 0.2612 time to fit residues: 412.2431 Evaluate side-chains 868 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 867 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 166 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 HIS ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 92 GLN k 7 ASN ** k 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 19610 Z= 0.222 Angle : 0.684 14.230 26647 Z= 0.353 Chirality : 0.042 0.201 3268 Planarity : 0.004 0.035 3401 Dihedral : 4.061 23.649 2941 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.06 % Allowed : 1.53 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.16), residues: 2771 helix: 1.86 (0.11), residues: 2154 sheet: -3.24 (0.88), residues: 18 loop : -0.81 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP b 67 HIS 0.008 0.001 HIS b 128 PHE 0.033 0.002 PHE L 52 TYR 0.047 0.002 TYR l 68 ARG 0.007 0.001 ARG h 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 986 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 52 ILE cc_start: 0.9337 (tp) cc_final: 0.8991 (tp) REVERT: H 56 MET cc_start: 0.9053 (mmp) cc_final: 0.8822 (mmm) REVERT: H 60 GLU cc_start: 0.9349 (mm-30) cc_final: 0.8993 (mm-30) REVERT: H 85 GLN cc_start: 0.9315 (mm-40) cc_final: 0.8852 (mm-40) REVERT: H 119 TYR cc_start: 0.7446 (p90) cc_final: 0.7075 (p90) REVERT: L 11 ILE cc_start: 0.9680 (mp) cc_final: 0.9276 (mm) REVERT: L 44 THR cc_start: 0.9574 (t) cc_final: 0.8996 (p) REVERT: L 47 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8813 (mt-10) REVERT: L 53 ARG cc_start: 0.8347 (ttp-110) cc_final: 0.8093 (ttp-110) REVERT: L 54 GLN cc_start: 0.8606 (mt0) cc_final: 0.8239 (tp-100) REVERT: L 67 ASN cc_start: 0.9081 (m110) cc_final: 0.8522 (m110) REVERT: L 69 TYR cc_start: 0.8516 (p90) cc_final: 0.8059 (p90) REVERT: L 72 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8639 (mm-30) REVERT: L 73 MET cc_start: 0.8673 (mtt) cc_final: 0.8444 (mtt) REVERT: L 79 ASP cc_start: 0.9384 (m-30) cc_final: 0.9115 (m-30) REVERT: L 90 GLU cc_start: 0.8992 (mp0) cc_final: 0.8081 (tt0) REVERT: L 99 ASP cc_start: 0.8887 (t0) cc_final: 0.6247 (t0) REVERT: b 4 LEU cc_start: 0.9460 (mm) cc_final: 0.9059 (mm) REVERT: b 8 TYR cc_start: 0.8800 (m-80) cc_final: 0.8404 (m-80) REVERT: b 19 MET cc_start: 0.8774 (mtp) cc_final: 0.8377 (mtp) REVERT: b 41 LEU cc_start: 0.9123 (mm) cc_final: 0.8843 (mm) REVERT: b 48 MET cc_start: 0.9280 (ttm) cc_final: 0.8873 (ttp) REVERT: b 51 ASN cc_start: 0.8757 (p0) cc_final: 0.8002 (p0) REVERT: b 90 ASN cc_start: 0.9128 (m110) cc_final: 0.8742 (m110) REVERT: b 91 LEU cc_start: 0.9467 (tp) cc_final: 0.9191 (tp) REVERT: b 102 ILE cc_start: 0.9719 (mm) cc_final: 0.9489 (mm) REVERT: b 103 TYR cc_start: 0.8811 (m-10) cc_final: 0.8306 (m-10) REVERT: b 116 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7387 (mm-30) REVERT: b 130 ASN cc_start: 0.9122 (m-40) cc_final: 0.8892 (m110) REVERT: b 131 TYR cc_start: 0.9227 (m-80) cc_final: 0.8395 (m-80) REVERT: b 137 MET cc_start: 0.9462 (mtm) cc_final: 0.9195 (mtm) REVERT: b 164 LEU cc_start: 0.9662 (mp) cc_final: 0.9293 (mm) REVERT: b 168 GLN cc_start: 0.9048 (mp-120) cc_final: 0.8806 (mp10) REVERT: b 169 ASN cc_start: 0.8225 (t0) cc_final: 0.7650 (t0) REVERT: b 172 LEU cc_start: 0.9361 (mt) cc_final: 0.8750 (mt) REVERT: b 186 ILE cc_start: 0.9627 (mt) cc_final: 0.9209 (mt) REVERT: b 189 PHE cc_start: 0.9086 (m-10) cc_final: 0.8819 (m-80) REVERT: b 197 GLN cc_start: 0.8978 (mt0) cc_final: 0.8663 (mt0) REVERT: b 202 LYS cc_start: 0.8372 (tptp) cc_final: 0.8027 (mptt) REVERT: b 203 MET cc_start: 0.8759 (ptp) cc_final: 0.8419 (pmm) REVERT: d 28 LEU cc_start: 0.9175 (mt) cc_final: 0.8700 (mm) REVERT: d 44 ASP cc_start: 0.9105 (m-30) cc_final: 0.8831 (m-30) REVERT: d 48 HIS cc_start: 0.8876 (m90) cc_final: 0.8433 (m90) REVERT: d 76 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8711 (mt-10) REVERT: d 105 MET cc_start: 0.9015 (mmm) cc_final: 0.8336 (tpt) REVERT: d 125 LEU cc_start: 0.9140 (mt) cc_final: 0.8825 (mt) REVERT: d 128 LYS cc_start: 0.9432 (mmtt) cc_final: 0.8922 (mmmt) REVERT: d 129 CYS cc_start: 0.8326 (m) cc_final: 0.7703 (m) REVERT: d 181 ILE cc_start: 0.9022 (mt) cc_final: 0.8791 (mt) REVERT: d 183 ASN cc_start: 0.9453 (t0) cc_final: 0.9181 (t0) REVERT: d 213 GLU cc_start: 0.8237 (pp20) cc_final: 0.7616 (tt0) REVERT: d 233 SER cc_start: 0.8954 (p) cc_final: 0.8421 (p) REVERT: d 235 GLU cc_start: 0.9181 (mp0) cc_final: 0.8868 (pm20) REVERT: d 262 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8239 (tm-30) REVERT: d 291 GLU cc_start: 0.9666 (mm-30) cc_final: 0.9436 (mm-30) REVERT: d 315 PHE cc_start: 0.9744 (m-80) cc_final: 0.9388 (m-80) REVERT: d 325 GLU cc_start: 0.9554 (tt0) cc_final: 0.8899 (tm-30) REVERT: d 326 CYS cc_start: 0.9622 (t) cc_final: 0.9418 (t) REVERT: d 348 ILE cc_start: 0.9510 (mm) cc_final: 0.9237 (mp) REVERT: g 14 PHE cc_start: 0.9739 (m-10) cc_final: 0.9466 (m-10) REVERT: g 28 MET cc_start: 0.9839 (mtm) cc_final: 0.9421 (mtm) REVERT: g 32 TYR cc_start: 0.8984 (t80) cc_final: 0.8241 (t80) REVERT: g 48 ARG cc_start: 0.8532 (mtp180) cc_final: 0.7888 (mtp180) REVERT: g 51 LEU cc_start: 0.8678 (mm) cc_final: 0.8090 (mm) REVERT: g 53 MET cc_start: 0.8629 (mtm) cc_final: 0.7886 (ttp) REVERT: g 57 ILE cc_start: 0.9524 (mt) cc_final: 0.9059 (mt) REVERT: g 70 LEU cc_start: 0.9527 (tp) cc_final: 0.9310 (tp) REVERT: g 80 LEU cc_start: 0.9567 (mt) cc_final: 0.9227 (mt) REVERT: g 90 PHE cc_start: 0.9089 (m-80) cc_final: 0.8558 (m-80) REVERT: g 112 ILE cc_start: 0.9469 (mm) cc_final: 0.9116 (mm) REVERT: g 131 MET cc_start: 0.9477 (ttm) cc_final: 0.9114 (mtp) REVERT: g 141 LEU cc_start: 0.9422 (mt) cc_final: 0.9068 (mt) REVERT: g 144 TYR cc_start: 0.8878 (m-80) cc_final: 0.8639 (m-80) REVERT: h 13 PHE cc_start: 0.9479 (t80) cc_final: 0.9273 (t80) REVERT: h 17 MET cc_start: 0.9468 (mtt) cc_final: 0.9220 (mtp) REVERT: h 24 VAL cc_start: 0.9529 (p) cc_final: 0.9254 (p) REVERT: h 28 MET cc_start: 0.8852 (mtp) cc_final: 0.8456 (ptp) REVERT: h 32 TYR cc_start: 0.8846 (t80) cc_final: 0.8424 (t80) REVERT: h 44 MET cc_start: 0.8347 (tmm) cc_final: 0.7838 (tmm) REVERT: h 48 ARG cc_start: 0.8163 (ttm170) cc_final: 0.7384 (ttm-80) REVERT: h 51 LEU cc_start: 0.8628 (mt) cc_final: 0.8336 (mt) REVERT: h 57 ILE cc_start: 0.9625 (mt) cc_final: 0.9245 (mt) REVERT: h 60 VAL cc_start: 0.9216 (p) cc_final: 0.8999 (m) REVERT: h 112 ILE cc_start: 0.9460 (mm) cc_final: 0.9140 (tp) REVERT: h 128 PHE cc_start: 0.9138 (t80) cc_final: 0.8684 (t80) REVERT: h 137 PHE cc_start: 0.9128 (m-80) cc_final: 0.8625 (m-80) REVERT: h 144 TYR cc_start: 0.9611 (m-10) cc_final: 0.9140 (m-10) REVERT: h 152 LEU cc_start: 0.9565 (mt) cc_final: 0.9345 (mt) REVERT: i 17 MET cc_start: 0.9575 (mmt) cc_final: 0.9016 (mmm) REVERT: i 61 MET cc_start: 0.9135 (mtp) cc_final: 0.8920 (mtp) REVERT: i 64 ILE cc_start: 0.9498 (mm) cc_final: 0.9283 (mm) REVERT: i 90 PHE cc_start: 0.8896 (m-10) cc_final: 0.8293 (m-80) REVERT: i 92 GLN cc_start: 0.9291 (mt0) cc_final: 0.8981 (tt0) REVERT: i 101 LEU cc_start: 0.9327 (mt) cc_final: 0.9108 (mt) REVERT: i 131 MET cc_start: 0.8918 (ttp) cc_final: 0.8508 (ttt) REVERT: i 135 LEU cc_start: 0.9509 (mm) cc_final: 0.9118 (mm) REVERT: i 152 LEU cc_start: 0.9657 (mt) cc_final: 0.9443 (mt) REVERT: j 28 MET cc_start: 0.8992 (mtp) cc_final: 0.8285 (tpt) REVERT: j 47 MET cc_start: 0.9029 (mmm) cc_final: 0.8183 (mmm) REVERT: j 84 ILE cc_start: 0.8314 (mm) cc_final: 0.7763 (pt) REVERT: j 97 LEU cc_start: 0.9142 (tt) cc_final: 0.8823 (pp) REVERT: j 108 PHE cc_start: 0.8826 (m-80) cc_final: 0.8466 (m-80) REVERT: j 121 THR cc_start: 0.8614 (m) cc_final: 0.8240 (m) REVERT: j 124 GLN cc_start: 0.8680 (tp-100) cc_final: 0.7827 (tm-30) REVERT: j 127 LEU cc_start: 0.8987 (tp) cc_final: 0.8423 (tp) REVERT: j 141 LEU cc_start: 0.9037 (mt) cc_final: 0.8508 (mt) REVERT: j 144 TYR cc_start: 0.9207 (m-10) cc_final: 0.8991 (m-80) REVERT: j 147 ILE cc_start: 0.9528 (mm) cc_final: 0.9316 (mm) REVERT: j 152 LEU cc_start: 0.9390 (tp) cc_final: 0.9107 (tp) REVERT: k 23 MET cc_start: 0.9103 (mmm) cc_final: 0.8562 (mmm) REVERT: k 32 TYR cc_start: 0.8102 (t80) cc_final: 0.7851 (t80) REVERT: k 65 ILE cc_start: 0.9419 (mt) cc_final: 0.9113 (mt) REVERT: k 68 TYR cc_start: 0.8807 (m-10) cc_final: 0.8295 (m-80) REVERT: k 90 PHE cc_start: 0.8806 (m-10) cc_final: 0.8449 (m-80) REVERT: k 91 LEU cc_start: 0.9134 (mt) cc_final: 0.8817 (mt) REVERT: k 118 VAL cc_start: 0.9470 (t) cc_final: 0.9171 (t) REVERT: k 124 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8719 (tm-30) REVERT: k 131 MET cc_start: 0.8248 (mtt) cc_final: 0.7686 (mtt) REVERT: l 17 MET cc_start: 0.9285 (mmp) cc_final: 0.8915 (mmp) REVERT: l 23 MET cc_start: 0.9586 (mmp) cc_final: 0.9344 (mmm) REVERT: l 32 TYR cc_start: 0.8033 (t80) cc_final: 0.7475 (t80) REVERT: l 48 ARG cc_start: 0.8494 (mtt90) cc_final: 0.8274 (ttt180) REVERT: l 124 GLN cc_start: 0.8658 (tp-100) cc_final: 0.8343 (tm-30) REVERT: l 127 LEU cc_start: 0.8298 (tp) cc_final: 0.7928 (tp) REVERT: l 131 MET cc_start: 0.9459 (ttp) cc_final: 0.9071 (ttm) REVERT: l 155 LYS cc_start: 0.8579 (tptt) cc_final: 0.8305 (tptt) REVERT: m 11 SER cc_start: 0.8526 (p) cc_final: 0.7880 (t) REVERT: m 14 PHE cc_start: 0.9663 (m-80) cc_final: 0.9169 (m-80) REVERT: m 17 MET cc_start: 0.9125 (mtp) cc_final: 0.8780 (mmm) REVERT: m 21 SER cc_start: 0.9060 (m) cc_final: 0.8812 (p) REVERT: m 23 MET cc_start: 0.9463 (tpt) cc_final: 0.9188 (tpt) REVERT: m 48 ARG cc_start: 0.8567 (mmm160) cc_final: 0.8130 (mmp-170) REVERT: m 51 LEU cc_start: 0.8503 (mt) cc_final: 0.8230 (mt) REVERT: m 53 MET cc_start: 0.8837 (mmm) cc_final: 0.8128 (tmm) REVERT: m 61 MET cc_start: 0.9472 (mmm) cc_final: 0.9264 (mmm) REVERT: m 86 LEU cc_start: 0.9423 (tp) cc_final: 0.8882 (tp) REVERT: m 89 SER cc_start: 0.9420 (m) cc_final: 0.8707 (t) REVERT: m 90 PHE cc_start: 0.8947 (m-10) cc_final: 0.8631 (m-80) REVERT: m 92 GLN cc_start: 0.9368 (mt0) cc_final: 0.8953 (mt0) REVERT: m 144 TYR cc_start: 0.9631 (m-10) cc_final: 0.9209 (m-10) REVERT: n 25 PHE cc_start: 0.8849 (m-80) cc_final: 0.8570 (m-80) REVERT: n 47 MET cc_start: 0.9301 (mmm) cc_final: 0.8793 (mmm) REVERT: n 61 MET cc_start: 0.9363 (mmp) cc_final: 0.8426 (mmm) REVERT: n 68 TYR cc_start: 0.9233 (m-10) cc_final: 0.8877 (m-10) REVERT: n 90 PHE cc_start: 0.8818 (m-80) cc_final: 0.8335 (m-80) REVERT: n 146 LEU cc_start: 0.8881 (mt) cc_final: 0.8483 (mt) REVERT: o 13 PHE cc_start: 0.8870 (t80) cc_final: 0.8340 (t80) REVERT: o 17 MET cc_start: 0.9074 (mmp) cc_final: 0.8803 (mmt) REVERT: o 47 MET cc_start: 0.8828 (tmm) cc_final: 0.8342 (tmm) REVERT: o 48 ARG cc_start: 0.8982 (ptm160) cc_final: 0.8692 (ptp-170) REVERT: o 51 LEU cc_start: 0.8573 (mt) cc_final: 0.8352 (mt) REVERT: o 57 ILE cc_start: 0.9038 (mt) cc_final: 0.8776 (mm) REVERT: o 61 MET cc_start: 0.9412 (mmp) cc_final: 0.9204 (mmm) REVERT: o 64 ILE cc_start: 0.9283 (mt) cc_final: 0.9028 (mt) REVERT: o 65 ILE cc_start: 0.9639 (mp) cc_final: 0.9247 (mp) REVERT: o 68 TYR cc_start: 0.9392 (m-10) cc_final: 0.8811 (m-80) REVERT: o 76 ILE cc_start: 0.9512 (mp) cc_final: 0.9063 (tt) REVERT: o 128 PHE cc_start: 0.8233 (t80) cc_final: 0.7717 (t80) REVERT: o 131 MET cc_start: 0.8658 (ppp) cc_final: 0.8373 (ppp) REVERT: o 132 ILE cc_start: 0.8696 (mm) cc_final: 0.8119 (mt) REVERT: o 144 TYR cc_start: 0.9052 (m-10) cc_final: 0.8765 (m-10) REVERT: p 303 TYR cc_start: 0.8758 (t80) cc_final: 0.8245 (t80) REVERT: p 313 ILE cc_start: 0.9688 (pt) cc_final: 0.9480 (pt) REVERT: p 314 MET cc_start: 0.9531 (mmp) cc_final: 0.9246 (mmp) REVERT: p 330 ASN cc_start: 0.8829 (t0) cc_final: 0.8484 (t0) outliers start: 1 outliers final: 1 residues processed: 986 average time/residue: 0.2631 time to fit residues: 413.7801 Evaluate side-chains 891 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 890 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 257 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 chunk 250 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 226 optimal weight: 0.1980 chunk 237 optimal weight: 0.7980 chunk 249 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 HIS H 137 ASN b 148 ASN ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 92 GLN ** k 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.6119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19610 Z= 0.217 Angle : 0.681 13.026 26647 Z= 0.346 Chirality : 0.042 0.366 3268 Planarity : 0.004 0.070 3401 Dihedral : 4.052 20.782 2941 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.16), residues: 2771 helix: 1.89 (0.11), residues: 2154 sheet: -2.77 (0.99), residues: 16 loop : -0.77 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP c 420 HIS 0.006 0.001 HIS b 128 PHE 0.073 0.002 PHE j 90 TYR 0.052 0.002 TYR k 144 ARG 0.006 0.000 ARG h 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 982 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 52 ILE cc_start: 0.9314 (tp) cc_final: 0.8943 (tp) REVERT: H 56 MET cc_start: 0.9037 (mmp) cc_final: 0.8811 (mmm) REVERT: H 60 GLU cc_start: 0.9359 (mm-30) cc_final: 0.9023 (mm-30) REVERT: H 64 GLU cc_start: 0.9349 (tp30) cc_final: 0.8528 (tm-30) REVERT: H 85 GLN cc_start: 0.9263 (mm-40) cc_final: 0.8819 (mm-40) REVERT: L 11 ILE cc_start: 0.9686 (mp) cc_final: 0.9111 (mm) REVERT: L 14 GLU cc_start: 0.9081 (pm20) cc_final: 0.8877 (pm20) REVERT: L 44 THR cc_start: 0.9596 (t) cc_final: 0.9011 (p) REVERT: L 47 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8793 (mt-10) REVERT: L 53 ARG cc_start: 0.8272 (ttp-110) cc_final: 0.7923 (ttp-110) REVERT: L 54 GLN cc_start: 0.8529 (mt0) cc_final: 0.8183 (tp-100) REVERT: L 67 ASN cc_start: 0.8974 (m110) cc_final: 0.8365 (m110) REVERT: L 69 TYR cc_start: 0.8384 (p90) cc_final: 0.7969 (p90) REVERT: L 70 ILE cc_start: 0.9464 (mt) cc_final: 0.9210 (mt) REVERT: L 72 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8638 (mm-30) REVERT: L 73 MET cc_start: 0.8720 (mtt) cc_final: 0.8502 (mtt) REVERT: L 79 ASP cc_start: 0.9353 (m-30) cc_final: 0.9106 (m-30) REVERT: L 90 GLU cc_start: 0.8869 (mp0) cc_final: 0.8150 (tt0) REVERT: L 99 ASP cc_start: 0.8897 (t0) cc_final: 0.6592 (t0) REVERT: b 4 LEU cc_start: 0.9442 (mm) cc_final: 0.9018 (mm) REVERT: b 8 TYR cc_start: 0.8781 (m-80) cc_final: 0.8380 (m-80) REVERT: b 19 MET cc_start: 0.8764 (mtp) cc_final: 0.8360 (mtp) REVERT: b 41 LEU cc_start: 0.9076 (mm) cc_final: 0.8809 (mm) REVERT: b 48 MET cc_start: 0.9333 (ttm) cc_final: 0.8673 (mtp) REVERT: b 51 ASN cc_start: 0.8778 (p0) cc_final: 0.8100 (p0) REVERT: b 87 LYS cc_start: 0.9472 (ptmt) cc_final: 0.9098 (ttmt) REVERT: b 90 ASN cc_start: 0.9031 (m110) cc_final: 0.8639 (m110) REVERT: b 91 LEU cc_start: 0.9463 (tp) cc_final: 0.9172 (tp) REVERT: b 102 ILE cc_start: 0.9707 (mm) cc_final: 0.9476 (mm) REVERT: b 103 TYR cc_start: 0.8827 (m-10) cc_final: 0.8354 (m-10) REVERT: b 116 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7370 (mm-30) REVERT: b 130 ASN cc_start: 0.9093 (m-40) cc_final: 0.8838 (m110) REVERT: b 131 TYR cc_start: 0.9205 (m-80) cc_final: 0.8380 (m-80) REVERT: b 137 MET cc_start: 0.9469 (mtm) cc_final: 0.9200 (mtm) REVERT: b 164 LEU cc_start: 0.9606 (mp) cc_final: 0.9192 (mm) REVERT: b 168 GLN cc_start: 0.8985 (mp-120) cc_final: 0.8746 (mp10) REVERT: b 169 ASN cc_start: 0.8217 (t0) cc_final: 0.7682 (t0) REVERT: b 172 LEU cc_start: 0.9411 (mt) cc_final: 0.8834 (mt) REVERT: b 186 ILE cc_start: 0.9593 (mt) cc_final: 0.9168 (mt) REVERT: b 189 PHE cc_start: 0.9108 (m-10) cc_final: 0.8900 (m-80) REVERT: b 191 VAL cc_start: 0.9473 (t) cc_final: 0.9272 (m) REVERT: b 203 MET cc_start: 0.8687 (ptp) cc_final: 0.8440 (pmm) REVERT: d 28 LEU cc_start: 0.9174 (mt) cc_final: 0.8663 (mm) REVERT: d 44 ASP cc_start: 0.9098 (m-30) cc_final: 0.8828 (m-30) REVERT: d 48 HIS cc_start: 0.8868 (m90) cc_final: 0.8423 (m90) REVERT: d 76 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8723 (mt-10) REVERT: d 105 MET cc_start: 0.8971 (mmm) cc_final: 0.8255 (tpt) REVERT: d 125 LEU cc_start: 0.9147 (mt) cc_final: 0.8831 (mt) REVERT: d 128 LYS cc_start: 0.9405 (mmtt) cc_final: 0.8944 (mmmt) REVERT: d 129 CYS cc_start: 0.8309 (m) cc_final: 0.7763 (m) REVERT: d 135 PHE cc_start: 0.8439 (m-80) cc_final: 0.8214 (m-80) REVERT: d 181 ILE cc_start: 0.8998 (mt) cc_final: 0.8771 (mt) REVERT: d 183 ASN cc_start: 0.9425 (t0) cc_final: 0.9129 (t0) REVERT: d 233 SER cc_start: 0.8917 (p) cc_final: 0.8390 (p) REVERT: d 235 GLU cc_start: 0.9170 (mp0) cc_final: 0.8869 (pm20) REVERT: d 262 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8237 (tm-30) REVERT: d 277 LEU cc_start: 0.9125 (mm) cc_final: 0.8875 (tp) REVERT: d 291 GLU cc_start: 0.9681 (mm-30) cc_final: 0.9459 (mm-30) REVERT: d 315 PHE cc_start: 0.9748 (m-80) cc_final: 0.9370 (m-80) REVERT: d 322 LYS cc_start: 0.9685 (mtpt) cc_final: 0.9460 (mtpp) REVERT: d 325 GLU cc_start: 0.9565 (tt0) cc_final: 0.8863 (tm-30) REVERT: d 326 CYS cc_start: 0.9631 (t) cc_final: 0.9430 (t) REVERT: g 28 MET cc_start: 0.9831 (mtm) cc_final: 0.9411 (mtm) REVERT: g 32 TYR cc_start: 0.9005 (t80) cc_final: 0.8319 (t80) REVERT: g 48 ARG cc_start: 0.8543 (mtp180) cc_final: 0.8331 (mtp180) REVERT: g 51 LEU cc_start: 0.8642 (mm) cc_final: 0.7916 (mm) REVERT: g 53 MET cc_start: 0.8738 (mtm) cc_final: 0.7907 (ttp) REVERT: g 54 LYS cc_start: 0.8662 (pttm) cc_final: 0.7784 (ptpt) REVERT: g 57 ILE cc_start: 0.9528 (mt) cc_final: 0.9091 (mt) REVERT: g 68 TYR cc_start: 0.9605 (m-80) cc_final: 0.9264 (m-80) REVERT: g 90 PHE cc_start: 0.9134 (m-80) cc_final: 0.8434 (m-80) REVERT: g 121 THR cc_start: 0.9505 (m) cc_final: 0.9079 (m) REVERT: g 128 PHE cc_start: 0.8881 (t80) cc_final: 0.8643 (t80) REVERT: g 131 MET cc_start: 0.9478 (ttm) cc_final: 0.9179 (mtp) REVERT: g 141 LEU cc_start: 0.9392 (mt) cc_final: 0.9040 (mt) REVERT: g 144 TYR cc_start: 0.8906 (m-80) cc_final: 0.8668 (m-80) REVERT: h 17 MET cc_start: 0.9432 (mtt) cc_final: 0.9146 (mtp) REVERT: h 24 VAL cc_start: 0.9525 (p) cc_final: 0.9320 (p) REVERT: h 28 MET cc_start: 0.8834 (mtp) cc_final: 0.8455 (ptp) REVERT: h 32 TYR cc_start: 0.8826 (t80) cc_final: 0.8390 (t80) REVERT: h 44 MET cc_start: 0.8364 (tmm) cc_final: 0.7876 (tmm) REVERT: h 48 ARG cc_start: 0.8223 (ttm170) cc_final: 0.7428 (ttm-80) REVERT: h 51 LEU cc_start: 0.8595 (mt) cc_final: 0.8319 (mt) REVERT: h 57 ILE cc_start: 0.9603 (mt) cc_final: 0.9216 (mt) REVERT: h 112 ILE cc_start: 0.9471 (mm) cc_final: 0.9195 (tp) REVERT: h 128 PHE cc_start: 0.9139 (t80) cc_final: 0.8662 (t80) REVERT: h 137 PHE cc_start: 0.9070 (m-80) cc_final: 0.8599 (m-80) REVERT: h 144 TYR cc_start: 0.9623 (m-10) cc_final: 0.9145 (m-10) REVERT: h 146 LEU cc_start: 0.9469 (tp) cc_final: 0.9269 (tp) REVERT: h 152 LEU cc_start: 0.9561 (mt) cc_final: 0.9349 (mt) REVERT: i 17 MET cc_start: 0.9518 (mmt) cc_final: 0.9211 (mmt) REVERT: i 28 MET cc_start: 0.9416 (mpp) cc_final: 0.9195 (mpp) REVERT: i 64 ILE cc_start: 0.9500 (mm) cc_final: 0.9269 (mm) REVERT: i 90 PHE cc_start: 0.8946 (m-10) cc_final: 0.8269 (m-80) REVERT: i 92 GLN cc_start: 0.9307 (mt0) cc_final: 0.8979 (tt0) REVERT: i 101 LEU cc_start: 0.9324 (mt) cc_final: 0.9103 (mt) REVERT: i 131 MET cc_start: 0.8888 (ttp) cc_final: 0.8429 (ttt) REVERT: i 135 LEU cc_start: 0.9446 (mm) cc_final: 0.9032 (mm) REVERT: i 152 LEU cc_start: 0.9657 (mt) cc_final: 0.9444 (mt) REVERT: j 28 MET cc_start: 0.8944 (mtp) cc_final: 0.8311 (mmm) REVERT: j 47 MET cc_start: 0.9126 (mmm) cc_final: 0.8769 (mmm) REVERT: j 61 MET cc_start: 0.8613 (ttp) cc_final: 0.8229 (ttm) REVERT: j 84 ILE cc_start: 0.8428 (mm) cc_final: 0.8223 (mm) REVERT: j 97 LEU cc_start: 0.9132 (tt) cc_final: 0.8801 (pp) REVERT: j 108 PHE cc_start: 0.8752 (m-80) cc_final: 0.8429 (m-80) REVERT: j 121 THR cc_start: 0.8247 (m) cc_final: 0.7906 (p) REVERT: j 124 GLN cc_start: 0.8612 (tp-100) cc_final: 0.7943 (tm-30) REVERT: j 127 LEU cc_start: 0.8928 (tp) cc_final: 0.8525 (tp) REVERT: j 141 LEU cc_start: 0.8965 (mt) cc_final: 0.8456 (mt) REVERT: j 144 TYR cc_start: 0.9197 (m-10) cc_final: 0.8983 (m-80) REVERT: j 147 ILE cc_start: 0.9526 (mm) cc_final: 0.9325 (mm) REVERT: j 152 LEU cc_start: 0.9423 (tp) cc_final: 0.9176 (tp) REVERT: k 17 MET cc_start: 0.9026 (mtm) cc_final: 0.8797 (mtm) REVERT: k 23 MET cc_start: 0.9090 (mmm) cc_final: 0.8656 (mmm) REVERT: k 32 TYR cc_start: 0.8086 (t80) cc_final: 0.7819 (t80) REVERT: k 65 ILE cc_start: 0.9365 (mt) cc_final: 0.9047 (mt) REVERT: k 68 TYR cc_start: 0.8899 (m-10) cc_final: 0.8415 (m-80) REVERT: k 90 PHE cc_start: 0.8785 (m-10) cc_final: 0.8402 (m-80) REVERT: k 91 LEU cc_start: 0.9126 (mt) cc_final: 0.8808 (mt) REVERT: k 118 VAL cc_start: 0.9449 (t) cc_final: 0.9120 (t) REVERT: k 124 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8515 (tm-30) REVERT: k 131 MET cc_start: 0.8299 (mtt) cc_final: 0.7597 (mtt) REVERT: l 13 PHE cc_start: 0.9129 (t80) cc_final: 0.8665 (t80) REVERT: l 17 MET cc_start: 0.9270 (mmp) cc_final: 0.8880 (mmp) REVERT: l 32 TYR cc_start: 0.8039 (t80) cc_final: 0.7377 (t80) REVERT: l 48 ARG cc_start: 0.8495 (mtt90) cc_final: 0.8268 (ttt180) REVERT: l 65 ILE cc_start: 0.9406 (mp) cc_final: 0.9174 (mp) REVERT: l 68 TYR cc_start: 0.8924 (m-80) cc_final: 0.8256 (m-80) REVERT: l 124 GLN cc_start: 0.8692 (tp-100) cc_final: 0.8376 (tm-30) REVERT: l 127 LEU cc_start: 0.8358 (tp) cc_final: 0.7940 (tp) REVERT: l 131 MET cc_start: 0.9462 (ttp) cc_final: 0.9077 (ttm) REVERT: l 143 LEU cc_start: 0.9276 (mm) cc_final: 0.8968 (mm) REVERT: l 146 LEU cc_start: 0.9205 (tt) cc_final: 0.8863 (pp) REVERT: m 14 PHE cc_start: 0.9707 (m-80) cc_final: 0.9207 (m-80) REVERT: m 17 MET cc_start: 0.9118 (mtp) cc_final: 0.8804 (mmm) REVERT: m 21 SER cc_start: 0.9055 (m) cc_final: 0.8797 (p) REVERT: m 48 ARG cc_start: 0.8732 (mmm160) cc_final: 0.8403 (mmp-170) REVERT: m 53 MET cc_start: 0.8851 (mmm) cc_final: 0.8181 (tmm) REVERT: m 86 LEU cc_start: 0.9426 (tp) cc_final: 0.8910 (tp) REVERT: m 89 SER cc_start: 0.9412 (m) cc_final: 0.8702 (t) REVERT: m 90 PHE cc_start: 0.8885 (m-10) cc_final: 0.8544 (m-80) REVERT: m 92 GLN cc_start: 0.9364 (mt0) cc_final: 0.8962 (mt0) REVERT: m 133 LEU cc_start: 0.8605 (tt) cc_final: 0.8123 (tp) REVERT: m 137 PHE cc_start: 0.9190 (m-80) cc_final: 0.8837 (m-80) REVERT: n 25 PHE cc_start: 0.8852 (m-80) cc_final: 0.8632 (m-80) REVERT: n 47 MET cc_start: 0.9287 (mmm) cc_final: 0.8753 (mmm) REVERT: n 61 MET cc_start: 0.9374 (mmp) cc_final: 0.8766 (mmm) REVERT: n 68 TYR cc_start: 0.9230 (m-10) cc_final: 0.8888 (m-10) REVERT: n 90 PHE cc_start: 0.8773 (m-80) cc_final: 0.8286 (m-80) REVERT: n 135 LEU cc_start: 0.9534 (mt) cc_final: 0.9222 (mt) REVERT: n 146 LEU cc_start: 0.8867 (mt) cc_final: 0.8479 (mt) REVERT: o 13 PHE cc_start: 0.8890 (t80) cc_final: 0.8303 (t80) REVERT: o 17 MET cc_start: 0.9070 (mmp) cc_final: 0.8792 (mmt) REVERT: o 25 PHE cc_start: 0.8003 (m-10) cc_final: 0.7802 (m-10) REVERT: o 47 MET cc_start: 0.8836 (tmm) cc_final: 0.8247 (tmm) REVERT: o 48 ARG cc_start: 0.8927 (ptm160) cc_final: 0.8593 (ptp-170) REVERT: o 51 LEU cc_start: 0.8588 (mt) cc_final: 0.8378 (mt) REVERT: o 57 ILE cc_start: 0.9005 (mt) cc_final: 0.8755 (mm) REVERT: o 64 ILE cc_start: 0.9281 (mt) cc_final: 0.9030 (mt) REVERT: o 65 ILE cc_start: 0.9649 (mp) cc_final: 0.9261 (mp) REVERT: o 68 TYR cc_start: 0.9314 (m-10) cc_final: 0.8832 (m-80) REVERT: o 90 PHE cc_start: 0.9352 (m-80) cc_final: 0.8958 (m-80) REVERT: o 128 PHE cc_start: 0.8233 (t80) cc_final: 0.7772 (t80) REVERT: o 132 ILE cc_start: 0.8698 (mm) cc_final: 0.8337 (mm) REVERT: o 144 TYR cc_start: 0.9067 (m-10) cc_final: 0.8730 (m-10) REVERT: p 303 TYR cc_start: 0.8617 (t80) cc_final: 0.8054 (t80) REVERT: p 330 ASN cc_start: 0.8861 (t0) cc_final: 0.8490 (t0) outliers start: 0 outliers final: 0 residues processed: 982 average time/residue: 0.2610 time to fit residues: 408.9376 Evaluate side-chains 893 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 893 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 264 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 175 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 HIS H 137 ASN L 81 HIS ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 92 GLN k 7 ASN ** k 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.6284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 19610 Z= 0.229 Angle : 0.692 15.349 26647 Z= 0.355 Chirality : 0.043 0.280 3268 Planarity : 0.004 0.035 3401 Dihedral : 4.007 23.401 2941 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.06 % Allowed : 0.35 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.16), residues: 2771 helix: 1.82 (0.11), residues: 2159 sheet: -2.73 (1.07), residues: 16 loop : -0.81 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP c 420 HIS 0.006 0.001 HIS b 128 PHE 0.047 0.002 PHE j 90 TYR 0.045 0.002 TYR l 68 ARG 0.012 0.001 ARG j 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 975 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 52 ILE cc_start: 0.9320 (tp) cc_final: 0.8933 (tp) REVERT: H 56 MET cc_start: 0.9025 (mmp) cc_final: 0.8812 (mmm) REVERT: H 60 GLU cc_start: 0.9358 (mm-30) cc_final: 0.9025 (mm-30) REVERT: H 85 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8743 (mm-40) REVERT: H 91 GLN cc_start: 0.8133 (tp-100) cc_final: 0.7796 (tt0) REVERT: L 11 ILE cc_start: 0.9682 (mp) cc_final: 0.9155 (mm) REVERT: L 47 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8888 (mm-30) REVERT: L 51 THR cc_start: 0.8847 (p) cc_final: 0.8353 (p) REVERT: L 53 ARG cc_start: 0.8310 (ttp-110) cc_final: 0.8093 (ttp-110) REVERT: L 54 GLN cc_start: 0.8579 (mt0) cc_final: 0.8295 (mp10) REVERT: L 67 ASN cc_start: 0.8952 (m110) cc_final: 0.8284 (m110) REVERT: L 69 TYR cc_start: 0.8457 (p90) cc_final: 0.8028 (p90) REVERT: L 72 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8639 (mm-30) REVERT: L 79 ASP cc_start: 0.9347 (m-30) cc_final: 0.9080 (m-30) REVERT: L 90 GLU cc_start: 0.8847 (mp0) cc_final: 0.8272 (tt0) REVERT: L 99 ASP cc_start: 0.8905 (t0) cc_final: 0.6542 (t0) REVERT: b 19 MET cc_start: 0.8733 (mtp) cc_final: 0.8351 (mtp) REVERT: b 41 LEU cc_start: 0.9059 (mm) cc_final: 0.8837 (mm) REVERT: b 48 MET cc_start: 0.9253 (ttm) cc_final: 0.8710 (mtp) REVERT: b 51 ASN cc_start: 0.8716 (p0) cc_final: 0.8121 (p0) REVERT: b 87 LYS cc_start: 0.9383 (ptmt) cc_final: 0.9075 (ttmt) REVERT: b 91 LEU cc_start: 0.9440 (tp) cc_final: 0.9135 (tp) REVERT: b 103 TYR cc_start: 0.8851 (m-10) cc_final: 0.8376 (m-10) REVERT: b 116 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7450 (mm-30) REVERT: b 126 ILE cc_start: 0.8176 (mm) cc_final: 0.7941 (mm) REVERT: b 130 ASN cc_start: 0.9073 (m-40) cc_final: 0.8813 (m110) REVERT: b 131 TYR cc_start: 0.9211 (m-80) cc_final: 0.8503 (m-80) REVERT: b 137 MET cc_start: 0.9467 (mtm) cc_final: 0.9203 (mtm) REVERT: b 164 LEU cc_start: 0.9621 (mp) cc_final: 0.9214 (mm) REVERT: b 168 GLN cc_start: 0.8987 (mp-120) cc_final: 0.8717 (mp10) REVERT: b 169 ASN cc_start: 0.8195 (t0) cc_final: 0.7636 (t0) REVERT: b 172 LEU cc_start: 0.9364 (mt) cc_final: 0.8794 (mt) REVERT: b 186 ILE cc_start: 0.9571 (mt) cc_final: 0.9144 (mt) REVERT: b 191 VAL cc_start: 0.9522 (t) cc_final: 0.9315 (m) REVERT: b 202 LYS cc_start: 0.8139 (tptp) cc_final: 0.7852 (mptt) REVERT: d 28 LEU cc_start: 0.9167 (mt) cc_final: 0.8656 (mm) REVERT: d 44 ASP cc_start: 0.9040 (m-30) cc_final: 0.8804 (m-30) REVERT: d 48 HIS cc_start: 0.8844 (m90) cc_final: 0.8406 (m90) REVERT: d 76 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8697 (mt-10) REVERT: d 105 MET cc_start: 0.9009 (mmm) cc_final: 0.8297 (tpt) REVERT: d 125 LEU cc_start: 0.9182 (mt) cc_final: 0.8870 (mt) REVERT: d 128 LYS cc_start: 0.9431 (mmtt) cc_final: 0.8914 (mmmt) REVERT: d 129 CYS cc_start: 0.8302 (m) cc_final: 0.7792 (m) REVERT: d 135 PHE cc_start: 0.8464 (m-80) cc_final: 0.8230 (m-80) REVERT: d 183 ASN cc_start: 0.9430 (t0) cc_final: 0.9134 (t0) REVERT: d 233 SER cc_start: 0.8903 (p) cc_final: 0.8369 (p) REVERT: d 235 GLU cc_start: 0.9159 (mp0) cc_final: 0.8872 (pm20) REVERT: d 262 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8232 (tm-30) REVERT: d 277 LEU cc_start: 0.9142 (mm) cc_final: 0.8891 (tp) REVERT: d 315 PHE cc_start: 0.9755 (m-80) cc_final: 0.9416 (m-80) REVERT: d 322 LYS cc_start: 0.9712 (mtpt) cc_final: 0.9417 (mtpp) REVERT: d 325 GLU cc_start: 0.9582 (tt0) cc_final: 0.8844 (tm-30) REVERT: g 28 MET cc_start: 0.9842 (mtm) cc_final: 0.9477 (mtm) REVERT: g 32 TYR cc_start: 0.8966 (t80) cc_final: 0.8298 (t80) REVERT: g 48 ARG cc_start: 0.8561 (mtp180) cc_final: 0.8336 (mtp180) REVERT: g 51 LEU cc_start: 0.8685 (mm) cc_final: 0.8041 (mm) REVERT: g 53 MET cc_start: 0.8706 (mtm) cc_final: 0.8261 (ttm) REVERT: g 54 LYS cc_start: 0.8560 (pttm) cc_final: 0.7742 (ptpt) REVERT: g 57 ILE cc_start: 0.9526 (mt) cc_final: 0.9127 (mt) REVERT: g 68 TYR cc_start: 0.9587 (m-80) cc_final: 0.9253 (m-80) REVERT: g 80 LEU cc_start: 0.9525 (mt) cc_final: 0.9277 (mt) REVERT: g 90 PHE cc_start: 0.9064 (m-80) cc_final: 0.8613 (m-80) REVERT: g 121 THR cc_start: 0.9547 (m) cc_final: 0.9138 (m) REVERT: g 128 PHE cc_start: 0.8898 (t80) cc_final: 0.8670 (t80) REVERT: g 131 MET cc_start: 0.9480 (ttm) cc_final: 0.9189 (mtp) REVERT: h 13 PHE cc_start: 0.9446 (t80) cc_final: 0.9234 (t80) REVERT: h 17 MET cc_start: 0.9471 (mtt) cc_final: 0.9210 (mtp) REVERT: h 24 VAL cc_start: 0.9524 (p) cc_final: 0.9320 (p) REVERT: h 28 MET cc_start: 0.8738 (mtp) cc_final: 0.8366 (ptp) REVERT: h 32 TYR cc_start: 0.8872 (t80) cc_final: 0.8427 (t80) REVERT: h 44 MET cc_start: 0.8347 (tmm) cc_final: 0.7692 (tmm) REVERT: h 47 MET cc_start: 0.9217 (mmp) cc_final: 0.8610 (tmm) REVERT: h 48 ARG cc_start: 0.8246 (ttm170) cc_final: 0.7604 (ttm-80) REVERT: h 51 LEU cc_start: 0.8617 (mt) cc_final: 0.8312 (mt) REVERT: h 57 ILE cc_start: 0.9587 (mt) cc_final: 0.9184 (mt) REVERT: h 90 PHE cc_start: 0.9036 (m-10) cc_final: 0.8552 (m-80) REVERT: h 92 GLN cc_start: 0.9091 (mp10) cc_final: 0.8154 (mp10) REVERT: h 112 ILE cc_start: 0.9487 (mm) cc_final: 0.9281 (tp) REVERT: h 128 PHE cc_start: 0.9166 (t80) cc_final: 0.8815 (t80) REVERT: h 137 PHE cc_start: 0.9065 (m-80) cc_final: 0.8588 (m-80) REVERT: h 144 TYR cc_start: 0.9648 (m-10) cc_final: 0.9156 (m-10) REVERT: h 152 LEU cc_start: 0.9563 (mt) cc_final: 0.9351 (mt) REVERT: i 13 PHE cc_start: 0.8351 (t80) cc_final: 0.7933 (t80) REVERT: i 17 MET cc_start: 0.9468 (mmt) cc_final: 0.8969 (mmm) REVERT: i 64 ILE cc_start: 0.9487 (mm) cc_final: 0.9247 (mm) REVERT: i 90 PHE cc_start: 0.8867 (m-10) cc_final: 0.8265 (m-80) REVERT: i 92 GLN cc_start: 0.9298 (mt0) cc_final: 0.9032 (tt0) REVERT: i 101 LEU cc_start: 0.9327 (mt) cc_final: 0.9113 (mt) REVERT: i 131 MET cc_start: 0.8918 (ttp) cc_final: 0.8496 (ttt) REVERT: i 135 LEU cc_start: 0.9500 (mm) cc_final: 0.9075 (mm) REVERT: i 152 LEU cc_start: 0.9658 (mt) cc_final: 0.9438 (mt) REVERT: j 28 MET cc_start: 0.8990 (mtp) cc_final: 0.8331 (mmm) REVERT: j 47 MET cc_start: 0.9262 (mmm) cc_final: 0.8918 (mmm) REVERT: j 61 MET cc_start: 0.8618 (ttp) cc_final: 0.8190 (ttm) REVERT: j 91 LEU cc_start: 0.9266 (mt) cc_final: 0.9056 (mt) REVERT: j 97 LEU cc_start: 0.9123 (tt) cc_final: 0.8790 (pp) REVERT: j 108 PHE cc_start: 0.8741 (m-80) cc_final: 0.8405 (m-80) REVERT: j 121 THR cc_start: 0.8351 (m) cc_final: 0.7746 (p) REVERT: j 124 GLN cc_start: 0.8634 (tp-100) cc_final: 0.7857 (tm-30) REVERT: j 127 LEU cc_start: 0.8955 (tp) cc_final: 0.8470 (tp) REVERT: j 141 LEU cc_start: 0.8968 (mt) cc_final: 0.8449 (mt) REVERT: j 144 TYR cc_start: 0.9166 (m-10) cc_final: 0.8959 (m-80) REVERT: j 147 ILE cc_start: 0.9515 (mm) cc_final: 0.9313 (mm) REVERT: j 152 LEU cc_start: 0.9441 (tp) cc_final: 0.9171 (tp) REVERT: k 17 MET cc_start: 0.8977 (mtm) cc_final: 0.8736 (mtm) REVERT: k 23 MET cc_start: 0.9101 (mmm) cc_final: 0.8667 (mmm) REVERT: k 32 TYR cc_start: 0.8038 (t80) cc_final: 0.7768 (t80) REVERT: k 65 ILE cc_start: 0.9338 (mt) cc_final: 0.9015 (mt) REVERT: k 68 TYR cc_start: 0.8963 (m-10) cc_final: 0.8459 (m-80) REVERT: k 90 PHE cc_start: 0.8771 (m-10) cc_final: 0.8361 (m-80) REVERT: k 91 LEU cc_start: 0.9156 (mt) cc_final: 0.8830 (mt) REVERT: k 118 VAL cc_start: 0.9463 (t) cc_final: 0.9205 (t) REVERT: k 127 LEU cc_start: 0.8524 (mp) cc_final: 0.8248 (mp) REVERT: k 131 MET cc_start: 0.8241 (mtt) cc_final: 0.7585 (mtt) REVERT: l 13 PHE cc_start: 0.9138 (t80) cc_final: 0.8632 (t80) REVERT: l 17 MET cc_start: 0.9262 (mmp) cc_final: 0.8851 (mmp) REVERT: l 32 TYR cc_start: 0.8047 (t80) cc_final: 0.7382 (t80) REVERT: l 48 ARG cc_start: 0.8512 (mtt90) cc_final: 0.8265 (ttt180) REVERT: l 65 ILE cc_start: 0.9386 (mp) cc_final: 0.9133 (mp) REVERT: l 68 TYR cc_start: 0.8913 (m-80) cc_final: 0.8259 (m-80) REVERT: l 118 VAL cc_start: 0.9167 (m) cc_final: 0.8963 (m) REVERT: l 124 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8346 (tm-30) REVERT: l 127 LEU cc_start: 0.8408 (tp) cc_final: 0.7880 (tp) REVERT: l 131 MET cc_start: 0.9475 (ttp) cc_final: 0.9081 (ttm) REVERT: l 143 LEU cc_start: 0.9252 (mm) cc_final: 0.8942 (mm) REVERT: l 146 LEU cc_start: 0.9231 (tt) cc_final: 0.8852 (pp) REVERT: m 11 SER cc_start: 0.8577 (p) cc_final: 0.7979 (t) REVERT: m 14 PHE cc_start: 0.9725 (m-80) cc_final: 0.9206 (m-80) REVERT: m 17 MET cc_start: 0.9078 (mtp) cc_final: 0.8785 (mmm) REVERT: m 21 SER cc_start: 0.9047 (m) cc_final: 0.8776 (p) REVERT: m 53 MET cc_start: 0.8827 (mmm) cc_final: 0.8198 (tmm) REVERT: m 61 MET cc_start: 0.9478 (tpt) cc_final: 0.9266 (mmm) REVERT: m 86 LEU cc_start: 0.9420 (tp) cc_final: 0.8870 (tp) REVERT: m 89 SER cc_start: 0.9447 (m) cc_final: 0.8774 (t) REVERT: m 90 PHE cc_start: 0.8861 (m-10) cc_final: 0.8532 (m-80) REVERT: m 92 GLN cc_start: 0.9369 (mt0) cc_final: 0.8974 (mt0) REVERT: n 25 PHE cc_start: 0.8844 (m-80) cc_final: 0.8632 (m-80) REVERT: n 47 MET cc_start: 0.9270 (mmm) cc_final: 0.8721 (mmm) REVERT: n 61 MET cc_start: 0.9326 (mmp) cc_final: 0.8763 (mmm) REVERT: n 68 TYR cc_start: 0.9257 (m-10) cc_final: 0.8926 (m-10) REVERT: n 90 PHE cc_start: 0.8733 (m-10) cc_final: 0.8226 (m-80) REVERT: n 135 LEU cc_start: 0.9527 (mt) cc_final: 0.9246 (mt) REVERT: n 144 TYR cc_start: 0.8825 (m-10) cc_final: 0.8619 (m-10) REVERT: n 146 LEU cc_start: 0.8883 (mt) cc_final: 0.8485 (mt) REVERT: o 13 PHE cc_start: 0.8943 (t80) cc_final: 0.8400 (t80) REVERT: o 17 MET cc_start: 0.9021 (mmp) cc_final: 0.8789 (mmt) REVERT: o 51 LEU cc_start: 0.8586 (mt) cc_final: 0.8323 (mt) REVERT: o 57 ILE cc_start: 0.8972 (mt) cc_final: 0.8533 (mm) REVERT: o 64 ILE cc_start: 0.9266 (mt) cc_final: 0.9049 (mt) REVERT: o 65 ILE cc_start: 0.9659 (mp) cc_final: 0.9332 (mp) REVERT: o 68 TYR cc_start: 0.9118 (m-10) cc_final: 0.8743 (m-80) REVERT: o 90 PHE cc_start: 0.9339 (m-80) cc_final: 0.8913 (m-80) REVERT: o 128 PHE cc_start: 0.8204 (t80) cc_final: 0.7871 (t80) REVERT: o 144 TYR cc_start: 0.9036 (m-10) cc_final: 0.8747 (m-10) REVERT: p 303 TYR cc_start: 0.8676 (t80) cc_final: 0.8120 (t80) REVERT: p 330 ASN cc_start: 0.8834 (t0) cc_final: 0.8482 (t0) outliers start: 1 outliers final: 1 residues processed: 975 average time/residue: 0.2622 time to fit residues: 408.8343 Evaluate side-chains 883 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 882 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 204 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 HIS H 137 ASN L 81 HIS ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 92 GLN k 7 ASN ** k 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.090029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.071300 restraints weight = 65711.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.073865 restraints weight = 40497.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.075803 restraints weight = 27686.178| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.6415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 19610 Z= 0.220 Angle : 0.695 12.798 26647 Z= 0.354 Chirality : 0.044 0.394 3268 Planarity : 0.004 0.035 3401 Dihedral : 3.985 23.686 2941 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.16), residues: 2771 helix: 1.81 (0.11), residues: 2163 sheet: -2.68 (1.13), residues: 16 loop : -0.77 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP c 420 HIS 0.006 0.001 HIS b 128 PHE 0.043 0.002 PHE b 189 TYR 0.045 0.002 TYR l 68 ARG 0.006 0.001 ARG L 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6609.46 seconds wall clock time: 118 minutes 21.46 seconds (7101.46 seconds total)