Starting phenix.real_space_refine on Thu Apr 11 00:00:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqg_21349/04_2024/6vqg_21349.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqg_21349/04_2024/6vqg_21349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqg_21349/04_2024/6vqg_21349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqg_21349/04_2024/6vqg_21349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqg_21349/04_2024/6vqg_21349.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqg_21349/04_2024/6vqg_21349.pdb" } resolution = 4.2 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= 0.060 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 134 5.16 5 C 13732 2.51 5 N 3383 2.21 5 O 3697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 388": "OE1" <-> "OE2" Residue "a TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 828": "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 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 98": "OE1" <-> "OE2" Residue "b PHE 118": "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 "b PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 54": "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 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 67": "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 GLU 139": "OE1" <-> "OE2" Residue "h PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 139": "OE1" <-> "OE2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "k PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 137": "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 "l GLU 139": "OE1" <-> "OE2" 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 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 25": "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 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 139": "OE1" <-> "OE2" Residue "p TYR 293": "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-5288/modules/chem_data/mon_lib" Total number of atoms: 20946 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: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3477 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 18, 'TRANS': 422} Chain breaks: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 56 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: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "f" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 452 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain breaks: 1 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 107 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: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 432 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Time building chain proxies: 10.98, per 1000 atoms: 0.52 Number of scatterers: 20946 At special positions: 0 Unit cell: (119.78, 126.14, 160.06, 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 134 16.00 O 3697 8.00 N 3383 7.00 C 13732 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: 9.15 Conformation dependent library (CDL) restraints added in 4.1 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: 120 helices and 3 sheets defined 81.4% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 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: 3.887A 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: 3.742A pdb=" N LEU L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 3.668A 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 371 through 380 Processing helix chain 'a' and resid 391 through 407 removed outlier: 4.914A 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 removed outlier: 3.519A pdb=" N LEU a 452 " --> pdb=" O TYR a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 481 through 488 Processing helix chain 'a' and resid 492 through 497 removed outlier: 4.390A 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: 4.568A pdb=" N ASN a 534 " --> pdb=" O LEU a 530 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER a 556 " --> pdb=" O GLY a 552 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU a 557 " --> pdb=" O VAL a 553 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE a 558 " --> pdb=" O SER a 554 " (cutoff:3.500A) Processing helix chain 'a' and resid 565 through 571 removed outlier: 3.728A pdb=" N ILE a 569 " --> pdb=" O LYS a 565 " (cutoff:3.500A) Processing helix chain 'a' and resid 572 through 598 removed outlier: 4.305A pdb=" N TYR a 586 " --> pdb=" O SER a 582 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU a 587 " --> pdb=" O LEU a 583 " (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 667 removed outlier: 3.707A pdb=" N VAL a 648 " --> pdb=" O ALA a 644 " (cutoff:3.500A) Proline residue: a 649 - end of helix removed outlier: 5.751A 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 Processing helix chain 'a' and resid 739 through 759 removed outlier: 4.214A 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 removed outlier: 3.518A pdb=" N PHE a 778 " --> pdb=" O LEU a 774 " (cutoff:3.500A) 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: 3.618A pdb=" N SER b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 3.567A 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: 4.221A pdb=" N LYS b 89 " --> pdb=" O ARG b 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 113 removed outlier: 3.760A pdb=" N GLY b 104 " --> pdb=" O VAL b 100 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 169 removed outlier: 3.861A pdb=" N GLN b 168 " --> pdb=" O LEU b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 172 through 198 removed outlier: 4.093A pdb=" N ILE b 178 " --> pdb=" O VAL b 174 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL b 179 " --> pdb=" O LYS b 175 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU b 180 " --> pdb=" O ILE b 176 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY b 187 " --> pdb=" O GLY b 183 " (cutoff:3.500A) Processing helix chain 'c' and resid 416 through 442 Processing helix chain 'd' and resid 8 through 25 removed outlier: 4.241A pdb=" N ASP d 12 " --> pdb=" O TYR d 8 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR d 15 " --> pdb=" O VAL d 11 " (cutoff:3.500A) removed outlier: 5.156A 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: 4.715A pdb=" N PHE d 96 " --> pdb=" O PRO d 92 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE d 100 " --> pdb=" O PHE d 96 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR d 114 " --> pdb=" O ILE d 110 " (cutoff:3.500A) removed outlier: 3.801A 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: 4.209A pdb=" N ALA d 162 " --> pdb=" O PRO d 159 " (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: 3.608A 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: 4.448A 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 339 removed outlier: 3.611A 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 Processing helix chain 'f' and resid 8 through 36 Processing helix chain 'f' and resid 54 through 90 removed outlier: 4.191A pdb=" N ILE f 58 " --> pdb=" O GLY f 54 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 46 removed outlier: 3.645A pdb=" N PHE g 14 " --> pdb=" O TYR g 10 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER g 26 " --> pdb=" O ALA g 22 " (cutoff:3.500A) removed outlier: 3.964A 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 removed outlier: 3.543A pdb=" N ARG g 119 " --> pdb=" O ASP g 115 " (cutoff:3.500A) Processing helix chain 'g' and resid 127 through 153 removed outlier: 3.781A pdb=" N SER g 153 " --> pdb=" O ALA g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 45 removed outlier: 4.636A pdb=" N GLY h 15 " --> pdb=" O SER h 11 " (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: 4.586A pdb=" N GLY h 130 " --> pdb=" O ARG h 126 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY h 145 " --> pdb=" O LEU h 141 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR h 154 " --> pdb=" O LEU h 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 11 through 48 removed outlier: 4.316A pdb=" N GLY i 15 " --> pdb=" O SER i 11 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET i 23 " --> pdb=" O ALA i 19 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER i 26 " --> pdb=" O ALA i 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL i 46 " --> pdb=" O ALA i 42 " (cutoff:3.500A) removed outlier: 3.669A 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: 3.830A pdb=" N GLN i 123 " --> pdb=" O ARG i 119 " (cutoff:3.500A) Processing helix chain 'i' and resid 126 through 154 removed outlier: 4.572A pdb=" N GLY i 130 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY i 145 " --> pdb=" O LEU i 141 " (cutoff:3.500A) Processing helix chain 'j' and resid 12 through 48 removed outlier: 3.554A pdb=" N MET j 23 " --> pdb=" O ALA j 19 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL j 46 " --> pdb=" O ALA j 42 " (cutoff:3.500A) removed outlier: 4.456A 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: 3.751A pdb=" N ILE j 64 " --> pdb=" O VAL j 60 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE j 65 " --> pdb=" O MET j 61 " (cutoff:3.500A) removed outlier: 4.017A 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: 4.469A pdb=" N GLY j 130 " --> pdb=" O ARG j 126 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY j 145 " --> pdb=" O LEU j 141 " (cutoff:3.500A) Processing helix chain 'k' and resid 10 through 48 removed outlier: 3.953A pdb=" N PHE k 14 " --> pdb=" O TYR k 10 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY k 15 " --> pdb=" O SER k 11 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET k 23 " --> pdb=" O ALA k 19 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA k 43 " --> pdb=" O THR k 39 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL k 46 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 3.972A 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: 4.420A pdb=" N GLY l 15 " --> pdb=" O SER l 11 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL l 46 " --> pdb=" O ALA l 42 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET l 47 " --> pdb=" O ALA l 43 " (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: 3.870A pdb=" N GLN l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 126 through 155 removed outlier: 4.339A pdb=" N GLY l 130 " --> pdb=" O ARG l 126 " (cutoff:3.500A) Processing helix chain 'm' and resid 10 through 45 removed outlier: 3.608A 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: 4.677A 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: 3.944A pdb=" N GLN m 123 " --> pdb=" O ARG m 119 " (cutoff:3.500A) Processing helix chain 'm' and resid 126 through 154 removed outlier: 4.523A pdb=" N GLY m 130 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE m 137 " --> pdb=" O LEU m 133 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR m 154 " --> pdb=" O LEU m 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 10 through 46 removed outlier: 4.389A pdb=" N PHE n 14 " --> pdb=" O TYR n 10 " (cutoff:3.500A) removed outlier: 4.274A 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: 3.992A 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 Processing helix chain 'n' and resid 86 through 123 removed outlier: 3.622A pdb=" N ARG n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 126 through 154 removed outlier: 4.652A pdb=" N GLY n 130 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY n 145 " --> pdb=" O LEU n 141 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR n 154 " --> pdb=" O LEU n 150 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 48 removed outlier: 4.410A pdb=" N GLY o 15 " --> pdb=" O SER o 11 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET o 23 " --> pdb=" O ALA o 19 " (cutoff:3.500A) removed outlier: 3.987A 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: 3.510A pdb=" N VAL o 72 " --> pdb=" O TYR o 68 " (cutoff:3.500A) Processing helix chain 'o' and resid 86 through 124 Processing helix chain 'o' and resid 126 through 154 removed outlier: 4.696A pdb=" N GLY o 130 " --> pdb=" O ARG o 126 " (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: 8.521A pdb=" N LEU L 37 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL L 10 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA L 9 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ASN L 67 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE L 11 " --> pdb=" O ASN L 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 362 through 363 1744 hydrogen bonds defined for protein. 5124 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: 7.01 Time building geometry restraints manager: 9.77 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: 3287 1.30 - 1.43: 5485 1.43 - 1.56: 12346 1.56 - 1.68: 0 1.68 - 1.81: 248 Bond restraints: 21366 Sorted by residual: bond pdb=" C PRO H 107 " pdb=" O PRO H 107 " ideal model delta sigma weight residual 1.233 1.172 0.061 1.13e-02 7.83e+03 2.93e+01 bond pdb=" N PRO c 417 " pdb=" CD PRO c 417 " ideal model delta sigma weight residual 1.473 1.541 -0.068 1.40e-02 5.10e+03 2.39e+01 bond pdb=" N PRO L 86 " pdb=" CD PRO L 86 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.15e+01 bond pdb=" N GLN h 124 " pdb=" CA GLN h 124 " ideal model delta sigma weight residual 1.462 1.418 0.044 1.06e-02 8.90e+03 1.70e+01 bond pdb=" CA ALA L 109 " pdb=" CB ALA L 109 " ideal model delta sigma weight residual 1.530 1.474 0.056 1.43e-02 4.89e+03 1.53e+01 ... (remaining 21361 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.39: 570 106.39 - 113.24: 11685 113.24 - 120.10: 8332 120.10 - 126.96: 8200 126.96 - 133.82: 179 Bond angle restraints: 28966 Sorted by residual: angle pdb=" N GLN d 171 " pdb=" CA GLN d 171 " pdb=" C GLN d 171 " ideal model delta sigma weight residual 111.28 102.51 8.77 1.09e+00 8.42e-01 6.48e+01 angle pdb=" C ILE L 91 " pdb=" N PRO L 92 " pdb=" CA PRO L 92 " ideal model delta sigma weight residual 119.76 127.78 -8.02 1.03e+00 9.43e-01 6.07e+01 angle pdb=" N SER L 104 " pdb=" CA SER L 104 " pdb=" C SER L 104 " ideal model delta sigma weight residual 111.36 103.09 8.27 1.09e+00 8.42e-01 5.76e+01 angle pdb=" C ARG L 108 " pdb=" N ALA L 109 " pdb=" CA ALA L 109 " ideal model delta sigma weight residual 122.72 112.37 10.35 1.38e+00 5.25e-01 5.63e+01 angle pdb=" C ASN m 7 " pdb=" N PRO m 8 " pdb=" CA PRO m 8 " ideal model delta sigma weight residual 119.76 127.21 -7.45 1.03e+00 9.43e-01 5.23e+01 ... (remaining 28961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11933 17.95 - 35.89: 352 35.89 - 53.84: 99 53.84 - 71.78: 19 71.78 - 89.73: 28 Dihedral angle restraints: 12431 sinusoidal: 4505 harmonic: 7926 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 -159.85 -20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA MET h 44 " pdb=" C MET h 44 " pdb=" N SER h 45 " pdb=" CA SER h 45 " ideal model delta harmonic sigma weight residual -180.00 -161.92 -18.08 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" N PRO d 5 " pdb=" C PRO d 5 " pdb=" CA PRO d 5 " pdb=" CB PRO d 5 " ideal model delta harmonic sigma weight residual 115.10 106.48 8.62 0 2.50e+00 1.60e-01 1.19e+01 ... (remaining 12428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2325 0.065 - 0.129: 944 0.129 - 0.194: 75 0.194 - 0.259: 78 0.259 - 0.324: 8 Chirality restraints: 3430 Sorted by residual: chirality pdb=" CA TYR h 68 " pdb=" N TYR h 68 " pdb=" C TYR h 68 " pdb=" CB TYR h 68 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.62e+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 2.82 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA TYR n 68 " pdb=" N TYR n 68 " pdb=" C TYR n 68 " pdb=" CB TYR n 68 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 3427 not shown) Planarity restraints: 3602 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 2.11e+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 4.34e-02 1.89e+01 pdb=" C ASN k 7 " 0.075 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 3.98e-02 1.58e+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 3599 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3292 2.76 - 3.29: 23730 3.29 - 3.83: 35865 3.83 - 4.36: 43948 4.36 - 4.90: 71613 Nonbonded interactions: 178448 Sorted by model distance: nonbonded pdb=" OG SER a 738 " pdb=" NH1 ARG a 741 " model vdw 2.219 2.520 nonbonded pdb=" NZ LYS H 55 " pdb=" OD2 ASP L 103 " model vdw 2.332 2.520 nonbonded pdb=" NZ LYS H 55 " pdb=" OD2 ASP L 99 " model vdw 2.352 2.520 nonbonded pdb=" OG SER a 738 " pdb=" OE2 GLU a 810 " model vdw 2.355 2.440 nonbonded pdb=" O SER m 11 " pdb=" OG SER m 89 " model vdw 2.356 2.440 ... (remaining 178443 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: 2.330 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: 0.020 Extract box with map and model: 9.170 Check model and map are aligned: 0.330 Set scattering table: 0.220 Process input model: 57.800 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.170 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: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 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 0.068 21366 Z= 0.545 Angle : 0.982 10.859 28966 Z= 0.743 Chirality : 0.069 0.324 3430 Planarity : 0.005 0.046 3602 Dihedral : 11.367 89.727 7401 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.56 % Favored : 97.19 % Rotamer: Outliers : 1.36 % Allowed : 0.94 % Favored : 97.70 % 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: 0.61 (0.15), residues: 2771 helix: 0.83 (0.10), residues: 2145 sheet: -0.53 (1.08), residues: 18 loop : -0.83 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP b 49 HIS 0.000 0.000 HIS d 340 PHE 0.011 0.000 PHE n 137 TYR 0.011 0.001 TYR d 33 ARG 0.001 0.000 ARG d 182 *********************** 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 1497 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1468 time to evaluate : 2.529 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 56 MET cc_start: 0.9149 (tmm) cc_final: 0.8930 (tmm) REVERT: H 61 VAL cc_start: 0.8818 (t) cc_final: 0.8351 (p) REVERT: H 62 MET cc_start: 0.8682 (mmt) cc_final: 0.8347 (mmp) REVERT: H 67 PHE cc_start: 0.8705 (t80) cc_final: 0.8154 (t80) REVERT: H 68 SER cc_start: 0.9256 (m) cc_final: 0.8466 (t) REVERT: H 71 GLU cc_start: 0.9263 (tt0) cc_final: 0.8924 (tt0) REVERT: H 91 GLN cc_start: 0.7634 (tt0) cc_final: 0.7141 (tt0) REVERT: H 93 LYS cc_start: 0.8280 (mttt) cc_final: 0.8017 (mmmt) REVERT: H 112 TYR cc_start: 0.9236 (t80) cc_final: 0.8413 (t80) REVERT: H 140 LYS cc_start: 0.9388 (tttt) cc_final: 0.9085 (ttpt) REVERT: L 11 ILE cc_start: 0.9298 (mt) cc_final: 0.8985 (mt) REVERT: L 28 LEU cc_start: 0.7460 (mt) cc_final: 0.7010 (mp) REVERT: L 35 ASN cc_start: 0.8190 (p0) cc_final: 0.7368 (p0) REVERT: L 38 VAL cc_start: 0.8841 (t) cc_final: 0.8554 (p) REVERT: L 40 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8772 (mp0) REVERT: L 46 ASN cc_start: 0.8613 (m-40) cc_final: 0.8367 (m-40) REVERT: L 49 GLU cc_start: 0.8894 (tt0) cc_final: 0.8644 (pp20) REVERT: L 67 ASN cc_start: 0.9101 (m110) cc_final: 0.8498 (p0) REVERT: L 68 GLN cc_start: 0.7719 (tt0) cc_final: 0.7387 (tp40) REVERT: L 78 LEU cc_start: 0.8494 (mp) cc_final: 0.7978 (tt) REVERT: L 89 LEU cc_start: 0.7837 (mt) cc_final: 0.7528 (mp) REVERT: L 90 GLU cc_start: 0.7929 (mt-10) cc_final: 0.6575 (mt-10) REVERT: L 99 ASP cc_start: 0.6889 (p0) cc_final: 0.6279 (p0) REVERT: L 105 ILE cc_start: 0.8764 (mm) cc_final: 0.8475 (mp) REVERT: a 9 GLU cc_start: 0.6111 (mp0) cc_final: 0.5842 (pp20) REVERT: a 397 ILE cc_start: 0.8826 (mm) cc_final: 0.8624 (tp) REVERT: a 401 PHE cc_start: 0.9148 (t80) cc_final: 0.8648 (t80) REVERT: a 447 ARG cc_start: 0.8471 (ptt-90) cc_final: 0.7623 (ptt-90) REVERT: a 458 ILE cc_start: 0.9235 (mt) cc_final: 0.8973 (mm) REVERT: a 538 MET cc_start: 0.8621 (ttt) cc_final: 0.7976 (tmm) REVERT: a 543 ILE cc_start: 0.9227 (mt) cc_final: 0.9001 (mt) REVERT: a 580 MET cc_start: 0.9557 (ttm) cc_final: 0.9223 (ttm) REVERT: a 634 LYS cc_start: 0.8077 (mttt) cc_final: 0.7492 (tttp) REVERT: a 642 VAL cc_start: 0.9444 (t) cc_final: 0.8840 (p) REVERT: a 717 THR cc_start: 0.9027 (m) cc_final: 0.8776 (p) REVERT: a 721 GLN cc_start: 0.8802 (tp40) cc_final: 0.8164 (tp-100) REVERT: a 729 CYS cc_start: 0.9140 (m) cc_final: 0.8711 (p) REVERT: a 732 CYS cc_start: 0.8826 (m) cc_final: 0.8574 (p) REVERT: a 754 GLU cc_start: 0.9535 (tt0) cc_final: 0.8958 (pt0) REVERT: a 804 LEU cc_start: 0.9391 (tp) cc_final: 0.9152 (tt) REVERT: a 808 TRP cc_start: 0.8935 (m-10) cc_final: 0.8665 (m-10) REVERT: a 809 VAL cc_start: 0.8580 (t) cc_final: 0.8251 (t) REVERT: a 810 GLU cc_start: 0.7526 (mp0) cc_final: 0.7069 (mp0) REVERT: a 814 LYS cc_start: 0.7679 (mmtm) cc_final: 0.7445 (mmtm) REVERT: a 815 PHE cc_start: 0.8255 (p90) cc_final: 0.7979 (p90) REVERT: b 8 TYR cc_start: 0.8963 (m-80) cc_final: 0.8423 (m-80) REVERT: b 19 MET cc_start: 0.8799 (mtp) cc_final: 0.8436 (mtp) REVERT: b 24 ILE cc_start: 0.9418 (tt) cc_final: 0.9214 (tp) REVERT: b 25 CYS cc_start: 0.9120 (m) cc_final: 0.8747 (t) REVERT: b 34 ARG cc_start: 0.8285 (mmm160) cc_final: 0.6383 (tpt170) REVERT: b 44 THR cc_start: 0.8011 (m) cc_final: 0.7671 (m) REVERT: b 48 MET cc_start: 0.9046 (ttt) cc_final: 0.8423 (tmm) REVERT: b 52 LEU cc_start: 0.9601 (mt) cc_final: 0.9181 (mt) REVERT: b 74 SER cc_start: 0.9506 (m) cc_final: 0.9120 (p) REVERT: b 75 SER cc_start: 0.9743 (m) cc_final: 0.9531 (p) REVERT: b 82 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8500 (mmtp) REVERT: b 88 THR cc_start: 0.7359 (m) cc_final: 0.7064 (m) REVERT: b 90 ASN cc_start: 0.8723 (m-40) cc_final: 0.8340 (m-40) REVERT: b 92 VAL cc_start: 0.9026 (p) cc_final: 0.8769 (m) REVERT: b 93 SER cc_start: 0.9503 (p) cc_final: 0.8973 (p) REVERT: b 96 PHE cc_start: 0.8584 (m-80) cc_final: 0.8148 (m-80) REVERT: b 107 MET cc_start: 0.9506 (tpt) cc_final: 0.8901 (tpt) REVERT: b 130 ASN cc_start: 0.9039 (m-40) cc_final: 0.8836 (m-40) REVERT: b 137 MET cc_start: 0.9270 (mtp) cc_final: 0.8952 (ttm) REVERT: b 151 CYS cc_start: 0.9323 (t) cc_final: 0.8987 (t) REVERT: b 154 CYS cc_start: 0.9411 (t) cc_final: 0.9182 (t) REVERT: b 166 ASP cc_start: 0.8857 (t70) cc_final: 0.8638 (t0) REVERT: b 169 ASN cc_start: 0.8966 (t0) cc_final: 0.8648 (t0) REVERT: b 172 LEU cc_start: 0.9089 (mt) cc_final: 0.8258 (mt) REVERT: b 180 GLU cc_start: 0.9709 (mt-10) cc_final: 0.9254 (mt-10) REVERT: b 192 ILE cc_start: 0.9457 (mt) cc_final: 0.9106 (tp) REVERT: c 419 ILE cc_start: 0.8777 (mt) cc_final: 0.8569 (mt) REVERT: c 439 MET cc_start: 0.9498 (mmm) cc_final: 0.9155 (mmm) REVERT: d 50 GLN cc_start: 0.8661 (mt0) cc_final: 0.8304 (tp40) REVERT: d 69 VAL cc_start: 0.9381 (t) cc_final: 0.9159 (p) REVERT: d 81 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8743 (mm-30) REVERT: d 88 HIS cc_start: 0.8699 (m-70) cc_final: 0.8230 (m-70) REVERT: d 91 GLU cc_start: 0.8787 (tt0) cc_final: 0.8382 (tm-30) REVERT: d 98 ASP cc_start: 0.9061 (m-30) cc_final: 0.8394 (t70) REVERT: d 105 MET cc_start: 0.9059 (mtt) cc_final: 0.8539 (mpp) REVERT: d 106 ILE cc_start: 0.9432 (mt) cc_final: 0.9221 (mt) REVERT: d 108 ASN cc_start: 0.9183 (m-40) cc_final: 0.8726 (m-40) REVERT: d 118 HIS cc_start: 0.9065 (m-70) cc_final: 0.8718 (m90) REVERT: d 124 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8634 (mp0) REVERT: d 128 LYS cc_start: 0.9176 (mmtt) cc_final: 0.8599 (mmmm) REVERT: d 191 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8479 (mm-30) REVERT: d 221 PHE cc_start: 0.8406 (m-80) cc_final: 0.7900 (m-80) REVERT: d 236 ASP cc_start: 0.9309 (m-30) cc_final: 0.8983 (t0) REVERT: d 241 PHE cc_start: 0.8192 (m-10) cc_final: 0.7676 (m-10) REVERT: d 244 CYS cc_start: 0.7573 (m) cc_final: 0.7129 (m) REVERT: d 260 ASP cc_start: 0.8196 (t70) cc_final: 0.7950 (t70) REVERT: d 262 GLU cc_start: 0.9068 (tt0) cc_final: 0.8614 (tm-30) REVERT: d 263 GLN cc_start: 0.9292 (mt0) cc_final: 0.8934 (mt0) REVERT: d 266 ASN cc_start: 0.8832 (m-40) cc_final: 0.8509 (m110) REVERT: d 290 LEU cc_start: 0.8433 (tp) cc_final: 0.8176 (tp) REVERT: d 292 ASP cc_start: 0.8971 (m-30) cc_final: 0.8058 (t0) REVERT: d 297 HIS cc_start: 0.8600 (t70) cc_final: 0.8337 (t70) REVERT: d 312 PHE cc_start: 0.8263 (m-10) cc_final: 0.8045 (m-10) REVERT: d 340 HIS cc_start: 0.7331 (m-70) cc_final: 0.6694 (m-70) REVERT: e 13 PHE cc_start: 0.7526 (m-80) cc_final: 0.7070 (m-10) REVERT: e 47 CYS cc_start: 0.7745 (p) cc_final: 0.7440 (p) REVERT: e 54 ILE cc_start: 0.9649 (mt) cc_final: 0.9296 (mt) REVERT: g 25 PHE cc_start: 0.9053 (m-10) cc_final: 0.8747 (m-80) REVERT: g 41 ILE cc_start: 0.9545 (mt) cc_final: 0.9324 (mm) REVERT: g 54 LYS cc_start: 0.8531 (mttt) cc_final: 0.8255 (mmmt) REVERT: g 88 ARG cc_start: 0.8824 (mmm160) cc_final: 0.8294 (tpm170) REVERT: g 91 LEU cc_start: 0.9186 (mt) cc_final: 0.8687 (mt) REVERT: g 144 TYR cc_start: 0.8928 (m-10) cc_final: 0.8609 (m-80) REVERT: g 152 LEU cc_start: 0.8970 (mt) cc_final: 0.8553 (tp) REVERT: h 10 TYR cc_start: 0.9107 (p90) cc_final: 0.8682 (p90) REVERT: h 13 PHE cc_start: 0.9002 (t80) cc_final: 0.8483 (t80) REVERT: h 17 MET cc_start: 0.9175 (mmp) cc_final: 0.8897 (mmm) REVERT: h 41 ILE cc_start: 0.9237 (mt) cc_final: 0.8960 (mt) REVERT: h 85 THR cc_start: 0.9410 (p) cc_final: 0.9179 (p) REVERT: h 91 LEU cc_start: 0.8919 (mt) cc_final: 0.8585 (mt) REVERT: h 108 PHE cc_start: 0.9579 (m-80) cc_final: 0.9352 (m-80) REVERT: h 139 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8100 (mm-30) REVERT: i 23 MET cc_start: 0.9340 (tpt) cc_final: 0.9125 (ttm) REVERT: i 47 MET cc_start: 0.8721 (mmm) cc_final: 0.8450 (mmp) REVERT: i 52 ILE cc_start: 0.9624 (tt) cc_final: 0.9270 (mm) REVERT: i 53 MET cc_start: 0.8728 (mmp) cc_final: 0.8498 (ptt) REVERT: j 44 MET cc_start: 0.7800 (tmm) cc_final: 0.7358 (tmm) REVERT: j 51 LEU cc_start: 0.8815 (mt) cc_final: 0.8502 (mt) REVERT: j 64 ILE cc_start: 0.8621 (mt) cc_final: 0.8044 (mt) REVERT: j 68 TYR cc_start: 0.8744 (m-10) cc_final: 0.8298 (m-80) REVERT: j 72 VAL cc_start: 0.9808 (t) cc_final: 0.9585 (p) REVERT: j 75 LEU cc_start: 0.9367 (tp) cc_final: 0.9036 (tp) REVERT: j 84 ILE cc_start: 0.8355 (mm) cc_final: 0.7767 (mm) REVERT: j 88 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7533 (mmm160) REVERT: j 91 LEU cc_start: 0.9517 (mt) cc_final: 0.9223 (mp) REVERT: j 121 THR cc_start: 0.8308 (m) cc_final: 0.7854 (p) REVERT: j 127 LEU cc_start: 0.9164 (tp) cc_final: 0.8852 (tt) REVERT: j 140 VAL cc_start: 0.9715 (t) cc_final: 0.9425 (t) REVERT: j 148 VAL cc_start: 0.9450 (t) cc_final: 0.9248 (p) REVERT: k 23 MET cc_start: 0.9072 (tpt) cc_final: 0.8831 (tpt) REVERT: k 54 LYS cc_start: 0.8210 (mttt) cc_final: 0.7770 (mtpp) REVERT: k 55 SER cc_start: 0.8637 (p) cc_final: 0.8220 (p) REVERT: k 76 ILE cc_start: 0.9278 (mt) cc_final: 0.8484 (tt) REVERT: k 85 THR cc_start: 0.9279 (p) cc_final: 0.8924 (p) REVERT: k 119 ARG cc_start: 0.8673 (mtt-85) cc_final: 0.8261 (mtt-85) REVERT: k 121 THR cc_start: 0.9018 (m) cc_final: 0.8674 (p) REVERT: k 127 LEU cc_start: 0.8767 (mp) cc_final: 0.7904 (mp) REVERT: k 131 MET cc_start: 0.9028 (ttp) cc_final: 0.8770 (ptm) REVERT: l 12 SER cc_start: 0.9487 (p) cc_final: 0.9238 (t) REVERT: l 17 MET cc_start: 0.8927 (mmm) cc_final: 0.8629 (mmm) REVERT: l 44 MET cc_start: 0.8591 (tmm) cc_final: 0.8185 (tmm) REVERT: l 52 ILE cc_start: 0.9187 (mt) cc_final: 0.8733 (mt) REVERT: l 53 MET cc_start: 0.8942 (mmp) cc_final: 0.8712 (tmm) REVERT: l 54 LYS cc_start: 0.8796 (mttt) cc_final: 0.8459 (mmtt) REVERT: l 80 LEU cc_start: 0.9309 (tp) cc_final: 0.8730 (tp) REVERT: l 82 ASP cc_start: 0.8950 (p0) cc_final: 0.8724 (t70) REVERT: l 91 LEU cc_start: 0.9387 (mt) cc_final: 0.8996 (mt) REVERT: l 113 VAL cc_start: 0.9474 (t) cc_final: 0.9225 (p) REVERT: l 118 VAL cc_start: 0.9697 (t) cc_final: 0.9326 (m) REVERT: l 119 ARG cc_start: 0.8311 (mtt-85) cc_final: 0.8027 (mtt90) REVERT: l 124 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8478 (tm-30) REVERT: l 131 MET cc_start: 0.9104 (ttp) cc_final: 0.8569 (ttp) REVERT: l 152 LEU cc_start: 0.9338 (mt) cc_final: 0.8790 (tp) REVERT: m 8 PRO cc_start: 0.9113 (Cg_exo) cc_final: 0.8529 (Cg_endo) REVERT: m 17 MET cc_start: 0.9106 (mmm) cc_final: 0.8859 (mmm) REVERT: m 21 SER cc_start: 0.9284 (m) cc_final: 0.8968 (p) REVERT: m 41 ILE cc_start: 0.9560 (mt) cc_final: 0.9320 (mt) REVERT: m 52 ILE cc_start: 0.8108 (mt) cc_final: 0.7806 (mt) REVERT: m 57 ILE cc_start: 0.8737 (mt) cc_final: 0.8441 (mp) REVERT: m 74 VAL cc_start: 0.9575 (t) cc_final: 0.9302 (p) REVERT: m 81 THR cc_start: 0.8642 (t) cc_final: 0.8331 (m) REVERT: m 112 ILE cc_start: 0.8868 (mt) cc_final: 0.8592 (tp) REVERT: m 119 ARG cc_start: 0.8872 (mtt-85) cc_final: 0.8498 (mtt180) REVERT: m 126 ARG cc_start: 0.8927 (mtt90) cc_final: 0.8726 (mtp85) REVERT: m 135 LEU cc_start: 0.9607 (mt) cc_final: 0.9406 (mt) REVERT: m 139 GLU cc_start: 0.9377 (tt0) cc_final: 0.8909 (tt0) REVERT: m 153 SER cc_start: 0.9051 (p) cc_final: 0.8808 (p) REVERT: n 13 PHE cc_start: 0.8891 (t80) cc_final: 0.8444 (t80) REVERT: n 36 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8196 (mttt) REVERT: n 53 MET cc_start: 0.9358 (mmp) cc_final: 0.9105 (mmm) REVERT: n 79 SER cc_start: 0.8634 (m) cc_final: 0.8319 (t) REVERT: n 88 ARG cc_start: 0.8511 (ttm-80) cc_final: 0.8191 (mmm-85) REVERT: n 90 PHE cc_start: 0.9605 (m-80) cc_final: 0.9305 (m-10) REVERT: n 99 VAL cc_start: 0.9803 (p) cc_final: 0.9546 (m) REVERT: n 126 ARG cc_start: 0.8238 (mtt-85) cc_final: 0.7966 (mmm160) REVERT: n 127 LEU cc_start: 0.9345 (tp) cc_final: 0.9134 (tp) REVERT: n 129 VAL cc_start: 0.9014 (t) cc_final: 0.8651 (t) REVERT: n 131 MET cc_start: 0.9299 (ttp) cc_final: 0.8953 (ttt) REVERT: n 144 TYR cc_start: 0.9112 (m-10) cc_final: 0.8780 (m-10) REVERT: o 6 ASN cc_start: 0.9349 (p0) cc_final: 0.9142 (p0) REVERT: o 39 THR cc_start: 0.9294 (m) cc_final: 0.9013 (m) REVERT: o 53 MET cc_start: 0.9199 (mmp) cc_final: 0.8660 (tmm) REVERT: o 61 MET cc_start: 0.7938 (mmp) cc_final: 0.7646 (mmp) REVERT: o 90 PHE cc_start: 0.9499 (m-80) cc_final: 0.9209 (m-80) REVERT: o 124 GLN cc_start: 0.8337 (tp-100) cc_final: 0.8050 (tm-30) REVERT: o 144 TYR cc_start: 0.9238 (m-10) cc_final: 0.8986 (m-10) REVERT: p 313 ILE cc_start: 0.9264 (mt) cc_final: 0.8868 (mt) REVERT: p 330 ASN cc_start: 0.9457 (t0) cc_final: 0.9154 (t0) outliers start: 29 outliers final: 12 residues processed: 1474 average time/residue: 0.3141 time to fit residues: 720.7838 Evaluate side-chains 1010 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 998 time to evaluate : 2.382 ------------------------------------------------------------------------------- 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: 0.8980 chunk 211 optimal weight: 4.9990 chunk 117 optimal weight: 0.0770 chunk 72 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 253 optimal weight: 5.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN ** a 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 601 HIS ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 88 HIS d 142 ASN ** d 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 297 HIS d 328 ASN ** d 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN i 78 ASN j 92 GLN k 92 GLN o 92 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21366 Z= 0.242 Angle : 0.678 11.132 28966 Z= 0.367 Chirality : 0.042 0.208 3430 Planarity : 0.005 0.057 3602 Dihedral : 4.115 19.007 2978 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.33 % Allowed : 1.60 % Favored : 98.08 % 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: 2.14 (0.15), residues: 2771 helix: 2.04 (0.11), residues: 2089 sheet: -0.34 (0.98), residues: 18 loop : -0.53 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP b 16 HIS 0.008 0.002 HIS a 548 PHE 0.037 0.002 PHE b 189 TYR 0.034 0.002 TYR j 144 ARG 0.009 0.001 ARG a 741 *********************** 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 1234 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1227 time to evaluate : 2.437 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: H 56 MET cc_start: 0.9201 (tmm) cc_final: 0.8978 (tmm) REVERT: H 58 MET cc_start: 0.8858 (tmm) cc_final: 0.8411 (tmm) REVERT: H 61 VAL cc_start: 0.8663 (t) cc_final: 0.8177 (p) REVERT: H 62 MET cc_start: 0.8745 (mmt) cc_final: 0.8431 (mmp) REVERT: H 64 GLU cc_start: 0.8762 (tp30) cc_final: 0.8506 (tp30) REVERT: H 67 PHE cc_start: 0.8521 (t80) cc_final: 0.7988 (t80) REVERT: H 68 SER cc_start: 0.9285 (m) cc_final: 0.8737 (t) REVERT: H 91 GLN cc_start: 0.7958 (tt0) cc_final: 0.7471 (tt0) REVERT: H 93 LYS cc_start: 0.8362 (mttt) cc_final: 0.8129 (mtpp) REVERT: H 137 ASN cc_start: 0.8968 (m110) cc_final: 0.8538 (m110) REVERT: H 140 LYS cc_start: 0.9335 (tttt) cc_final: 0.9011 (ttpt) REVERT: H 152 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8500 (pp30) REVERT: L 22 LEU cc_start: 0.9553 (mt) cc_final: 0.9291 (mt) REVERT: L 40 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8693 (mp0) REVERT: L 49 GLU cc_start: 0.9071 (tt0) cc_final: 0.8862 (pt0) REVERT: L 67 ASN cc_start: 0.8684 (m110) cc_final: 0.8409 (p0) REVERT: L 89 LEU cc_start: 0.7816 (mt) cc_final: 0.7582 (mp) REVERT: L 90 GLU cc_start: 0.8241 (mt-10) cc_final: 0.6511 (mt-10) REVERT: L 99 ASP cc_start: 0.6996 (p0) cc_final: 0.5851 (t0) REVERT: a 9 GLU cc_start: 0.6689 (mp0) cc_final: 0.6051 (pp20) REVERT: a 388 GLU cc_start: 0.8187 (tp30) cc_final: 0.7031 (tt0) REVERT: a 397 ILE cc_start: 0.9174 (mm) cc_final: 0.8912 (tp) REVERT: a 401 PHE cc_start: 0.8959 (t80) cc_final: 0.8643 (t80) REVERT: a 409 ASP cc_start: 0.8668 (t0) cc_final: 0.8030 (t70) REVERT: a 430 ILE cc_start: 0.8033 (mm) cc_final: 0.7827 (mm) REVERT: a 447 ARG cc_start: 0.8125 (ptt-90) cc_final: 0.7555 (ptt90) REVERT: a 504 ASN cc_start: 0.8709 (t0) cc_final: 0.8509 (t0) REVERT: a 538 MET cc_start: 0.8858 (ttt) cc_final: 0.8313 (tmm) REVERT: a 540 MET cc_start: 0.9331 (tpt) cc_final: 0.8931 (tpt) REVERT: a 615 ASN cc_start: 0.8932 (t0) cc_final: 0.8658 (t0) REVERT: a 634 LYS cc_start: 0.7891 (mttt) cc_final: 0.7644 (ptmt) REVERT: a 651 MET cc_start: 0.8657 (mmm) cc_final: 0.8421 (mmm) REVERT: a 721 GLN cc_start: 0.8726 (tp40) cc_final: 0.8063 (tp-100) REVERT: a 729 CYS cc_start: 0.9183 (m) cc_final: 0.8979 (p) REVERT: a 732 CYS cc_start: 0.8480 (m) cc_final: 0.7909 (m) REVERT: a 759 MET cc_start: 0.8149 (mmm) cc_final: 0.7542 (tmm) REVERT: a 794 MET cc_start: 0.9581 (tmm) cc_final: 0.9339 (tmm) REVERT: a 806 LEU cc_start: 0.9045 (mm) cc_final: 0.8804 (mm) REVERT: a 808 TRP cc_start: 0.8973 (m-10) cc_final: 0.8754 (m-10) REVERT: a 810 GLU cc_start: 0.7067 (mp0) cc_final: 0.6800 (mp0) REVERT: a 814 LYS cc_start: 0.8257 (mmtm) cc_final: 0.8044 (mmtt) REVERT: a 815 PHE cc_start: 0.8396 (p90) cc_final: 0.8170 (p90) REVERT: b 8 TYR cc_start: 0.8980 (m-80) cc_final: 0.8634 (m-80) REVERT: b 19 MET cc_start: 0.8693 (mtp) cc_final: 0.8276 (mtp) REVERT: b 25 CYS cc_start: 0.9110 (m) cc_final: 0.8821 (t) REVERT: b 34 ARG cc_start: 0.8331 (mmm160) cc_final: 0.6444 (tpt170) REVERT: b 48 MET cc_start: 0.8994 (ttt) cc_final: 0.8643 (tmm) REVERT: b 70 TYR cc_start: 0.9123 (p90) cc_final: 0.8874 (p90) REVERT: b 71 ILE cc_start: 0.9595 (mm) cc_final: 0.9386 (mm) REVERT: b 74 SER cc_start: 0.9423 (m) cc_final: 0.9006 (t) REVERT: b 75 SER cc_start: 0.9792 (m) cc_final: 0.9439 (p) REVERT: b 82 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8425 (mmtp) REVERT: b 90 ASN cc_start: 0.8639 (m-40) cc_final: 0.7239 (m-40) REVERT: b 98 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8150 (mt-10) REVERT: b 107 MET cc_start: 0.9474 (tpt) cc_final: 0.8940 (tpt) REVERT: b 148 ASN cc_start: 0.9779 (m110) cc_final: 0.9566 (m110) REVERT: b 151 CYS cc_start: 0.9423 (t) cc_final: 0.9111 (t) REVERT: b 166 ASP cc_start: 0.8504 (t70) cc_final: 0.8145 (p0) REVERT: b 169 ASN cc_start: 0.8908 (t0) cc_final: 0.8707 (t0) REVERT: b 172 LEU cc_start: 0.8985 (mt) cc_final: 0.8207 (mt) REVERT: c 435 TYR cc_start: 0.8595 (t80) cc_final: 0.8058 (t80) REVERT: c 439 MET cc_start: 0.9463 (mmm) cc_final: 0.9080 (mmm) REVERT: c 440 ILE cc_start: 0.9583 (mt) cc_final: 0.9346 (mt) REVERT: d 50 GLN cc_start: 0.8656 (mt0) cc_final: 0.8212 (tp40) REVERT: d 65 LEU cc_start: 0.9176 (mp) cc_final: 0.8922 (pt) REVERT: d 85 MET cc_start: 0.8963 (mtp) cc_final: 0.8576 (ttp) REVERT: d 98 ASP cc_start: 0.8977 (m-30) cc_final: 0.8415 (t0) REVERT: d 124 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8570 (mp0) REVERT: d 128 LYS cc_start: 0.9163 (mmtt) cc_final: 0.8385 (mttt) REVERT: d 129 CYS cc_start: 0.8501 (m) cc_final: 0.8163 (m) REVERT: d 154 ILE cc_start: 0.9100 (mt) cc_final: 0.8861 (mt) REVERT: d 158 THR cc_start: 0.9036 (m) cc_final: 0.8583 (p) REVERT: d 176 MET cc_start: 0.7727 (mtt) cc_final: 0.7255 (mtt) REVERT: d 181 ILE cc_start: 0.8910 (mt) cc_final: 0.8655 (mt) REVERT: d 191 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8520 (mm-30) REVERT: d 241 PHE cc_start: 0.8171 (m-10) cc_final: 0.7764 (m-10) REVERT: d 244 CYS cc_start: 0.7809 (m) cc_final: 0.7325 (m) REVERT: d 260 ASP cc_start: 0.8150 (t70) cc_final: 0.7863 (t0) REVERT: d 262 GLU cc_start: 0.9014 (tt0) cc_final: 0.8717 (tm-30) REVERT: d 263 GLN cc_start: 0.9223 (mt0) cc_final: 0.8906 (mt0) REVERT: d 269 ASP cc_start: 0.9154 (m-30) cc_final: 0.8893 (m-30) REVERT: d 292 ASP cc_start: 0.8841 (m-30) cc_final: 0.8017 (t0) REVERT: d 297 HIS cc_start: 0.8545 (t-90) cc_final: 0.8272 (t70) REVERT: d 340 HIS cc_start: 0.7385 (m-70) cc_final: 0.6493 (m-70) REVERT: d 344 ILE cc_start: 0.9052 (tp) cc_final: 0.8519 (mm) REVERT: e 9 PRO cc_start: 0.7212 (Cg_exo) cc_final: 0.6578 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7603 (m-80) cc_final: 0.7067 (m-80) REVERT: e 47 CYS cc_start: 0.7912 (p) cc_final: 0.7421 (p) REVERT: e 54 ILE cc_start: 0.9583 (mt) cc_final: 0.9358 (mt) REVERT: e 68 LEU cc_start: 0.8864 (tp) cc_final: 0.8576 (tp) REVERT: g 10 TYR cc_start: 0.6548 (m-80) cc_final: 0.6077 (m-80) REVERT: g 41 ILE cc_start: 0.9427 (mt) cc_final: 0.9216 (mm) REVERT: g 54 LYS cc_start: 0.8575 (mttt) cc_final: 0.8236 (mmmt) REVERT: g 61 MET cc_start: 0.7852 (mmt) cc_final: 0.7496 (mmm) REVERT: g 87 TYR cc_start: 0.8736 (t80) cc_final: 0.8430 (t80) REVERT: g 88 ARG cc_start: 0.8459 (mmm160) cc_final: 0.7824 (tpm170) REVERT: g 91 LEU cc_start: 0.8904 (mt) cc_final: 0.8619 (mt) REVERT: g 110 ILE cc_start: 0.9617 (mm) cc_final: 0.9407 (mm) REVERT: g 124 GLN cc_start: 0.8126 (tp-100) cc_final: 0.7918 (tm-30) REVERT: g 131 MET cc_start: 0.9388 (ttt) cc_final: 0.9188 (ttt) REVERT: g 141 LEU cc_start: 0.9577 (mt) cc_final: 0.9245 (mt) REVERT: g 144 TYR cc_start: 0.9263 (m-10) cc_final: 0.8850 (m-80) REVERT: g 152 LEU cc_start: 0.9068 (mt) cc_final: 0.8552 (tp) REVERT: h 10 TYR cc_start: 0.8811 (p90) cc_final: 0.8377 (p90) REVERT: h 13 PHE cc_start: 0.8745 (t80) cc_final: 0.8321 (t80) REVERT: h 17 MET cc_start: 0.8954 (mmp) cc_final: 0.8690 (mmm) REVERT: h 108 PHE cc_start: 0.9553 (m-80) cc_final: 0.8904 (m-10) REVERT: h 127 LEU cc_start: 0.8773 (tp) cc_final: 0.8460 (tp) REVERT: h 152 LEU cc_start: 0.9387 (tp) cc_final: 0.9173 (tp) REVERT: i 17 MET cc_start: 0.9490 (mmp) cc_final: 0.9286 (mmp) REVERT: i 51 LEU cc_start: 0.9335 (mt) cc_final: 0.9133 (mt) REVERT: i 52 ILE cc_start: 0.9620 (tt) cc_final: 0.9195 (mm) REVERT: i 53 MET cc_start: 0.8686 (mmp) cc_final: 0.8438 (ptt) REVERT: i 110 ILE cc_start: 0.9468 (mt) cc_final: 0.9069 (tt) REVERT: i 119 ARG cc_start: 0.8757 (ttm110) cc_final: 0.8142 (ttm110) REVERT: i 139 GLU cc_start: 0.9222 (tp30) cc_final: 0.8952 (tp30) REVERT: j 61 MET cc_start: 0.9030 (tpp) cc_final: 0.8435 (tpp) REVERT: j 64 ILE cc_start: 0.8799 (mt) cc_final: 0.8504 (mt) REVERT: j 68 TYR cc_start: 0.9002 (m-10) cc_final: 0.8740 (m-80) REVERT: j 70 LEU cc_start: 0.9422 (tp) cc_final: 0.9137 (tp) REVERT: j 108 PHE cc_start: 0.9282 (m-80) cc_final: 0.8942 (m-80) REVERT: j 118 VAL cc_start: 0.9433 (t) cc_final: 0.9143 (m) REVERT: k 32 TYR cc_start: 0.8709 (t80) cc_final: 0.8192 (t80) REVERT: k 41 ILE cc_start: 0.9091 (mm) cc_final: 0.8671 (mm) REVERT: k 44 MET cc_start: 0.7855 (ttp) cc_final: 0.7597 (ppp) REVERT: k 47 MET cc_start: 0.8900 (mmp) cc_final: 0.8698 (mpp) REVERT: k 48 ARG cc_start: 0.7447 (mmt90) cc_final: 0.7040 (mmt90) REVERT: k 51 LEU cc_start: 0.9027 (mt) cc_final: 0.8781 (tt) REVERT: k 54 LYS cc_start: 0.8181 (mttt) cc_final: 0.7604 (mtpt) REVERT: k 76 ILE cc_start: 0.9187 (mt) cc_final: 0.8324 (tt) REVERT: k 80 LEU cc_start: 0.9237 (mt) cc_final: 0.8959 (mt) REVERT: k 92 GLN cc_start: 0.9037 (mt0) cc_final: 0.8596 (mt0) REVERT: k 121 THR cc_start: 0.8800 (m) cc_final: 0.8418 (p) REVERT: k 124 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8249 (tm-30) REVERT: k 137 PHE cc_start: 0.8914 (m-80) cc_final: 0.8436 (m-80) REVERT: k 143 LEU cc_start: 0.9380 (tp) cc_final: 0.9112 (mp) REVERT: k 147 ILE cc_start: 0.9652 (mt) cc_final: 0.9305 (tp) REVERT: k 151 ILE cc_start: 0.9550 (mt) cc_final: 0.9301 (mt) REVERT: l 47 MET cc_start: 0.8111 (tmm) cc_final: 0.7855 (tmm) REVERT: l 48 ARG cc_start: 0.8899 (ptp-110) cc_final: 0.8430 (ptp-110) REVERT: l 50 GLU cc_start: 0.8977 (mp0) cc_final: 0.8762 (mp0) REVERT: l 52 ILE cc_start: 0.9205 (mt) cc_final: 0.8807 (mt) REVERT: l 54 LYS cc_start: 0.8724 (mttt) cc_final: 0.8368 (mmtt) REVERT: l 55 SER cc_start: 0.9429 (m) cc_final: 0.9035 (p) REVERT: l 61 MET cc_start: 0.8644 (mmm) cc_final: 0.7773 (mmm) REVERT: l 70 LEU cc_start: 0.9211 (tt) cc_final: 0.8904 (tt) REVERT: l 91 LEU cc_start: 0.9326 (mt) cc_final: 0.9117 (mt) REVERT: l 101 LEU cc_start: 0.9097 (mt) cc_final: 0.8890 (mt) REVERT: l 118 VAL cc_start: 0.9685 (t) cc_final: 0.9397 (m) REVERT: l 124 GLN cc_start: 0.9071 (tp-100) cc_final: 0.8651 (tm-30) REVERT: l 136 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9144 (mp) REVERT: l 152 LEU cc_start: 0.9336 (mt) cc_final: 0.9088 (tp) REVERT: m 8 PRO cc_start: 0.9038 (Cg_exo) cc_final: 0.8615 (Cg_endo) REVERT: m 17 MET cc_start: 0.9035 (mmm) cc_final: 0.8778 (mmm) REVERT: m 21 SER cc_start: 0.9269 (m) cc_final: 0.8965 (p) REVERT: m 44 MET cc_start: 0.8893 (ppp) cc_final: 0.8684 (ppp) REVERT: m 52 ILE cc_start: 0.8276 (mt) cc_final: 0.7981 (mt) REVERT: m 92 GLN cc_start: 0.9158 (mt0) cc_final: 0.8845 (mt0) REVERT: m 112 ILE cc_start: 0.8942 (mt) cc_final: 0.8733 (tp) REVERT: m 132 ILE cc_start: 0.9143 (mm) cc_final: 0.8869 (mm) REVERT: n 17 MET cc_start: 0.9307 (mmt) cc_final: 0.9098 (mmm) REVERT: n 36 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7878 (mttt) REVERT: n 53 MET cc_start: 0.9383 (mmp) cc_final: 0.9141 (mmm) REVERT: n 54 LYS cc_start: 0.8595 (mttt) cc_final: 0.8194 (mtmt) REVERT: n 57 ILE cc_start: 0.9407 (mm) cc_final: 0.9205 (mm) REVERT: n 61 MET cc_start: 0.8700 (mmp) cc_final: 0.8478 (mmm) REVERT: n 76 ILE cc_start: 0.9677 (mt) cc_final: 0.9419 (mt) REVERT: n 79 SER cc_start: 0.8599 (m) cc_final: 0.8377 (t) REVERT: n 80 LEU cc_start: 0.9220 (tp) cc_final: 0.8601 (mt) REVERT: n 84 ILE cc_start: 0.9180 (mt) cc_final: 0.8893 (mp) REVERT: n 88 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.7979 (mmm-85) REVERT: n 126 ARG cc_start: 0.8347 (mtt-85) cc_final: 0.7972 (mmm160) REVERT: n 127 LEU cc_start: 0.9269 (tp) cc_final: 0.9022 (tp) REVERT: n 141 LEU cc_start: 0.9565 (mt) cc_final: 0.9326 (mt) REVERT: o 32 TYR cc_start: 0.7816 (t80) cc_final: 0.7498 (t80) REVERT: o 47 MET cc_start: 0.8928 (tpp) cc_final: 0.8655 (tpp) REVERT: o 51 LEU cc_start: 0.9285 (mt) cc_final: 0.8876 (pt) REVERT: o 90 PHE cc_start: 0.9364 (m-80) cc_final: 0.8910 (m-10) REVERT: o 110 ILE cc_start: 0.9356 (mt) cc_final: 0.9007 (mt) REVERT: o 144 TYR cc_start: 0.9120 (m-10) cc_final: 0.8848 (m-10) REVERT: p 305 VAL cc_start: 0.9373 (t) cc_final: 0.8949 (p) REVERT: p 313 ILE cc_start: 0.9291 (mt) cc_final: 0.9082 (mt) REVERT: p 341 ARG cc_start: 0.8689 (ptm-80) cc_final: 0.8298 (ptm-80) outliers start: 7 outliers final: 0 residues processed: 1230 average time/residue: 0.3324 time to fit residues: 656.1165 Evaluate side-chains 980 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 978 time to evaluate : 2.517 ------------------------------------------------------------------------------- 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: 5.9990 chunk 78 optimal weight: 0.9980 chunk 210 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 253 optimal weight: 0.8980 chunk 274 optimal weight: 7.9990 chunk 226 optimal weight: 0.9990 chunk 251 optimal weight: 7.9990 chunk 86 optimal weight: 0.5980 chunk 203 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 560 HIS a 637 GLN b 132 HIS d 328 ASN ** d 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN i 78 ASN j 124 GLN n 123 GLN o 92 GLN ** o 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21366 Z= 0.232 Angle : 0.652 10.446 28966 Z= 0.347 Chirality : 0.042 0.411 3430 Planarity : 0.005 0.044 3602 Dihedral : 4.140 24.798 2978 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.28 % Allowed : 2.30 % Favored : 97.42 % 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: 1.82 (0.15), residues: 2771 helix: 1.81 (0.11), residues: 2095 sheet: -0.77 (1.00), residues: 18 loop : -0.64 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP b 16 HIS 0.005 0.001 HIS a 720 PHE 0.028 0.002 PHE b 12 TYR 0.037 0.002 TYR H 138 ARG 0.007 0.000 ARG H 63 *********************** 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 1188 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1182 time to evaluate : 2.354 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 56 MET cc_start: 0.9281 (tmm) cc_final: 0.8979 (tmm) REVERT: H 58 MET cc_start: 0.8969 (tmm) cc_final: 0.8434 (tmm) REVERT: H 61 VAL cc_start: 0.8738 (t) cc_final: 0.8363 (p) REVERT: H 62 MET cc_start: 0.8803 (mmt) cc_final: 0.8469 (mmp) REVERT: H 63 ARG cc_start: 0.8137 (ttm110) cc_final: 0.7391 (mtp85) REVERT: H 64 GLU cc_start: 0.8689 (tp30) cc_final: 0.8340 (tp30) REVERT: H 68 SER cc_start: 0.9287 (m) cc_final: 0.8742 (t) REVERT: H 91 GLN cc_start: 0.8051 (tt0) cc_final: 0.7553 (tt0) REVERT: H 93 LYS cc_start: 0.8331 (mttt) cc_final: 0.7992 (mtpp) REVERT: H 134 LEU cc_start: 0.9085 (tp) cc_final: 0.8844 (tp) REVERT: H 137 ASN cc_start: 0.8979 (m110) cc_final: 0.8532 (m110) REVERT: L 22 LEU cc_start: 0.9516 (mt) cc_final: 0.9307 (mt) REVERT: L 40 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8736 (mp0) REVERT: L 46 ASN cc_start: 0.8695 (m-40) cc_final: 0.8277 (p0) REVERT: L 89 LEU cc_start: 0.7711 (mt) cc_final: 0.7388 (mp) REVERT: L 90 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7383 (mt-10) REVERT: a 9 GLU cc_start: 0.6890 (mp0) cc_final: 0.6171 (pp20) REVERT: a 388 GLU cc_start: 0.8212 (tp30) cc_final: 0.7065 (tt0) REVERT: a 397 ILE cc_start: 0.9157 (mm) cc_final: 0.8879 (tp) REVERT: a 401 PHE cc_start: 0.9023 (t80) cc_final: 0.8600 (t80) REVERT: a 409 ASP cc_start: 0.8416 (t0) cc_final: 0.8062 (t70) REVERT: a 423 MET cc_start: 0.9532 (mpp) cc_final: 0.8993 (mpp) REVERT: a 467 CYS cc_start: 0.7216 (t) cc_final: 0.6964 (t) REVERT: a 519 ILE cc_start: 0.7004 (mp) cc_final: 0.6784 (mp) REVERT: a 538 MET cc_start: 0.8626 (ttt) cc_final: 0.8126 (tmm) REVERT: a 540 MET cc_start: 0.9376 (tpt) cc_final: 0.9096 (tpt) REVERT: a 576 GLU cc_start: 0.9271 (mt-10) cc_final: 0.9032 (mp0) REVERT: a 580 MET cc_start: 0.8916 (mmp) cc_final: 0.8454 (mmm) REVERT: a 616 MET cc_start: 0.9127 (ttp) cc_final: 0.8764 (ttp) REVERT: a 637 GLN cc_start: 0.8318 (mt0) cc_final: 0.7984 (mt0) REVERT: a 651 MET cc_start: 0.9095 (mmm) cc_final: 0.8481 (mmm) REVERT: a 721 GLN cc_start: 0.8774 (tp40) cc_final: 0.8120 (tp-100) REVERT: a 729 CYS cc_start: 0.9183 (m) cc_final: 0.8973 (p) REVERT: a 759 MET cc_start: 0.8100 (mmm) cc_final: 0.7440 (tmm) REVERT: a 810 GLU cc_start: 0.7341 (mp0) cc_final: 0.7123 (mp0) REVERT: a 815 PHE cc_start: 0.8298 (p90) cc_final: 0.8061 (p90) REVERT: b 19 MET cc_start: 0.8711 (mtp) cc_final: 0.8330 (mtp) REVERT: b 25 CYS cc_start: 0.9155 (m) cc_final: 0.8771 (t) REVERT: b 34 ARG cc_start: 0.8397 (mmm160) cc_final: 0.6350 (tpt170) REVERT: b 36 ASP cc_start: 0.7862 (t70) cc_final: 0.7442 (t0) REVERT: b 48 MET cc_start: 0.9062 (ttt) cc_final: 0.8263 (tmm) REVERT: b 52 LEU cc_start: 0.9530 (mt) cc_final: 0.9231 (mt) REVERT: b 71 ILE cc_start: 0.9575 (mm) cc_final: 0.9251 (mm) REVERT: b 74 SER cc_start: 0.9451 (m) cc_final: 0.9052 (t) REVERT: b 75 SER cc_start: 0.9756 (m) cc_final: 0.9358 (p) REVERT: b 82 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8531 (mtpp) REVERT: b 90 ASN cc_start: 0.8796 (m-40) cc_final: 0.6317 (m-40) REVERT: b 92 VAL cc_start: 0.9149 (m) cc_final: 0.8606 (m) REVERT: b 96 PHE cc_start: 0.8799 (m-80) cc_final: 0.8545 (m-80) REVERT: b 114 MET cc_start: 0.7979 (mtm) cc_final: 0.7592 (mtm) REVERT: b 129 ARG cc_start: 0.9033 (mpp80) cc_final: 0.8772 (mmm-85) REVERT: b 130 ASN cc_start: 0.9055 (m-40) cc_final: 0.8829 (m-40) REVERT: b 137 MET cc_start: 0.9423 (ttt) cc_final: 0.9075 (ttm) REVERT: b 148 ASN cc_start: 0.9755 (m110) cc_final: 0.9443 (m110) REVERT: b 151 CYS cc_start: 0.9466 (t) cc_final: 0.9194 (t) REVERT: b 154 CYS cc_start: 0.9284 (t) cc_final: 0.9083 (t) REVERT: b 158 VAL cc_start: 0.9634 (p) cc_final: 0.9168 (p) REVERT: b 164 LEU cc_start: 0.9352 (mm) cc_final: 0.9014 (mt) REVERT: b 166 ASP cc_start: 0.8494 (t70) cc_final: 0.8191 (p0) REVERT: b 168 GLN cc_start: 0.9275 (mt0) cc_final: 0.9016 (mp10) REVERT: b 172 LEU cc_start: 0.8987 (mt) cc_final: 0.8053 (mt) REVERT: b 173 PHE cc_start: 0.8721 (t80) cc_final: 0.8236 (t80) REVERT: b 188 LEU cc_start: 0.9165 (tt) cc_final: 0.8960 (tt) REVERT: c 419 ILE cc_start: 0.8178 (mm) cc_final: 0.7932 (mm) REVERT: c 423 LEU cc_start: 0.9084 (mt) cc_final: 0.8837 (mt) REVERT: c 435 TYR cc_start: 0.8465 (t80) cc_final: 0.8194 (t80) REVERT: c 439 MET cc_start: 0.9608 (mmm) cc_final: 0.9394 (mmm) REVERT: d 28 LEU cc_start: 0.9096 (mm) cc_final: 0.8878 (mm) REVERT: d 30 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8449 (tm-30) REVERT: d 50 GLN cc_start: 0.8746 (mt0) cc_final: 0.8295 (tp40) REVERT: d 73 LYS cc_start: 0.8840 (mmmt) cc_final: 0.8576 (tppt) REVERT: d 76 GLU cc_start: 0.8619 (tt0) cc_final: 0.8225 (tp30) REVERT: d 85 MET cc_start: 0.8985 (mtp) cc_final: 0.8717 (ttp) REVERT: d 98 ASP cc_start: 0.8833 (m-30) cc_final: 0.8335 (t70) REVERT: d 105 MET cc_start: 0.8964 (mtm) cc_final: 0.8728 (mtp) REVERT: d 108 ASN cc_start: 0.8937 (m110) cc_final: 0.8689 (m110) REVERT: d 124 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8544 (mp0) REVERT: d 128 LYS cc_start: 0.9070 (mmtt) cc_final: 0.8304 (mttt) REVERT: d 129 CYS cc_start: 0.8655 (m) cc_final: 0.8341 (m) REVERT: d 164 PHE cc_start: 0.8273 (m-10) cc_final: 0.8023 (m-80) REVERT: d 241 PHE cc_start: 0.8357 (m-10) cc_final: 0.7967 (m-80) REVERT: d 244 CYS cc_start: 0.7881 (m) cc_final: 0.7230 (m) REVERT: d 260 ASP cc_start: 0.8181 (t70) cc_final: 0.7841 (t0) REVERT: d 263 GLN cc_start: 0.9255 (mt0) cc_final: 0.8848 (mt0) REVERT: d 292 ASP cc_start: 0.8762 (m-30) cc_final: 0.7865 (t70) REVERT: d 297 HIS cc_start: 0.8551 (t-90) cc_final: 0.8276 (t70) REVERT: d 312 PHE cc_start: 0.8299 (m-10) cc_final: 0.8017 (m-10) REVERT: d 344 ILE cc_start: 0.9118 (tp) cc_final: 0.8546 (mm) REVERT: e 9 PRO cc_start: 0.7234 (Cg_exo) cc_final: 0.6650 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7551 (m-80) cc_final: 0.7034 (m-10) REVERT: e 47 CYS cc_start: 0.7856 (p) cc_final: 0.7342 (p) REVERT: e 54 ILE cc_start: 0.9589 (mt) cc_final: 0.9348 (mt) REVERT: e 68 LEU cc_start: 0.8838 (tp) cc_final: 0.8510 (tp) REVERT: g 25 PHE cc_start: 0.8752 (m-80) cc_final: 0.8264 (m-80) REVERT: g 54 LYS cc_start: 0.8561 (mttt) cc_final: 0.8213 (mmmt) REVERT: g 61 MET cc_start: 0.7808 (mmt) cc_final: 0.7431 (mmm) REVERT: g 86 LEU cc_start: 0.8723 (tp) cc_final: 0.8395 (tp) REVERT: g 88 ARG cc_start: 0.8370 (mmm160) cc_final: 0.7945 (mmt180) REVERT: g 90 PHE cc_start: 0.8142 (m-80) cc_final: 0.7026 (m-80) REVERT: g 91 LEU cc_start: 0.8914 (mt) cc_final: 0.8439 (mt) REVERT: g 108 PHE cc_start: 0.9163 (m-80) cc_final: 0.8675 (m-80) REVERT: g 110 ILE cc_start: 0.9572 (mm) cc_final: 0.9322 (mm) REVERT: g 124 GLN cc_start: 0.8195 (tp-100) cc_final: 0.7910 (tm-30) REVERT: g 131 MET cc_start: 0.9411 (ttt) cc_final: 0.9187 (ttt) REVERT: g 133 LEU cc_start: 0.9065 (mp) cc_final: 0.8776 (mp) REVERT: g 135 LEU cc_start: 0.9020 (mt) cc_final: 0.8769 (mt) REVERT: g 137 PHE cc_start: 0.8665 (m-10) cc_final: 0.8128 (m-80) REVERT: g 141 LEU cc_start: 0.9562 (mt) cc_final: 0.8979 (mt) REVERT: g 144 TYR cc_start: 0.9257 (m-10) cc_final: 0.8587 (m-80) REVERT: g 152 LEU cc_start: 0.9331 (mt) cc_final: 0.8800 (tt) REVERT: h 10 TYR cc_start: 0.8826 (p90) cc_final: 0.8451 (p90) REVERT: h 17 MET cc_start: 0.8889 (mmp) cc_final: 0.8598 (mmm) REVERT: h 44 MET cc_start: 0.9017 (tmm) cc_final: 0.8812 (tmm) REVERT: h 70 LEU cc_start: 0.8893 (tp) cc_final: 0.8600 (tp) REVERT: h 127 LEU cc_start: 0.8773 (tp) cc_final: 0.8398 (tp) REVERT: h 152 LEU cc_start: 0.9396 (tp) cc_final: 0.9157 (tp) REVERT: i 14 PHE cc_start: 0.8711 (m-10) cc_final: 0.8305 (m-10) REVERT: i 51 LEU cc_start: 0.9325 (mt) cc_final: 0.9048 (mt) REVERT: i 52 ILE cc_start: 0.9577 (tt) cc_final: 0.9217 (mm) REVERT: i 53 MET cc_start: 0.8682 (mmp) cc_final: 0.8368 (ptt) REVERT: i 86 LEU cc_start: 0.9408 (tt) cc_final: 0.9160 (tp) REVERT: i 90 PHE cc_start: 0.7573 (m-10) cc_final: 0.7176 (m-80) REVERT: i 110 ILE cc_start: 0.9419 (mt) cc_final: 0.9064 (tt) REVERT: i 119 ARG cc_start: 0.8655 (ttm110) cc_final: 0.8227 (ttm110) REVERT: j 61 MET cc_start: 0.8727 (tpp) cc_final: 0.8420 (tpp) REVERT: j 70 LEU cc_start: 0.9536 (tp) cc_final: 0.9091 (tp) REVERT: j 108 PHE cc_start: 0.9231 (m-80) cc_final: 0.8920 (m-80) REVERT: j 118 VAL cc_start: 0.9252 (t) cc_final: 0.8697 (p) REVERT: j 127 LEU cc_start: 0.9358 (tp) cc_final: 0.9058 (tt) REVERT: j 136 ILE cc_start: 0.9223 (mm) cc_final: 0.8936 (mm) REVERT: j 146 LEU cc_start: 0.9577 (tp) cc_final: 0.9342 (tp) REVERT: k 23 MET cc_start: 0.9176 (tpt) cc_final: 0.8840 (tpt) REVERT: k 32 TYR cc_start: 0.8795 (t80) cc_final: 0.8271 (t80) REVERT: k 48 ARG cc_start: 0.7133 (mmt90) cc_final: 0.6680 (mmt90) REVERT: k 51 LEU cc_start: 0.9037 (mt) cc_final: 0.8678 (tt) REVERT: k 54 LYS cc_start: 0.7978 (mttt) cc_final: 0.7086 (mtpt) REVERT: k 70 LEU cc_start: 0.8535 (tp) cc_final: 0.8202 (tp) REVERT: k 76 ILE cc_start: 0.9232 (mt) cc_final: 0.8414 (tt) REVERT: k 80 LEU cc_start: 0.9289 (mt) cc_final: 0.8991 (mt) REVERT: k 90 PHE cc_start: 0.8978 (m-80) cc_final: 0.8286 (m-80) REVERT: k 92 GLN cc_start: 0.9132 (mt0) cc_final: 0.8625 (mt0) REVERT: k 123 GLN cc_start: 0.8669 (tp40) cc_final: 0.7741 (tm-30) REVERT: k 124 GLN cc_start: 0.8602 (tm-30) cc_final: 0.7803 (tm-30) REVERT: k 137 PHE cc_start: 0.8921 (m-80) cc_final: 0.8410 (m-80) REVERT: l 44 MET cc_start: 0.8562 (tmm) cc_final: 0.8212 (tmm) REVERT: l 47 MET cc_start: 0.8007 (tmm) cc_final: 0.7697 (tmm) REVERT: l 48 ARG cc_start: 0.8752 (ptp-110) cc_final: 0.8057 (ptp-110) REVERT: l 54 LYS cc_start: 0.8778 (mttt) cc_final: 0.8224 (mmtt) REVERT: l 70 LEU cc_start: 0.9333 (tt) cc_final: 0.9121 (tt) REVERT: l 91 LEU cc_start: 0.9289 (mt) cc_final: 0.9073 (mt) REVERT: l 118 VAL cc_start: 0.9731 (t) cc_final: 0.9508 (m) REVERT: l 123 GLN cc_start: 0.9133 (mp10) cc_final: 0.8880 (mp10) REVERT: l 152 LEU cc_start: 0.9359 (mt) cc_final: 0.8992 (tp) REVERT: m 17 MET cc_start: 0.9078 (mmm) cc_final: 0.8834 (mmm) REVERT: m 21 SER cc_start: 0.9264 (m) cc_final: 0.8933 (p) REVERT: m 41 ILE cc_start: 0.9546 (mt) cc_final: 0.9303 (mm) REVERT: m 44 MET cc_start: 0.9065 (ppp) cc_final: 0.8842 (ppp) REVERT: m 52 ILE cc_start: 0.8455 (mt) cc_final: 0.8129 (mt) REVERT: m 53 MET cc_start: 0.9324 (tpp) cc_final: 0.8804 (tpp) REVERT: m 61 MET cc_start: 0.9551 (mmm) cc_final: 0.9051 (mmm) REVERT: m 86 LEU cc_start: 0.9325 (tp) cc_final: 0.8933 (tp) REVERT: m 90 PHE cc_start: 0.9243 (m-80) cc_final: 0.8604 (m-80) REVERT: m 92 GLN cc_start: 0.9197 (mt0) cc_final: 0.8855 (mt0) REVERT: m 132 ILE cc_start: 0.9190 (mm) cc_final: 0.8877 (mm) REVERT: n 17 MET cc_start: 0.9360 (mmt) cc_final: 0.9022 (mmm) REVERT: n 36 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7748 (mttt) REVERT: n 53 MET cc_start: 0.9373 (mmp) cc_final: 0.9129 (mmm) REVERT: n 61 MET cc_start: 0.8939 (mmp) cc_final: 0.8682 (mmm) REVERT: n 76 ILE cc_start: 0.9761 (mt) cc_final: 0.9547 (mt) REVERT: n 80 LEU cc_start: 0.9235 (tp) cc_final: 0.8696 (mt) REVERT: n 81 THR cc_start: 0.8991 (p) cc_final: 0.8697 (t) REVERT: n 88 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.7779 (mmm-85) REVERT: n 90 PHE cc_start: 0.9652 (m-80) cc_final: 0.9361 (m-80) REVERT: n 119 ARG cc_start: 0.8028 (ttm110) cc_final: 0.7823 (mtm180) REVERT: n 126 ARG cc_start: 0.8345 (mtt-85) cc_final: 0.8002 (mmm160) REVERT: n 127 LEU cc_start: 0.9350 (tp) cc_final: 0.9083 (tp) REVERT: n 141 LEU cc_start: 0.9402 (mt) cc_final: 0.9187 (mt) REVERT: n 144 TYR cc_start: 0.9040 (m-10) cc_final: 0.8740 (m-10) REVERT: o 32 TYR cc_start: 0.7890 (t80) cc_final: 0.7516 (t80) REVERT: o 44 MET cc_start: 0.8630 (ttp) cc_final: 0.8340 (ttp) REVERT: o 61 MET cc_start: 0.8236 (mmp) cc_final: 0.8002 (mmp) REVERT: o 90 PHE cc_start: 0.9328 (m-80) cc_final: 0.9039 (m-10) REVERT: o 110 ILE cc_start: 0.9399 (mt) cc_final: 0.9034 (mt) REVERT: o 144 TYR cc_start: 0.9030 (m-10) cc_final: 0.8723 (m-10) REVERT: o 147 ILE cc_start: 0.9260 (mt) cc_final: 0.9035 (tp) REVERT: p 305 VAL cc_start: 0.9316 (t) cc_final: 0.8925 (p) REVERT: p 313 ILE cc_start: 0.9377 (mt) cc_final: 0.9084 (mt) REVERT: p 339 ILE cc_start: 0.7379 (mm) cc_final: 0.6954 (mt) outliers start: 6 outliers final: 0 residues processed: 1183 average time/residue: 0.2968 time to fit residues: 557.1412 Evaluate side-chains 977 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 977 time to evaluate : 2.476 ------------------------------------------------------------------------------- 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: 0.9990 chunk 131 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 170 optimal weight: 6.9990 chunk 254 optimal weight: 0.9980 chunk 269 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 751 GLN ** d 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 338 GLN e 33 ASN g 123 GLN ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 21366 Z= 0.233 Angle : 0.650 10.440 28966 Z= 0.341 Chirality : 0.041 0.255 3430 Planarity : 0.004 0.049 3602 Dihedral : 4.149 20.566 2978 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.78 % Favored : 97.19 % Rotamer: Outliers : 0.28 % Allowed : 2.02 % Favored : 97.70 % 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: 1.77 (0.15), residues: 2771 helix: 1.80 (0.11), residues: 2073 sheet: -0.68 (1.09), residues: 18 loop : -0.69 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP b 67 HIS 0.005 0.001 HIS H 111 PHE 0.029 0.002 PHE l 108 TYR 0.054 0.002 TYR j 144 ARG 0.005 0.000 ARG a 805 *********************** 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 1173 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1167 time to evaluate : 2.407 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 56 MET cc_start: 0.9217 (tmm) cc_final: 0.8918 (tmm) REVERT: H 58 MET cc_start: 0.9050 (tmm) cc_final: 0.8524 (tmm) REVERT: H 64 GLU cc_start: 0.8651 (tp30) cc_final: 0.8334 (tp30) REVERT: H 68 SER cc_start: 0.9334 (m) cc_final: 0.8819 (t) REVERT: H 91 GLN cc_start: 0.8253 (tt0) cc_final: 0.7655 (tt0) REVERT: H 134 LEU cc_start: 0.9085 (tp) cc_final: 0.8762 (tp) REVERT: H 137 ASN cc_start: 0.8967 (m110) cc_final: 0.8490 (m110) REVERT: H 138 TYR cc_start: 0.9086 (m-10) cc_final: 0.8863 (m-10) REVERT: L 22 LEU cc_start: 0.9538 (mt) cc_final: 0.9281 (mt) REVERT: L 29 ASN cc_start: 0.8739 (t0) cc_final: 0.7945 (m-40) REVERT: L 31 ASN cc_start: 0.8629 (p0) cc_final: 0.8246 (p0) REVERT: L 35 ASN cc_start: 0.8968 (p0) cc_final: 0.8639 (p0) REVERT: L 40 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8755 (mp0) REVERT: L 73 MET cc_start: 0.8419 (mtp) cc_final: 0.7943 (ptp) REVERT: L 89 LEU cc_start: 0.7620 (mt) cc_final: 0.7319 (mp) REVERT: L 90 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7141 (mt-10) REVERT: a 9 GLU cc_start: 0.6909 (mp0) cc_final: 0.6180 (pp20) REVERT: a 388 GLU cc_start: 0.8190 (tp30) cc_final: 0.7030 (tt0) REVERT: a 401 PHE cc_start: 0.9045 (t80) cc_final: 0.8577 (t80) REVERT: a 423 MET cc_start: 0.9487 (mpp) cc_final: 0.8918 (mpp) REVERT: a 449 ILE cc_start: 0.9558 (mt) cc_final: 0.9117 (mt) REVERT: a 467 CYS cc_start: 0.6682 (t) cc_final: 0.6425 (t) REVERT: a 519 ILE cc_start: 0.7062 (mp) cc_final: 0.6786 (mp) REVERT: a 538 MET cc_start: 0.8011 (ttt) cc_final: 0.7464 (tmm) REVERT: a 540 MET cc_start: 0.9273 (tpt) cc_final: 0.9038 (tpt) REVERT: a 576 GLU cc_start: 0.9354 (mt-10) cc_final: 0.9073 (mt-10) REVERT: a 580 MET cc_start: 0.9070 (mmp) cc_final: 0.8643 (mmm) REVERT: a 616 MET cc_start: 0.9086 (ttp) cc_final: 0.8741 (ttp) REVERT: a 642 VAL cc_start: 0.9232 (m) cc_final: 0.9015 (p) REVERT: a 651 MET cc_start: 0.9200 (mmm) cc_final: 0.8701 (mmm) REVERT: a 721 GLN cc_start: 0.8821 (tp40) cc_final: 0.8286 (tp-100) REVERT: a 729 CYS cc_start: 0.9115 (m) cc_final: 0.8868 (p) REVERT: a 759 MET cc_start: 0.8062 (mmm) cc_final: 0.7439 (tmm) REVERT: a 794 MET cc_start: 0.9610 (tmm) cc_final: 0.9185 (tmm) REVERT: a 810 GLU cc_start: 0.7594 (mp0) cc_final: 0.7313 (mp0) REVERT: a 811 PHE cc_start: 0.8317 (t80) cc_final: 0.8096 (t80) REVERT: b 19 MET cc_start: 0.8750 (mtp) cc_final: 0.8256 (mtt) REVERT: b 25 CYS cc_start: 0.9175 (m) cc_final: 0.8822 (t) REVERT: b 34 ARG cc_start: 0.8389 (mmm160) cc_final: 0.6340 (tpt170) REVERT: b 48 MET cc_start: 0.8898 (ttt) cc_final: 0.8667 (tmm) REVERT: b 70 TYR cc_start: 0.9038 (p90) cc_final: 0.8762 (p90) REVERT: b 71 ILE cc_start: 0.9561 (mm) cc_final: 0.9277 (mm) REVERT: b 74 SER cc_start: 0.9459 (m) cc_final: 0.9077 (t) REVERT: b 75 SER cc_start: 0.9746 (m) cc_final: 0.9355 (p) REVERT: b 82 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8558 (mtpp) REVERT: b 90 ASN cc_start: 0.8737 (m-40) cc_final: 0.7225 (m-40) REVERT: b 92 VAL cc_start: 0.9145 (m) cc_final: 0.8566 (m) REVERT: b 96 PHE cc_start: 0.9061 (m-80) cc_final: 0.8495 (m-80) REVERT: b 98 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8144 (mm-30) REVERT: b 114 MET cc_start: 0.7933 (mtm) cc_final: 0.6820 (mtm) REVERT: b 129 ARG cc_start: 0.9099 (mpp80) cc_final: 0.8806 (mmm-85) REVERT: b 137 MET cc_start: 0.9425 (ttt) cc_final: 0.8894 (tpt) REVERT: b 148 ASN cc_start: 0.9710 (m110) cc_final: 0.9411 (m110) REVERT: b 151 CYS cc_start: 0.9490 (t) cc_final: 0.9210 (t) REVERT: b 154 CYS cc_start: 0.9256 (t) cc_final: 0.9012 (t) REVERT: b 164 LEU cc_start: 0.9346 (mm) cc_final: 0.9003 (mt) REVERT: b 166 ASP cc_start: 0.8555 (t70) cc_final: 0.8208 (p0) REVERT: b 168 GLN cc_start: 0.9349 (mt0) cc_final: 0.9086 (mp10) REVERT: b 169 ASN cc_start: 0.8638 (t0) cc_final: 0.8435 (t0) REVERT: b 172 LEU cc_start: 0.8992 (mt) cc_final: 0.8318 (mt) REVERT: b 173 PHE cc_start: 0.8707 (t80) cc_final: 0.8409 (t80) REVERT: c 419 ILE cc_start: 0.8331 (mm) cc_final: 0.8082 (mm) REVERT: c 423 LEU cc_start: 0.9041 (mt) cc_final: 0.8803 (mt) REVERT: c 435 TYR cc_start: 0.8669 (t80) cc_final: 0.8266 (t80) REVERT: c 439 MET cc_start: 0.9579 (mmm) cc_final: 0.9325 (mmm) REVERT: d 30 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8432 (tm-30) REVERT: d 50 GLN cc_start: 0.8807 (mt0) cc_final: 0.8355 (tp40) REVERT: d 74 LEU cc_start: 0.9667 (mp) cc_final: 0.9439 (tp) REVERT: d 76 GLU cc_start: 0.8435 (tt0) cc_final: 0.8127 (tp30) REVERT: d 85 MET cc_start: 0.8987 (mtp) cc_final: 0.8781 (ttp) REVERT: d 98 ASP cc_start: 0.8846 (m-30) cc_final: 0.8362 (t70) REVERT: d 105 MET cc_start: 0.8974 (mtm) cc_final: 0.8681 (mtp) REVERT: d 108 ASN cc_start: 0.8948 (m110) cc_final: 0.8545 (m110) REVERT: d 124 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8467 (mt-10) REVERT: d 128 LYS cc_start: 0.9086 (mmtt) cc_final: 0.8226 (mttt) REVERT: d 176 MET cc_start: 0.7738 (mtt) cc_final: 0.7412 (mtt) REVERT: d 241 PHE cc_start: 0.8419 (m-10) cc_final: 0.7801 (m-10) REVERT: d 244 CYS cc_start: 0.8156 (m) cc_final: 0.7431 (p) REVERT: d 292 ASP cc_start: 0.8818 (m-30) cc_final: 0.7882 (t70) REVERT: d 297 HIS cc_start: 0.8647 (t-90) cc_final: 0.8372 (t70) REVERT: d 312 PHE cc_start: 0.8377 (m-10) cc_final: 0.8108 (m-10) REVERT: d 335 CYS cc_start: 0.8780 (m) cc_final: 0.8256 (t) REVERT: e 9 PRO cc_start: 0.7342 (Cg_exo) cc_final: 0.6755 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7568 (m-80) cc_final: 0.7012 (m-80) REVERT: e 47 CYS cc_start: 0.7898 (p) cc_final: 0.7276 (p) REVERT: e 54 ILE cc_start: 0.9607 (mt) cc_final: 0.9340 (mt) REVERT: e 68 LEU cc_start: 0.8798 (tp) cc_final: 0.8542 (tp) REVERT: g 25 PHE cc_start: 0.8770 (m-80) cc_final: 0.8239 (m-80) REVERT: g 61 MET cc_start: 0.7753 (mmt) cc_final: 0.7244 (mmm) REVERT: g 88 ARG cc_start: 0.8297 (mmm160) cc_final: 0.7656 (mmt180) REVERT: g 91 LEU cc_start: 0.8888 (mt) cc_final: 0.8660 (mt) REVERT: g 108 PHE cc_start: 0.9239 (m-80) cc_final: 0.8692 (m-80) REVERT: g 110 ILE cc_start: 0.9575 (mm) cc_final: 0.9346 (mm) REVERT: g 124 GLN cc_start: 0.8181 (tp-100) cc_final: 0.7834 (tm-30) REVERT: g 133 LEU cc_start: 0.9112 (mp) cc_final: 0.8756 (mp) REVERT: g 137 PHE cc_start: 0.8599 (m-10) cc_final: 0.8030 (m-80) REVERT: g 141 LEU cc_start: 0.9361 (mt) cc_final: 0.8989 (mt) REVERT: g 144 TYR cc_start: 0.9083 (m-10) cc_final: 0.8651 (m-80) REVERT: g 152 LEU cc_start: 0.9386 (mt) cc_final: 0.9001 (tp) REVERT: h 10 TYR cc_start: 0.8827 (p90) cc_final: 0.8478 (p90) REVERT: h 13 PHE cc_start: 0.8615 (t80) cc_final: 0.8333 (t80) REVERT: h 44 MET cc_start: 0.9051 (tmm) cc_final: 0.8818 (tmm) REVERT: h 70 LEU cc_start: 0.8920 (tp) cc_final: 0.8698 (tp) REVERT: h 127 LEU cc_start: 0.8774 (tp) cc_final: 0.8502 (tp) REVERT: h 152 LEU cc_start: 0.9399 (tp) cc_final: 0.9179 (tp) REVERT: i 52 ILE cc_start: 0.9569 (tt) cc_final: 0.9292 (mm) REVERT: i 53 MET cc_start: 0.8574 (mmp) cc_final: 0.8194 (ptt) REVERT: i 61 MET cc_start: 0.9246 (mtm) cc_final: 0.8684 (ptm) REVERT: i 110 ILE cc_start: 0.9410 (mt) cc_final: 0.9005 (tt) REVERT: i 119 ARG cc_start: 0.8648 (ttm110) cc_final: 0.8253 (ttm110) REVERT: i 144 TYR cc_start: 0.8848 (m-80) cc_final: 0.8533 (m-80) REVERT: j 17 MET cc_start: 0.9313 (mmp) cc_final: 0.9090 (tpt) REVERT: j 61 MET cc_start: 0.8839 (tpp) cc_final: 0.8524 (tpp) REVERT: j 136 ILE cc_start: 0.9228 (mm) cc_final: 0.8935 (mm) REVERT: k 23 MET cc_start: 0.9194 (tpt) cc_final: 0.8818 (tpt) REVERT: k 32 TYR cc_start: 0.8784 (t80) cc_final: 0.8233 (t80) REVERT: k 48 ARG cc_start: 0.7215 (mmt90) cc_final: 0.6930 (mmt90) REVERT: k 54 LYS cc_start: 0.7942 (mttt) cc_final: 0.7493 (mttt) REVERT: k 70 LEU cc_start: 0.8560 (tp) cc_final: 0.8272 (tp) REVERT: k 76 ILE cc_start: 0.9274 (mt) cc_final: 0.8347 (tt) REVERT: k 80 LEU cc_start: 0.9331 (mt) cc_final: 0.9088 (mt) REVERT: k 90 PHE cc_start: 0.8944 (m-80) cc_final: 0.8322 (m-80) REVERT: k 92 GLN cc_start: 0.9152 (mt0) cc_final: 0.8616 (mt0) REVERT: k 101 LEU cc_start: 0.9096 (mt) cc_final: 0.8849 (mp) REVERT: k 121 THR cc_start: 0.8815 (p) cc_final: 0.8523 (p) REVERT: k 123 GLN cc_start: 0.8740 (tp40) cc_final: 0.8266 (tp-100) REVERT: k 124 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8122 (tm-30) REVERT: k 128 PHE cc_start: 0.6725 (t80) cc_final: 0.6471 (t80) REVERT: k 147 ILE cc_start: 0.9545 (tp) cc_final: 0.9342 (tp) REVERT: k 150 LEU cc_start: 0.8958 (tt) cc_final: 0.8667 (mp) REVERT: l 13 PHE cc_start: 0.9436 (t80) cc_final: 0.9230 (t80) REVERT: l 54 LYS cc_start: 0.8742 (mttt) cc_final: 0.8156 (mmtt) REVERT: l 90 PHE cc_start: 0.9083 (m-10) cc_final: 0.8230 (m-80) REVERT: l 118 VAL cc_start: 0.9720 (t) cc_final: 0.9353 (m) REVERT: l 123 GLN cc_start: 0.9013 (mp10) cc_final: 0.8773 (mp10) REVERT: l 131 MET cc_start: 0.9173 (ttm) cc_final: 0.8954 (ttm) REVERT: l 152 LEU cc_start: 0.9349 (mt) cc_final: 0.9012 (tp) REVERT: m 17 MET cc_start: 0.9026 (mmm) cc_final: 0.8811 (mmm) REVERT: m 21 SER cc_start: 0.9235 (m) cc_final: 0.8869 (p) REVERT: m 44 MET cc_start: 0.9155 (ppp) cc_final: 0.8948 (ppp) REVERT: m 47 MET cc_start: 0.8327 (tpp) cc_final: 0.8123 (tpp) REVERT: m 48 ARG cc_start: 0.8215 (mmm-85) cc_final: 0.7856 (mmm-85) REVERT: m 52 ILE cc_start: 0.8542 (mt) cc_final: 0.8230 (mt) REVERT: m 61 MET cc_start: 0.9479 (mmm) cc_final: 0.9034 (mmm) REVERT: m 86 LEU cc_start: 0.9329 (tp) cc_final: 0.8954 (tp) REVERT: m 90 PHE cc_start: 0.9335 (m-10) cc_final: 0.8640 (m-80) REVERT: m 92 GLN cc_start: 0.9255 (mt0) cc_final: 0.8914 (mt0) REVERT: n 17 MET cc_start: 0.9321 (mmt) cc_final: 0.8864 (mmt) REVERT: n 36 LYS cc_start: 0.8062 (mmtt) cc_final: 0.7642 (mttt) REVERT: n 80 LEU cc_start: 0.9243 (tp) cc_final: 0.8672 (mt) REVERT: n 81 THR cc_start: 0.9196 (p) cc_final: 0.8947 (t) REVERT: n 88 ARG cc_start: 0.8290 (ttm-80) cc_final: 0.7504 (mmm-85) REVERT: n 119 ARG cc_start: 0.7898 (ttm110) cc_final: 0.7667 (mtm180) REVERT: n 126 ARG cc_start: 0.8328 (mtt-85) cc_final: 0.7925 (mmm160) REVERT: n 127 LEU cc_start: 0.9414 (tp) cc_final: 0.9198 (tp) REVERT: o 32 TYR cc_start: 0.7927 (t80) cc_final: 0.7544 (t80) REVERT: o 44 MET cc_start: 0.8695 (ttp) cc_final: 0.8366 (ttp) REVERT: o 80 LEU cc_start: 0.9312 (mm) cc_final: 0.9038 (mm) REVERT: o 90 PHE cc_start: 0.9278 (m-10) cc_final: 0.8699 (m-10) REVERT: o 110 ILE cc_start: 0.9425 (mt) cc_final: 0.9215 (mt) REVERT: o 144 TYR cc_start: 0.8881 (m-10) cc_final: 0.8617 (m-10) REVERT: p 305 VAL cc_start: 0.9339 (t) cc_final: 0.8982 (p) REVERT: p 326 TYR cc_start: 0.8217 (t80) cc_final: 0.7975 (t80) REVERT: p 330 ASN cc_start: 0.8805 (m-40) cc_final: 0.8520 (m-40) REVERT: p 341 ARG cc_start: 0.8892 (ptm-80) cc_final: 0.8438 (ptm160) outliers start: 6 outliers final: 0 residues processed: 1169 average time/residue: 0.2943 time to fit residues: 549.1131 Evaluate side-chains 967 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 967 time to evaluate : 2.335 ------------------------------------------------------------------------------- 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: 3.9990 chunk 153 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 137 optimal weight: 0.6980 chunk 242 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 751 GLN ** d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21366 Z= 0.223 Angle : 0.645 8.956 28966 Z= 0.336 Chirality : 0.041 0.268 3430 Planarity : 0.004 0.052 3602 Dihedral : 4.123 20.033 2978 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.56 % Favored : 97.40 % Rotamer: Outliers : 0.14 % Allowed : 1.69 % 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: 1.65 (0.16), residues: 2771 helix: 1.70 (0.11), residues: 2077 sheet: -0.45 (1.10), residues: 18 loop : -0.73 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP b 67 HIS 0.004 0.001 HIS a 720 PHE 0.032 0.002 PHE n 90 TYR 0.051 0.002 TYR m 144 ARG 0.005 0.000 ARG j 48 *********************** 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 1147 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1144 time to evaluate : 2.379 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: H 56 MET cc_start: 0.9144 (tmm) cc_final: 0.8829 (tmm) REVERT: H 57 LEU cc_start: 0.9375 (tt) cc_final: 0.9170 (tt) REVERT: H 58 MET cc_start: 0.9008 (tmm) cc_final: 0.8620 (tmm) REVERT: H 64 GLU cc_start: 0.8656 (tp30) cc_final: 0.8420 (tp30) REVERT: H 67 PHE cc_start: 0.8478 (t80) cc_final: 0.8170 (t80) REVERT: H 68 SER cc_start: 0.9324 (m) cc_final: 0.8778 (t) REVERT: H 91 GLN cc_start: 0.8219 (tt0) cc_final: 0.7714 (tt0) REVERT: H 134 LEU cc_start: 0.9043 (tp) cc_final: 0.8709 (tp) REVERT: H 137 ASN cc_start: 0.8980 (m110) cc_final: 0.8463 (m110) REVERT: L 6 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7667 (mmtt) REVERT: L 22 LEU cc_start: 0.9555 (mt) cc_final: 0.9282 (mt) REVERT: L 29 ASN cc_start: 0.8857 (t0) cc_final: 0.7943 (m-40) REVERT: L 30 LYS cc_start: 0.8999 (mmpt) cc_final: 0.8735 (tppt) REVERT: L 31 ASN cc_start: 0.8579 (p0) cc_final: 0.8226 (p0) REVERT: L 35 ASN cc_start: 0.9065 (p0) cc_final: 0.8604 (p0) REVERT: L 40 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8798 (mp0) REVERT: L 73 MET cc_start: 0.8386 (mtp) cc_final: 0.7892 (ptp) REVERT: L 89 LEU cc_start: 0.7529 (mt) cc_final: 0.7252 (mp) REVERT: L 90 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7229 (mt-10) REVERT: L 99 ASP cc_start: 0.5989 (t0) cc_final: 0.3753 (p0) REVERT: a 9 GLU cc_start: 0.7139 (mp0) cc_final: 0.6374 (pp20) REVERT: a 388 GLU cc_start: 0.8211 (tp30) cc_final: 0.7127 (tt0) REVERT: a 401 PHE cc_start: 0.9126 (t80) cc_final: 0.8599 (t80) REVERT: a 423 MET cc_start: 0.9472 (mpp) cc_final: 0.8951 (mpp) REVERT: a 426 ARG cc_start: 0.6578 (mmt180) cc_final: 0.6236 (tpp-160) REVERT: a 467 CYS cc_start: 0.6797 (t) cc_final: 0.6414 (t) REVERT: a 538 MET cc_start: 0.8262 (ttt) cc_final: 0.7883 (ttt) REVERT: a 540 MET cc_start: 0.9279 (tpt) cc_final: 0.9073 (tpt) REVERT: a 616 MET cc_start: 0.9084 (ttp) cc_final: 0.8714 (ttp) REVERT: a 642 VAL cc_start: 0.9226 (m) cc_final: 0.8552 (p) REVERT: a 645 MET cc_start: 0.8735 (ptt) cc_final: 0.8315 (ppp) REVERT: a 646 LEU cc_start: 0.8932 (mt) cc_final: 0.8574 (pp) REVERT: a 647 CYS cc_start: 0.9133 (m) cc_final: 0.8733 (m) REVERT: a 651 MET cc_start: 0.9087 (mmm) cc_final: 0.8593 (mmm) REVERT: a 721 GLN cc_start: 0.8823 (tp40) cc_final: 0.8300 (tp-100) REVERT: a 729 CYS cc_start: 0.9076 (m) cc_final: 0.8817 (p) REVERT: a 759 MET cc_start: 0.8019 (mmm) cc_final: 0.7384 (tmm) REVERT: a 794 MET cc_start: 0.9617 (tmm) cc_final: 0.9286 (tmm) REVERT: a 810 GLU cc_start: 0.7460 (mp0) cc_final: 0.6948 (mp0) REVERT: b 8 TYR cc_start: 0.8922 (m-80) cc_final: 0.8582 (m-80) REVERT: b 19 MET cc_start: 0.8731 (mtp) cc_final: 0.8254 (mtt) REVERT: b 25 CYS cc_start: 0.9157 (m) cc_final: 0.8814 (t) REVERT: b 34 ARG cc_start: 0.8438 (mmm160) cc_final: 0.6353 (tpt170) REVERT: b 36 ASP cc_start: 0.7426 (t70) cc_final: 0.7006 (t0) REVERT: b 48 MET cc_start: 0.8881 (ttt) cc_final: 0.8605 (tmm) REVERT: b 70 TYR cc_start: 0.9016 (p90) cc_final: 0.8684 (p90) REVERT: b 71 ILE cc_start: 0.9563 (mm) cc_final: 0.9243 (mm) REVERT: b 74 SER cc_start: 0.9440 (m) cc_final: 0.9080 (t) REVERT: b 75 SER cc_start: 0.9742 (m) cc_final: 0.9351 (p) REVERT: b 82 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8590 (mtpp) REVERT: b 90 ASN cc_start: 0.8725 (m-40) cc_final: 0.7071 (m-40) REVERT: b 114 MET cc_start: 0.8042 (mtm) cc_final: 0.7413 (mtm) REVERT: b 129 ARG cc_start: 0.9122 (mpp80) cc_final: 0.8844 (mmm-85) REVERT: b 130 ASN cc_start: 0.9046 (m-40) cc_final: 0.8625 (m-40) REVERT: b 137 MET cc_start: 0.9457 (ttt) cc_final: 0.9149 (tpp) REVERT: b 148 ASN cc_start: 0.9648 (m110) cc_final: 0.9342 (m110) REVERT: b 151 CYS cc_start: 0.9486 (t) cc_final: 0.9204 (t) REVERT: b 166 ASP cc_start: 0.8453 (t70) cc_final: 0.8138 (p0) REVERT: b 168 GLN cc_start: 0.9360 (mt0) cc_final: 0.9082 (mp10) REVERT: b 169 ASN cc_start: 0.8579 (t0) cc_final: 0.8230 (t0) REVERT: b 172 LEU cc_start: 0.8986 (mt) cc_final: 0.8284 (mt) REVERT: b 173 PHE cc_start: 0.8604 (t80) cc_final: 0.8357 (t80) REVERT: b 189 PHE cc_start: 0.8897 (m-80) cc_final: 0.8674 (m-80) REVERT: c 419 ILE cc_start: 0.8633 (mm) cc_final: 0.8391 (mm) REVERT: c 435 TYR cc_start: 0.8530 (t80) cc_final: 0.8128 (t80) REVERT: c 439 MET cc_start: 0.9536 (mmm) cc_final: 0.9182 (mtt) REVERT: d 74 LEU cc_start: 0.9619 (mp) cc_final: 0.9409 (tp) REVERT: d 76 GLU cc_start: 0.8417 (tt0) cc_final: 0.8174 (tp30) REVERT: d 79 VAL cc_start: 0.9464 (p) cc_final: 0.9260 (m) REVERT: d 85 MET cc_start: 0.8987 (mtp) cc_final: 0.8692 (ttp) REVERT: d 98 ASP cc_start: 0.8864 (m-30) cc_final: 0.8363 (t70) REVERT: d 124 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8480 (mt-10) REVERT: d 128 LYS cc_start: 0.9140 (mmtt) cc_final: 0.8300 (mttt) REVERT: d 176 MET cc_start: 0.7738 (mtt) cc_final: 0.7447 (mtt) REVERT: d 179 GLU cc_start: 0.8756 (mm-30) cc_final: 0.7536 (tt0) REVERT: d 241 PHE cc_start: 0.8481 (m-10) cc_final: 0.7872 (m-10) REVERT: d 292 ASP cc_start: 0.8803 (m-30) cc_final: 0.7866 (t70) REVERT: d 297 HIS cc_start: 0.8558 (t-90) cc_final: 0.8285 (t70) REVERT: d 312 PHE cc_start: 0.8304 (m-10) cc_final: 0.8080 (m-10) REVERT: d 335 CYS cc_start: 0.8759 (m) cc_final: 0.8291 (t) REVERT: e 9 PRO cc_start: 0.7333 (Cg_exo) cc_final: 0.6726 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7546 (m-80) cc_final: 0.7017 (m-80) REVERT: e 47 CYS cc_start: 0.7770 (p) cc_final: 0.7349 (p) REVERT: e 49 TYR cc_start: 0.7972 (t80) cc_final: 0.7593 (t80) REVERT: e 54 ILE cc_start: 0.9586 (mt) cc_final: 0.9344 (mt) REVERT: e 68 LEU cc_start: 0.8746 (tp) cc_final: 0.8454 (tp) REVERT: f 67 TYR cc_start: 0.8176 (m-80) cc_final: 0.7935 (m-80) REVERT: g 10 TYR cc_start: 0.6896 (m-80) cc_final: 0.6065 (m-80) REVERT: g 25 PHE cc_start: 0.8802 (m-80) cc_final: 0.8599 (m-80) REVERT: g 61 MET cc_start: 0.7662 (mmt) cc_final: 0.7310 (mmm) REVERT: g 88 ARG cc_start: 0.8611 (mmm160) cc_final: 0.7917 (tpm170) REVERT: g 91 LEU cc_start: 0.9014 (mt) cc_final: 0.8555 (mt) REVERT: g 108 PHE cc_start: 0.9294 (m-80) cc_final: 0.8898 (m-80) REVERT: g 110 ILE cc_start: 0.9565 (mm) cc_final: 0.9271 (mm) REVERT: g 124 GLN cc_start: 0.8251 (tp-100) cc_final: 0.7897 (tm-30) REVERT: g 133 LEU cc_start: 0.9121 (mp) cc_final: 0.8739 (mp) REVERT: g 137 PHE cc_start: 0.8628 (m-10) cc_final: 0.8124 (m-80) REVERT: g 141 LEU cc_start: 0.9257 (mt) cc_final: 0.8842 (mt) REVERT: g 144 TYR cc_start: 0.9069 (m-10) cc_final: 0.8649 (m-80) REVERT: g 152 LEU cc_start: 0.9410 (mt) cc_final: 0.9087 (mt) REVERT: h 10 TYR cc_start: 0.9005 (p90) cc_final: 0.8629 (p90) REVERT: h 44 MET cc_start: 0.9019 (tmm) cc_final: 0.8751 (tmm) REVERT: h 78 ASN cc_start: 0.8819 (t0) cc_final: 0.8396 (p0) REVERT: h 91 LEU cc_start: 0.9019 (mt) cc_final: 0.8731 (mt) REVERT: h 152 LEU cc_start: 0.9398 (tp) cc_final: 0.9164 (tp) REVERT: i 47 MET cc_start: 0.8918 (mmp) cc_final: 0.7952 (mtt) REVERT: i 52 ILE cc_start: 0.9629 (tt) cc_final: 0.9318 (mm) REVERT: i 53 MET cc_start: 0.8580 (mmp) cc_final: 0.8160 (ptt) REVERT: i 61 MET cc_start: 0.9267 (mtm) cc_final: 0.8668 (ptm) REVERT: i 119 ARG cc_start: 0.8674 (ttm110) cc_final: 0.8289 (ttm110) REVERT: i 144 TYR cc_start: 0.8797 (m-80) cc_final: 0.8597 (m-80) REVERT: j 17 MET cc_start: 0.9312 (mmp) cc_final: 0.9061 (tpt) REVERT: j 44 MET cc_start: 0.8666 (ptt) cc_final: 0.8454 (ptt) REVERT: j 61 MET cc_start: 0.8822 (tpp) cc_final: 0.8575 (tpp) REVERT: j 70 LEU cc_start: 0.9575 (tp) cc_final: 0.9344 (tp) REVERT: j 84 ILE cc_start: 0.8940 (mm) cc_final: 0.8419 (mm) REVERT: j 127 LEU cc_start: 0.8948 (tt) cc_final: 0.8674 (tt) REVERT: j 128 PHE cc_start: 0.8918 (t80) cc_final: 0.8705 (t80) REVERT: j 131 MET cc_start: 0.9189 (ttt) cc_final: 0.8978 (ttt) REVERT: j 136 ILE cc_start: 0.9244 (mm) cc_final: 0.8935 (mm) REVERT: k 23 MET cc_start: 0.9148 (tpt) cc_final: 0.8807 (tpt) REVERT: k 32 TYR cc_start: 0.8761 (t80) cc_final: 0.8212 (t80) REVERT: k 61 MET cc_start: 0.9454 (mtm) cc_final: 0.9041 (mpp) REVERT: k 65 ILE cc_start: 0.9417 (mt) cc_final: 0.9188 (tp) REVERT: k 70 LEU cc_start: 0.8579 (tp) cc_final: 0.8303 (tp) REVERT: k 76 ILE cc_start: 0.9300 (mt) cc_final: 0.8367 (tt) REVERT: k 80 LEU cc_start: 0.9335 (mt) cc_final: 0.9013 (mt) REVERT: k 92 GLN cc_start: 0.9070 (mt0) cc_final: 0.8532 (mt0) REVERT: k 123 GLN cc_start: 0.8765 (tp40) cc_final: 0.8311 (tp40) REVERT: k 124 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8142 (tm-30) REVERT: k 147 ILE cc_start: 0.9530 (tp) cc_final: 0.9307 (tp) REVERT: k 150 LEU cc_start: 0.8964 (tt) cc_final: 0.8686 (mt) REVERT: l 54 LYS cc_start: 0.8733 (mttt) cc_final: 0.8123 (mmtt) REVERT: l 86 LEU cc_start: 0.9084 (tt) cc_final: 0.8847 (tt) REVERT: l 90 PHE cc_start: 0.8448 (m-10) cc_final: 0.7401 (m-80) REVERT: l 101 LEU cc_start: 0.9078 (mt) cc_final: 0.8840 (mt) REVERT: l 118 VAL cc_start: 0.9713 (t) cc_final: 0.9451 (m) REVERT: l 123 GLN cc_start: 0.9017 (mp10) cc_final: 0.8788 (mp10) REVERT: m 21 SER cc_start: 0.9327 (m) cc_final: 0.8886 (p) REVERT: m 52 ILE cc_start: 0.8579 (mt) cc_final: 0.8277 (mt) REVERT: m 60 VAL cc_start: 0.9621 (m) cc_final: 0.9394 (m) REVERT: m 61 MET cc_start: 0.9472 (mmm) cc_final: 0.9125 (mmm) REVERT: m 92 GLN cc_start: 0.9306 (mt0) cc_final: 0.8984 (mt0) REVERT: n 17 MET cc_start: 0.9288 (mmt) cc_final: 0.8792 (mmt) REVERT: n 36 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7694 (mttt) REVERT: n 76 ILE cc_start: 0.9785 (mt) cc_final: 0.9578 (mt) REVERT: n 79 SER cc_start: 0.8812 (m) cc_final: 0.8330 (p) REVERT: n 80 LEU cc_start: 0.9258 (tp) cc_final: 0.8746 (mt) REVERT: n 81 THR cc_start: 0.9268 (p) cc_final: 0.9014 (t) REVERT: n 84 ILE cc_start: 0.9186 (mm) cc_final: 0.8957 (mp) REVERT: n 90 PHE cc_start: 0.9552 (m-80) cc_final: 0.9209 (m-80) REVERT: n 119 ARG cc_start: 0.7993 (ttm110) cc_final: 0.7756 (mtm180) REVERT: n 126 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.7934 (mmm160) REVERT: n 127 LEU cc_start: 0.9456 (tp) cc_final: 0.9196 (tp) REVERT: n 128 PHE cc_start: 0.9059 (t80) cc_final: 0.8855 (t80) REVERT: n 129 VAL cc_start: 0.8521 (m) cc_final: 0.8097 (m) REVERT: o 32 TYR cc_start: 0.8095 (t80) cc_final: 0.7682 (t80) REVERT: o 44 MET cc_start: 0.8691 (ttp) cc_final: 0.8382 (ttp) REVERT: o 90 PHE cc_start: 0.9275 (m-10) cc_final: 0.8849 (m-10) REVERT: o 110 ILE cc_start: 0.9434 (mt) cc_final: 0.9067 (mt) REVERT: p 305 VAL cc_start: 0.9357 (t) cc_final: 0.9010 (p) REVERT: p 330 ASN cc_start: 0.8739 (m-40) cc_final: 0.8434 (m-40) outliers start: 3 outliers final: 0 residues processed: 1144 average time/residue: 0.3000 time to fit residues: 547.6500 Evaluate side-chains 952 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 952 time to evaluate : 2.447 ------------------------------------------------------------------------------- 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: 4.9990 chunk 242 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 158 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 269 optimal weight: 0.8980 chunk 224 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 22 optimal weight: 0.0060 chunk 89 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 637 GLN a 751 GLN ** d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 324 GLN d 328 ASN ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 124 GLN m 7 ASN m 92 GLN ** o 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.5808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21366 Z= 0.204 Angle : 0.658 9.671 28966 Z= 0.337 Chirality : 0.041 0.234 3430 Planarity : 0.004 0.058 3602 Dihedral : 4.112 18.918 2978 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 0.09 % Allowed : 1.36 % Favored : 98.54 % 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: 1.67 (0.16), residues: 2771 helix: 1.74 (0.11), residues: 2077 sheet: -0.50 (1.16), residues: 18 loop : -0.79 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 743 HIS 0.005 0.001 HIS H 111 PHE 0.025 0.002 PHE m 90 TYR 0.056 0.002 TYR m 144 ARG 0.008 0.000 ARG p 341 *********************** 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 1141 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1139 time to evaluate : 2.490 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 56 MET cc_start: 0.9133 (tmm) cc_final: 0.8799 (tmm) REVERT: H 57 LEU cc_start: 0.9320 (tt) cc_final: 0.9097 (tt) REVERT: H 64 GLU cc_start: 0.8556 (tp30) cc_final: 0.8277 (tp30) REVERT: H 68 SER cc_start: 0.9335 (m) cc_final: 0.8816 (t) REVERT: H 91 GLN cc_start: 0.8363 (tt0) cc_final: 0.7780 (tt0) REVERT: H 134 LEU cc_start: 0.9060 (tp) cc_final: 0.8717 (tp) REVERT: H 137 ASN cc_start: 0.8952 (m110) cc_final: 0.8389 (m110) REVERT: H 147 GLU cc_start: 0.9112 (tt0) cc_final: 0.8806 (tp30) REVERT: H 151 LEU cc_start: 0.9081 (mm) cc_final: 0.8809 (mm) REVERT: L 6 LYS cc_start: 0.8124 (mmtt) cc_final: 0.7616 (mmmm) REVERT: L 8 ILE cc_start: 0.8399 (mt) cc_final: 0.8051 (mp) REVERT: L 22 LEU cc_start: 0.9485 (mt) cc_final: 0.9135 (mt) REVERT: L 29 ASN cc_start: 0.8862 (t0) cc_final: 0.7950 (m-40) REVERT: L 30 LYS cc_start: 0.9003 (mmpt) cc_final: 0.8738 (tppt) REVERT: L 31 ASN cc_start: 0.8559 (p0) cc_final: 0.8257 (p0) REVERT: L 35 ASN cc_start: 0.9123 (p0) cc_final: 0.8672 (p0) REVERT: L 40 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8801 (mp0) REVERT: L 49 GLU cc_start: 0.8902 (pt0) cc_final: 0.8178 (pp20) REVERT: L 57 ASN cc_start: 0.8943 (m110) cc_final: 0.8724 (m110) REVERT: L 58 ARG cc_start: 0.7663 (mtt90) cc_final: 0.7431 (ttm-80) REVERT: L 73 MET cc_start: 0.8402 (mtp) cc_final: 0.7917 (ptp) REVERT: L 90 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7220 (mt-10) REVERT: L 99 ASP cc_start: 0.6019 (t0) cc_final: 0.3923 (p0) REVERT: a 9 GLU cc_start: 0.7199 (mp0) cc_final: 0.6392 (pp20) REVERT: a 388 GLU cc_start: 0.8173 (tp30) cc_final: 0.7167 (tt0) REVERT: a 397 ILE cc_start: 0.9024 (mm) cc_final: 0.8706 (tp) REVERT: a 401 PHE cc_start: 0.9112 (t80) cc_final: 0.8615 (t80) REVERT: a 409 ASP cc_start: 0.8085 (t0) cc_final: 0.7884 (t70) REVERT: a 423 MET cc_start: 0.9468 (mpp) cc_final: 0.8956 (mpp) REVERT: a 426 ARG cc_start: 0.6526 (mmt180) cc_final: 0.6304 (tpp-160) REVERT: a 467 CYS cc_start: 0.6620 (t) cc_final: 0.6194 (t) REVERT: a 519 ILE cc_start: 0.6919 (mp) cc_final: 0.6522 (mp) REVERT: a 538 MET cc_start: 0.7859 (ttt) cc_final: 0.7517 (ttt) REVERT: a 580 MET cc_start: 0.9265 (mmm) cc_final: 0.9007 (mmm) REVERT: a 616 MET cc_start: 0.9085 (ttp) cc_final: 0.8657 (tmm) REVERT: a 636 ILE cc_start: 0.8846 (mm) cc_final: 0.8606 (tp) REVERT: a 637 GLN cc_start: 0.8698 (mt0) cc_final: 0.8028 (mt0) REVERT: a 642 VAL cc_start: 0.9220 (m) cc_final: 0.8522 (p) REVERT: a 645 MET cc_start: 0.8667 (ptt) cc_final: 0.8254 (ppp) REVERT: a 646 LEU cc_start: 0.8902 (mt) cc_final: 0.8553 (pp) REVERT: a 647 CYS cc_start: 0.9167 (m) cc_final: 0.8769 (m) REVERT: a 651 MET cc_start: 0.9070 (mmm) cc_final: 0.8562 (mmm) REVERT: a 721 GLN cc_start: 0.8835 (tp40) cc_final: 0.8286 (tp-100) REVERT: a 729 CYS cc_start: 0.9059 (m) cc_final: 0.8735 (p) REVERT: a 759 MET cc_start: 0.8039 (mmm) cc_final: 0.7406 (tmm) REVERT: a 794 MET cc_start: 0.9535 (tmm) cc_final: 0.9247 (tmm) REVERT: a 801 LEU cc_start: 0.9465 (tt) cc_final: 0.9262 (tt) REVERT: a 815 PHE cc_start: 0.8379 (p90) cc_final: 0.8143 (p90) REVERT: b 8 TYR cc_start: 0.8909 (m-80) cc_final: 0.8372 (m-80) REVERT: b 19 MET cc_start: 0.8734 (mtp) cc_final: 0.8282 (mtp) REVERT: b 25 CYS cc_start: 0.9117 (m) cc_final: 0.8808 (t) REVERT: b 34 ARG cc_start: 0.8407 (mmm160) cc_final: 0.6322 (tpt170) REVERT: b 36 ASP cc_start: 0.7751 (t70) cc_final: 0.7266 (t0) REVERT: b 48 MET cc_start: 0.8891 (ttt) cc_final: 0.8502 (tmm) REVERT: b 52 LEU cc_start: 0.9530 (mt) cc_final: 0.9072 (mt) REVERT: b 71 ILE cc_start: 0.9526 (mm) cc_final: 0.9221 (mm) REVERT: b 74 SER cc_start: 0.9441 (m) cc_final: 0.9105 (t) REVERT: b 75 SER cc_start: 0.9724 (m) cc_final: 0.9345 (p) REVERT: b 82 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8443 (mmtp) REVERT: b 90 ASN cc_start: 0.8662 (m-40) cc_final: 0.8070 (m-40) REVERT: b 96 PHE cc_start: 0.9204 (m-80) cc_final: 0.8585 (m-80) REVERT: b 98 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8198 (mm-30) REVERT: b 114 MET cc_start: 0.8105 (mtm) cc_final: 0.7064 (mtm) REVERT: b 129 ARG cc_start: 0.9138 (mpp80) cc_final: 0.8870 (mmm-85) REVERT: b 130 ASN cc_start: 0.9033 (m-40) cc_final: 0.8653 (m-40) REVERT: b 137 MET cc_start: 0.9469 (ttt) cc_final: 0.8754 (tpt) REVERT: b 148 ASN cc_start: 0.9577 (m110) cc_final: 0.9311 (m110) REVERT: b 164 LEU cc_start: 0.9369 (mm) cc_final: 0.9001 (mt) REVERT: b 168 GLN cc_start: 0.9353 (mt0) cc_final: 0.9074 (mp10) REVERT: b 169 ASN cc_start: 0.8489 (t0) cc_final: 0.7930 (t0) REVERT: b 172 LEU cc_start: 0.8993 (mt) cc_final: 0.8247 (mt) REVERT: b 186 ILE cc_start: 0.9232 (mt) cc_final: 0.8970 (mt) REVERT: b 203 MET cc_start: 0.8188 (mmp) cc_final: 0.7961 (mmm) REVERT: c 419 ILE cc_start: 0.8525 (mm) cc_final: 0.8051 (mm) REVERT: c 439 MET cc_start: 0.9510 (mmm) cc_final: 0.9256 (mtt) REVERT: d 23 LEU cc_start: 0.9070 (mm) cc_final: 0.8821 (mm) REVERT: d 76 GLU cc_start: 0.8411 (tt0) cc_final: 0.8132 (tp30) REVERT: d 79 VAL cc_start: 0.9477 (p) cc_final: 0.9265 (m) REVERT: d 85 MET cc_start: 0.8994 (mtp) cc_final: 0.8745 (ttp) REVERT: d 98 ASP cc_start: 0.8858 (m-30) cc_final: 0.8392 (t0) REVERT: d 124 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8489 (mt-10) REVERT: d 128 LYS cc_start: 0.9187 (mmtt) cc_final: 0.8385 (mttt) REVERT: d 176 MET cc_start: 0.7666 (mtt) cc_final: 0.7352 (mtt) REVERT: d 241 PHE cc_start: 0.8466 (m-10) cc_final: 0.8143 (m-80) REVERT: d 292 ASP cc_start: 0.8781 (m-30) cc_final: 0.7782 (t0) REVERT: d 297 HIS cc_start: 0.8572 (t-90) cc_final: 0.8330 (t70) REVERT: d 335 CYS cc_start: 0.8689 (m) cc_final: 0.8228 (t) REVERT: d 340 HIS cc_start: 0.8293 (m170) cc_final: 0.6891 (m170) REVERT: e 9 PRO cc_start: 0.7289 (Cg_exo) cc_final: 0.6694 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7441 (m-80) cc_final: 0.6932 (m-80) REVERT: e 47 CYS cc_start: 0.7776 (p) cc_final: 0.7250 (p) REVERT: e 54 ILE cc_start: 0.9593 (mt) cc_final: 0.9376 (mt) REVERT: e 68 LEU cc_start: 0.8721 (tp) cc_final: 0.8416 (tp) REVERT: f 67 TYR cc_start: 0.8278 (m-80) cc_final: 0.7993 (m-80) REVERT: g 10 TYR cc_start: 0.6918 (m-80) cc_final: 0.6102 (m-80) REVERT: g 44 MET cc_start: 0.9282 (ppp) cc_final: 0.8848 (ppp) REVERT: g 45 SER cc_start: 0.9671 (p) cc_final: 0.9296 (p) REVERT: g 61 MET cc_start: 0.7760 (mmt) cc_final: 0.7186 (mmm) REVERT: g 88 ARG cc_start: 0.8393 (mmm160) cc_final: 0.7969 (mmt180) REVERT: g 108 PHE cc_start: 0.9252 (m-80) cc_final: 0.8452 (m-80) REVERT: g 110 ILE cc_start: 0.9572 (mm) cc_final: 0.9186 (mm) REVERT: g 124 GLN cc_start: 0.8137 (tp-100) cc_final: 0.7783 (tm-30) REVERT: g 137 PHE cc_start: 0.8629 (m-10) cc_final: 0.8343 (m-80) REVERT: g 139 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7471 (mm-30) REVERT: g 141 LEU cc_start: 0.9227 (mt) cc_final: 0.8785 (mt) REVERT: g 144 TYR cc_start: 0.9072 (m-10) cc_final: 0.8664 (m-80) REVERT: g 152 LEU cc_start: 0.9457 (mt) cc_final: 0.9251 (mt) REVERT: h 10 TYR cc_start: 0.9029 (p90) cc_final: 0.8609 (p90) REVERT: h 13 PHE cc_start: 0.8378 (t80) cc_final: 0.7984 (t80) REVERT: h 17 MET cc_start: 0.8491 (mmm) cc_final: 0.7766 (mmm) REVERT: h 44 MET cc_start: 0.9011 (tmm) cc_final: 0.8730 (tmm) REVERT: h 146 LEU cc_start: 0.9497 (tt) cc_final: 0.9242 (tt) REVERT: i 52 ILE cc_start: 0.9622 (tt) cc_final: 0.9309 (mm) REVERT: i 53 MET cc_start: 0.8620 (mmp) cc_final: 0.8180 (ptt) REVERT: i 61 MET cc_start: 0.9317 (mtm) cc_final: 0.8722 (ptp) REVERT: i 65 ILE cc_start: 0.9399 (mm) cc_final: 0.8935 (mm) REVERT: i 90 PHE cc_start: 0.7576 (m-10) cc_final: 0.7063 (m-80) REVERT: i 119 ARG cc_start: 0.8632 (ttm110) cc_final: 0.8253 (ttm110) REVERT: i 139 GLU cc_start: 0.9227 (tp30) cc_final: 0.8871 (tp30) REVERT: i 144 TYR cc_start: 0.8827 (m-80) cc_final: 0.8587 (m-80) REVERT: j 41 ILE cc_start: 0.9093 (pt) cc_final: 0.8878 (pt) REVERT: j 61 MET cc_start: 0.8839 (tpp) cc_final: 0.8556 (tpp) REVERT: j 70 LEU cc_start: 0.9577 (tp) cc_final: 0.9350 (tp) REVERT: j 84 ILE cc_start: 0.8787 (mm) cc_final: 0.8178 (mm) REVERT: j 123 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8805 (mm-40) REVERT: j 127 LEU cc_start: 0.8924 (tt) cc_final: 0.8471 (tt) REVERT: j 131 MET cc_start: 0.9230 (ttt) cc_final: 0.8909 (ttt) REVERT: j 136 ILE cc_start: 0.9255 (mm) cc_final: 0.8952 (mm) REVERT: k 32 TYR cc_start: 0.8755 (t80) cc_final: 0.8195 (t80) REVERT: k 54 LYS cc_start: 0.7850 (mttt) cc_final: 0.7328 (tttt) REVERT: k 65 ILE cc_start: 0.9430 (mt) cc_final: 0.9221 (tp) REVERT: k 76 ILE cc_start: 0.9309 (mt) cc_final: 0.8397 (tt) REVERT: k 80 LEU cc_start: 0.9284 (mt) cc_final: 0.9006 (mt) REVERT: k 90 PHE cc_start: 0.8888 (m-80) cc_final: 0.8403 (m-80) REVERT: k 92 GLN cc_start: 0.9068 (mt0) cc_final: 0.8539 (mt0) REVERT: k 123 GLN cc_start: 0.8763 (tp40) cc_final: 0.8310 (tp40) REVERT: k 124 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8223 (tm-30) REVERT: k 137 PHE cc_start: 0.9064 (m-80) cc_final: 0.8444 (m-80) REVERT: k 143 LEU cc_start: 0.9405 (tp) cc_final: 0.9120 (mm) REVERT: k 147 ILE cc_start: 0.9479 (tp) cc_final: 0.9261 (tp) REVERT: k 150 LEU cc_start: 0.9013 (tt) cc_final: 0.8728 (mt) REVERT: l 54 LYS cc_start: 0.8652 (mttt) cc_final: 0.8019 (mmtt) REVERT: l 90 PHE cc_start: 0.8217 (m-10) cc_final: 0.7395 (m-80) REVERT: l 121 THR cc_start: 0.8990 (p) cc_final: 0.8733 (p) REVERT: l 123 GLN cc_start: 0.8952 (mp10) cc_final: 0.8717 (mp10) REVERT: l 152 LEU cc_start: 0.9352 (tp) cc_final: 0.8937 (tp) REVERT: m 13 PHE cc_start: 0.8775 (t80) cc_final: 0.8545 (t80) REVERT: m 17 MET cc_start: 0.9216 (mmm) cc_final: 0.8795 (mmm) REVERT: m 21 SER cc_start: 0.9348 (m) cc_final: 0.8801 (p) REVERT: m 25 PHE cc_start: 0.8357 (m-80) cc_final: 0.8044 (m-80) REVERT: m 47 MET cc_start: 0.8180 (tpp) cc_final: 0.7899 (tpp) REVERT: m 48 ARG cc_start: 0.8290 (mmm-85) cc_final: 0.7971 (mmm-85) REVERT: m 52 ILE cc_start: 0.8599 (mt) cc_final: 0.8320 (mt) REVERT: m 53 MET cc_start: 0.9370 (tpp) cc_final: 0.9019 (tpp) REVERT: m 61 MET cc_start: 0.9542 (mmm) cc_final: 0.9135 (mmm) REVERT: m 92 GLN cc_start: 0.9302 (mt0) cc_final: 0.9065 (mt0) REVERT: m 139 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8487 (tm-30) REVERT: n 17 MET cc_start: 0.9269 (mmt) cc_final: 0.8768 (mmt) REVERT: n 36 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7723 (mttt) REVERT: n 80 LEU cc_start: 0.9228 (tp) cc_final: 0.8752 (mt) REVERT: n 81 THR cc_start: 0.9274 (p) cc_final: 0.9005 (t) REVERT: n 90 PHE cc_start: 0.9492 (m-80) cc_final: 0.9102 (m-80) REVERT: n 126 ARG cc_start: 0.8204 (mtt-85) cc_final: 0.7896 (mmm160) REVERT: n 127 LEU cc_start: 0.9440 (tp) cc_final: 0.9138 (tp) REVERT: n 128 PHE cc_start: 0.9010 (t80) cc_final: 0.8771 (t80) REVERT: n 129 VAL cc_start: 0.8534 (m) cc_final: 0.8140 (t) REVERT: n 141 LEU cc_start: 0.9362 (mt) cc_final: 0.9156 (mt) REVERT: n 144 TYR cc_start: 0.9007 (m-10) cc_final: 0.8782 (m-10) REVERT: o 23 MET cc_start: 0.9428 (tpp) cc_final: 0.8970 (tpp) REVERT: o 32 TYR cc_start: 0.7955 (t80) cc_final: 0.7529 (t80) REVERT: o 44 MET cc_start: 0.8742 (ttp) cc_final: 0.8416 (ttp) REVERT: o 80 LEU cc_start: 0.9306 (mm) cc_final: 0.9054 (mm) REVERT: o 90 PHE cc_start: 0.9183 (m-10) cc_final: 0.8859 (m-10) REVERT: o 110 ILE cc_start: 0.9392 (mt) cc_final: 0.9191 (mt) REVERT: p 305 VAL cc_start: 0.9369 (t) cc_final: 0.9105 (p) REVERT: p 326 TYR cc_start: 0.8195 (t80) cc_final: 0.7981 (t80) REVERT: p 330 ASN cc_start: 0.8711 (m-40) cc_final: 0.8421 (m-40) REVERT: p 341 ARG cc_start: 0.8754 (ptm-80) cc_final: 0.8363 (ptm-80) outliers start: 2 outliers final: 0 residues processed: 1139 average time/residue: 0.3084 time to fit residues: 564.8038 Evaluate side-chains 963 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 963 time to evaluate : 2.644 ------------------------------------------------------------------------------- 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: 0.7980 chunk 30 optimal weight: 4.9990 chunk 153 optimal weight: 0.0570 chunk 197 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 227 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 168 optimal weight: 0.4980 chunk 163 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 751 GLN ** d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 124 GLN m 7 ASN o 7 ASN ** o 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.6068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21366 Z= 0.205 Angle : 0.676 13.570 28966 Z= 0.343 Chirality : 0.042 0.370 3430 Planarity : 0.004 0.056 3602 Dihedral : 4.111 20.487 2978 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.85 % Favored : 97.11 % Rotamer: Outliers : 0.09 % Allowed : 1.60 % Favored : 98.31 % 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: 1.67 (0.16), residues: 2771 helix: 1.74 (0.11), residues: 2078 sheet: -0.14 (1.16), residues: 18 loop : -0.82 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP a 743 HIS 0.005 0.001 HIS H 111 PHE 0.028 0.002 PHE b 189 TYR 0.042 0.002 TYR i 68 ARG 0.005 0.000 ARG n 48 *********************** 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 1150 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1148 time to evaluate : 2.387 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 56 MET cc_start: 0.9113 (tmm) cc_final: 0.8768 (tmm) REVERT: H 57 LEU cc_start: 0.9308 (tt) cc_final: 0.9087 (tt) REVERT: H 58 MET cc_start: 0.8913 (tmm) cc_final: 0.8703 (tmm) REVERT: H 64 GLU cc_start: 0.8538 (tp30) cc_final: 0.8264 (tp30) REVERT: H 68 SER cc_start: 0.9283 (m) cc_final: 0.8755 (t) REVERT: H 91 GLN cc_start: 0.8236 (tt0) cc_final: 0.7589 (tt0) REVERT: H 134 LEU cc_start: 0.9096 (tp) cc_final: 0.8715 (tp) REVERT: H 137 ASN cc_start: 0.8965 (m110) cc_final: 0.8403 (m110) REVERT: H 147 GLU cc_start: 0.8931 (tt0) cc_final: 0.8700 (tp30) REVERT: H 151 LEU cc_start: 0.9070 (mm) cc_final: 0.8778 (mm) REVERT: L 8 ILE cc_start: 0.8403 (mt) cc_final: 0.8081 (mp) REVERT: L 29 ASN cc_start: 0.8938 (t0) cc_final: 0.7986 (m-40) REVERT: L 30 LYS cc_start: 0.9007 (mmpt) cc_final: 0.8743 (tppt) REVERT: L 31 ASN cc_start: 0.8568 (p0) cc_final: 0.8253 (p0) REVERT: L 35 ASN cc_start: 0.9173 (p0) cc_final: 0.8707 (p0) REVERT: L 40 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8782 (mp0) REVERT: L 49 GLU cc_start: 0.8899 (pt0) cc_final: 0.8190 (pp20) REVERT: L 57 ASN cc_start: 0.8948 (m110) cc_final: 0.8726 (m110) REVERT: L 58 ARG cc_start: 0.7712 (mtt90) cc_final: 0.7472 (ttm-80) REVERT: L 73 MET cc_start: 0.8376 (mtm) cc_final: 0.7962 (ptp) REVERT: L 99 ASP cc_start: 0.6057 (t0) cc_final: 0.3922 (p0) REVERT: a 9 GLU cc_start: 0.7241 (mp0) cc_final: 0.6383 (pp20) REVERT: a 388 GLU cc_start: 0.8180 (tp30) cc_final: 0.7141 (tt0) REVERT: a 397 ILE cc_start: 0.9036 (mm) cc_final: 0.8695 (tp) REVERT: a 401 PHE cc_start: 0.9114 (t80) cc_final: 0.8497 (t80) REVERT: a 423 MET cc_start: 0.9470 (mpp) cc_final: 0.8926 (mpp) REVERT: a 426 ARG cc_start: 0.6546 (mmt180) cc_final: 0.6331 (tpp-160) REVERT: a 467 CYS cc_start: 0.6490 (t) cc_final: 0.6167 (t) REVERT: a 519 ILE cc_start: 0.6960 (mp) cc_final: 0.6588 (mp) REVERT: a 540 MET cc_start: 0.9573 (tpp) cc_final: 0.9234 (tpt) REVERT: a 580 MET cc_start: 0.9295 (mmm) cc_final: 0.9044 (mmm) REVERT: a 616 MET cc_start: 0.9091 (ttp) cc_final: 0.8692 (tmm) REVERT: a 636 ILE cc_start: 0.8897 (mm) cc_final: 0.8633 (tp) REVERT: a 637 GLN cc_start: 0.8589 (mt0) cc_final: 0.8250 (mt0) REVERT: a 642 VAL cc_start: 0.9212 (m) cc_final: 0.8518 (p) REVERT: a 645 MET cc_start: 0.8678 (ptt) cc_final: 0.8257 (ppp) REVERT: a 646 LEU cc_start: 0.8844 (mt) cc_final: 0.8522 (pp) REVERT: a 647 CYS cc_start: 0.9155 (m) cc_final: 0.8771 (m) REVERT: a 651 MET cc_start: 0.9069 (mmm) cc_final: 0.8574 (mmm) REVERT: a 721 GLN cc_start: 0.8834 (tp40) cc_final: 0.8320 (tp-100) REVERT: a 729 CYS cc_start: 0.8929 (m) cc_final: 0.8646 (p) REVERT: a 759 MET cc_start: 0.8025 (mmm) cc_final: 0.7381 (tmm) REVERT: a 801 LEU cc_start: 0.9428 (tt) cc_final: 0.9216 (tt) REVERT: a 811 PHE cc_start: 0.8317 (t80) cc_final: 0.7993 (t80) REVERT: b 19 MET cc_start: 0.8694 (mtp) cc_final: 0.8228 (mtm) REVERT: b 25 CYS cc_start: 0.9128 (m) cc_final: 0.8787 (t) REVERT: b 34 ARG cc_start: 0.8367 (mmm160) cc_final: 0.6367 (tpt170) REVERT: b 36 ASP cc_start: 0.7824 (t70) cc_final: 0.7296 (t0) REVERT: b 48 MET cc_start: 0.8905 (ttt) cc_final: 0.8500 (tmm) REVERT: b 52 LEU cc_start: 0.9523 (mt) cc_final: 0.9096 (mt) REVERT: b 70 TYR cc_start: 0.9033 (p90) cc_final: 0.8738 (p90) REVERT: b 71 ILE cc_start: 0.9511 (mm) cc_final: 0.9132 (mm) REVERT: b 74 SER cc_start: 0.9416 (m) cc_final: 0.9061 (t) REVERT: b 75 SER cc_start: 0.9725 (m) cc_final: 0.9353 (p) REVERT: b 82 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8508 (mmtp) REVERT: b 88 THR cc_start: 0.8604 (t) cc_final: 0.8375 (t) REVERT: b 90 ASN cc_start: 0.8639 (m-40) cc_final: 0.8240 (m-40) REVERT: b 114 MET cc_start: 0.7769 (mtm) cc_final: 0.7004 (mtm) REVERT: b 129 ARG cc_start: 0.9122 (mpp80) cc_final: 0.8826 (mmm-85) REVERT: b 137 MET cc_start: 0.9449 (ttt) cc_final: 0.9241 (tpp) REVERT: b 148 ASN cc_start: 0.9587 (m110) cc_final: 0.9349 (m110) REVERT: b 164 LEU cc_start: 0.9387 (mm) cc_final: 0.9016 (mt) REVERT: b 168 GLN cc_start: 0.9341 (mt0) cc_final: 0.9089 (mp10) REVERT: b 169 ASN cc_start: 0.8509 (t0) cc_final: 0.7871 (t0) REVERT: b 172 LEU cc_start: 0.8982 (mt) cc_final: 0.8240 (mt) REVERT: b 186 ILE cc_start: 0.9230 (mt) cc_final: 0.8999 (mt) REVERT: b 189 PHE cc_start: 0.8928 (m-80) cc_final: 0.8718 (m-80) REVERT: c 419 ILE cc_start: 0.8720 (mm) cc_final: 0.8468 (mm) REVERT: d 23 LEU cc_start: 0.9081 (mm) cc_final: 0.8808 (mp) REVERT: d 74 LEU cc_start: 0.9673 (tp) cc_final: 0.9388 (tp) REVERT: d 76 GLU cc_start: 0.8309 (tt0) cc_final: 0.8075 (tp30) REVERT: d 98 ASP cc_start: 0.8805 (m-30) cc_final: 0.8173 (t0) REVERT: d 124 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8492 (mt-10) REVERT: d 128 LYS cc_start: 0.9197 (mmtt) cc_final: 0.8398 (mttt) REVERT: d 176 MET cc_start: 0.7710 (mtt) cc_final: 0.7386 (mtt) REVERT: d 179 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8452 (mm-30) REVERT: d 241 PHE cc_start: 0.8483 (m-10) cc_final: 0.8190 (m-80) REVERT: d 292 ASP cc_start: 0.8795 (m-30) cc_final: 0.7823 (t0) REVERT: d 297 HIS cc_start: 0.8567 (t-90) cc_final: 0.8235 (t-90) REVERT: d 308 ASN cc_start: 0.7512 (m-40) cc_final: 0.7284 (m-40) REVERT: d 335 CYS cc_start: 0.8688 (m) cc_final: 0.8273 (t) REVERT: d 340 HIS cc_start: 0.8361 (m170) cc_final: 0.6934 (m170) REVERT: e 9 PRO cc_start: 0.7503 (Cg_exo) cc_final: 0.6958 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7593 (m-80) cc_final: 0.7045 (m-80) REVERT: e 47 CYS cc_start: 0.7790 (p) cc_final: 0.7031 (p) REVERT: f 67 TYR cc_start: 0.8337 (m-80) cc_final: 0.8024 (m-80) REVERT: g 10 TYR cc_start: 0.6905 (m-80) cc_final: 0.6061 (m-80) REVERT: g 61 MET cc_start: 0.7803 (mmt) cc_final: 0.7511 (mmt) REVERT: g 88 ARG cc_start: 0.8493 (mmm160) cc_final: 0.8062 (mmt180) REVERT: g 108 PHE cc_start: 0.9254 (m-80) cc_final: 0.8372 (m-80) REVERT: g 110 ILE cc_start: 0.9598 (mm) cc_final: 0.9337 (mm) REVERT: g 121 THR cc_start: 0.8612 (p) cc_final: 0.8394 (p) REVERT: g 124 GLN cc_start: 0.8107 (tp-100) cc_final: 0.7740 (tm-30) REVERT: g 131 MET cc_start: 0.9384 (ttt) cc_final: 0.8992 (ttt) REVERT: g 137 PHE cc_start: 0.8600 (m-10) cc_final: 0.8285 (m-80) REVERT: g 141 LEU cc_start: 0.9224 (mt) cc_final: 0.8817 (mt) REVERT: g 144 TYR cc_start: 0.9167 (m-10) cc_final: 0.8605 (m-80) REVERT: g 152 LEU cc_start: 0.9489 (mt) cc_final: 0.9265 (mt) REVERT: h 10 TYR cc_start: 0.9047 (p90) cc_final: 0.8652 (p90) REVERT: h 13 PHE cc_start: 0.8474 (t80) cc_final: 0.8100 (t80) REVERT: h 17 MET cc_start: 0.8528 (mmm) cc_final: 0.7783 (mmm) REVERT: h 44 MET cc_start: 0.9047 (tmm) cc_final: 0.8795 (tmm) REVERT: h 78 ASN cc_start: 0.9007 (t0) cc_final: 0.8657 (p0) REVERT: h 84 ILE cc_start: 0.8467 (mt) cc_final: 0.8142 (pt) REVERT: i 52 ILE cc_start: 0.9628 (tt) cc_final: 0.9303 (mm) REVERT: i 53 MET cc_start: 0.8615 (mmp) cc_final: 0.8270 (ptt) REVERT: i 61 MET cc_start: 0.9324 (mtm) cc_final: 0.8736 (ptp) REVERT: i 76 ILE cc_start: 0.9542 (tp) cc_final: 0.9275 (tp) REVERT: i 86 LEU cc_start: 0.9319 (tt) cc_final: 0.9021 (tp) REVERT: i 90 PHE cc_start: 0.7649 (m-10) cc_final: 0.7208 (m-80) REVERT: j 17 MET cc_start: 0.9289 (mmp) cc_final: 0.8701 (mmt) REVERT: j 41 ILE cc_start: 0.9146 (pt) cc_final: 0.8923 (pt) REVERT: j 61 MET cc_start: 0.8828 (tpp) cc_final: 0.8261 (tpp) REVERT: j 64 ILE cc_start: 0.8852 (mp) cc_final: 0.8634 (mp) REVERT: j 68 TYR cc_start: 0.8958 (m-80) cc_final: 0.8621 (m-80) REVERT: j 70 LEU cc_start: 0.9585 (tp) cc_final: 0.9378 (tp) REVERT: j 84 ILE cc_start: 0.8609 (mm) cc_final: 0.8027 (mm) REVERT: j 127 LEU cc_start: 0.8972 (tt) cc_final: 0.8432 (tt) REVERT: j 131 MET cc_start: 0.9230 (ttt) cc_final: 0.8916 (ttt) REVERT: k 32 TYR cc_start: 0.8654 (t80) cc_final: 0.8214 (t80) REVERT: k 54 LYS cc_start: 0.7798 (mttt) cc_final: 0.7141 (tttp) REVERT: k 61 MET cc_start: 0.9436 (mtm) cc_final: 0.9003 (mpp) REVERT: k 65 ILE cc_start: 0.9438 (mt) cc_final: 0.9233 (tp) REVERT: k 76 ILE cc_start: 0.9336 (mt) cc_final: 0.8423 (tt) REVERT: k 80 LEU cc_start: 0.9268 (mt) cc_final: 0.8986 (mt) REVERT: k 90 PHE cc_start: 0.8924 (m-80) cc_final: 0.8403 (m-80) REVERT: k 92 GLN cc_start: 0.9072 (mt0) cc_final: 0.8545 (mt0) REVERT: k 123 GLN cc_start: 0.8775 (tp40) cc_final: 0.8301 (tp40) REVERT: k 124 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8253 (tm-30) REVERT: k 133 LEU cc_start: 0.9252 (mt) cc_final: 0.8900 (mt) REVERT: k 137 PHE cc_start: 0.9117 (m-80) cc_final: 0.8563 (m-80) REVERT: k 143 LEU cc_start: 0.9401 (tp) cc_final: 0.9133 (mm) REVERT: k 147 ILE cc_start: 0.9485 (tp) cc_final: 0.9271 (tp) REVERT: k 150 LEU cc_start: 0.9006 (tt) cc_final: 0.8722 (mt) REVERT: l 54 LYS cc_start: 0.8595 (mttt) cc_final: 0.7964 (mmtt) REVERT: l 90 PHE cc_start: 0.8293 (m-10) cc_final: 0.7360 (m-80) REVERT: l 121 THR cc_start: 0.9027 (p) cc_final: 0.8712 (p) REVERT: l 123 GLN cc_start: 0.8919 (mp10) cc_final: 0.8671 (mp10) REVERT: l 131 MET cc_start: 0.9166 (ttm) cc_final: 0.8935 (ttm) REVERT: l 152 LEU cc_start: 0.9395 (tp) cc_final: 0.9082 (tp) REVERT: m 17 MET cc_start: 0.9216 (mmm) cc_final: 0.8796 (mmm) REVERT: m 21 SER cc_start: 0.9234 (m) cc_final: 0.8668 (p) REVERT: m 25 PHE cc_start: 0.8355 (m-80) cc_final: 0.8034 (m-80) REVERT: m 47 MET cc_start: 0.8175 (tpp) cc_final: 0.7592 (tpp) REVERT: m 48 ARG cc_start: 0.8312 (mmm-85) cc_final: 0.7776 (mmm-85) REVERT: m 53 MET cc_start: 0.9409 (tpp) cc_final: 0.9103 (tpp) REVERT: m 60 VAL cc_start: 0.9623 (m) cc_final: 0.9408 (m) REVERT: m 61 MET cc_start: 0.9587 (mmm) cc_final: 0.9167 (mmm) REVERT: m 139 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8427 (tm-30) REVERT: n 17 MET cc_start: 0.9269 (mmt) cc_final: 0.8758 (mmt) REVERT: n 36 LYS cc_start: 0.8078 (mmtt) cc_final: 0.7688 (mttt) REVERT: n 54 LYS cc_start: 0.8459 (mttt) cc_final: 0.8070 (ttmt) REVERT: n 60 VAL cc_start: 0.8839 (t) cc_final: 0.8625 (t) REVERT: n 79 SER cc_start: 0.8737 (m) cc_final: 0.8252 (p) REVERT: n 80 LEU cc_start: 0.9151 (tp) cc_final: 0.8667 (mt) REVERT: n 90 PHE cc_start: 0.9602 (m-80) cc_final: 0.9321 (m-80) REVERT: n 126 ARG cc_start: 0.8207 (mtt-85) cc_final: 0.7823 (mmm160) REVERT: n 127 LEU cc_start: 0.9452 (tp) cc_final: 0.9072 (tp) REVERT: n 141 LEU cc_start: 0.9276 (mt) cc_final: 0.8919 (mt) REVERT: n 144 TYR cc_start: 0.9053 (m-10) cc_final: 0.8528 (m-10) REVERT: o 32 TYR cc_start: 0.8026 (t80) cc_final: 0.7687 (t80) REVERT: o 44 MET cc_start: 0.8750 (ttp) cc_final: 0.8404 (ttp) REVERT: o 65 ILE cc_start: 0.9690 (mm) cc_final: 0.9465 (mm) REVERT: o 68 TYR cc_start: 0.8871 (m-10) cc_final: 0.8669 (m-80) REVERT: o 80 LEU cc_start: 0.9368 (mm) cc_final: 0.9088 (mm) REVERT: o 90 PHE cc_start: 0.8780 (m-10) cc_final: 0.8233 (m-10) REVERT: o 110 ILE cc_start: 0.9389 (mt) cc_final: 0.9189 (mt) REVERT: p 305 VAL cc_start: 0.9369 (t) cc_final: 0.9132 (p) REVERT: p 330 ASN cc_start: 0.8719 (m-40) cc_final: 0.8469 (m-40) REVERT: p 335 TYR cc_start: 0.7236 (m-80) cc_final: 0.6961 (m-10) REVERT: p 339 ILE cc_start: 0.7654 (mm) cc_final: 0.7195 (mt) REVERT: p 341 ARG cc_start: 0.8731 (ptm-80) cc_final: 0.8379 (ptm-80) outliers start: 2 outliers final: 0 residues processed: 1149 average time/residue: 0.2998 time to fit residues: 551.2825 Evaluate side-chains 953 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 953 time to evaluate : 2.364 ------------------------------------------------------------------------------- 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: 7.9990 chunk 107 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 124 GLN m 7 ASN m 92 GLN o 7 ASN ** p 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.6298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21366 Z= 0.227 Angle : 0.697 9.990 28966 Z= 0.355 Chirality : 0.042 0.254 3430 Planarity : 0.004 0.056 3602 Dihedral : 4.132 21.164 2978 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.00 % Favored : 96.97 % Rotamer: Outliers : 0.09 % Allowed : 1.03 % Favored : 98.87 % 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: 1.58 (0.16), residues: 2771 helix: 1.68 (0.11), residues: 2079 sheet: -0.29 (1.20), residues: 18 loop : -0.87 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP b 67 HIS 0.004 0.001 HIS a 548 PHE 0.026 0.002 PHE i 137 TYR 0.039 0.002 TYR i 68 ARG 0.005 0.000 ARG p 341 *********************** 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 1127 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1125 time to evaluate : 2.234 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 56 MET cc_start: 0.9125 (tmm) cc_final: 0.8772 (tmm) REVERT: H 57 LEU cc_start: 0.9310 (tt) cc_final: 0.9064 (tt) REVERT: H 64 GLU cc_start: 0.8545 (tp30) cc_final: 0.8256 (tp30) REVERT: H 68 SER cc_start: 0.9289 (m) cc_final: 0.8769 (t) REVERT: H 91 GLN cc_start: 0.8351 (tt0) cc_final: 0.7781 (tt0) REVERT: H 134 LEU cc_start: 0.9085 (tp) cc_final: 0.8672 (tp) REVERT: H 137 ASN cc_start: 0.8935 (m110) cc_final: 0.8379 (m110) REVERT: H 151 LEU cc_start: 0.9128 (mm) cc_final: 0.8877 (mm) REVERT: L 6 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7729 (mmmm) REVERT: L 35 ASN cc_start: 0.9190 (p0) cc_final: 0.8613 (p0) REVERT: L 40 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8790 (mp0) REVERT: L 49 GLU cc_start: 0.8906 (pt0) cc_final: 0.8211 (pp20) REVERT: L 57 ASN cc_start: 0.8960 (m110) cc_final: 0.8730 (m110) REVERT: L 58 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7433 (ttm-80) REVERT: L 73 MET cc_start: 0.8349 (mtm) cc_final: 0.7935 (ptp) REVERT: L 99 ASP cc_start: 0.5796 (t0) cc_final: 0.3793 (p0) REVERT: a 9 GLU cc_start: 0.7305 (mp0) cc_final: 0.6784 (pm20) REVERT: a 10 MET cc_start: 0.5019 (tpp) cc_final: 0.4770 (tpp) REVERT: a 388 GLU cc_start: 0.8232 (tp30) cc_final: 0.7103 (tt0) REVERT: a 401 PHE cc_start: 0.9123 (t80) cc_final: 0.8565 (t80) REVERT: a 423 MET cc_start: 0.9458 (mpp) cc_final: 0.8928 (mpp) REVERT: a 426 ARG cc_start: 0.6577 (mmt180) cc_final: 0.6370 (tpp-160) REVERT: a 467 CYS cc_start: 0.6527 (t) cc_final: 0.6096 (t) REVERT: a 519 ILE cc_start: 0.6968 (mp) cc_final: 0.6648 (mp) REVERT: a 537 LYS cc_start: 0.8984 (mttt) cc_final: 0.8671 (mttm) REVERT: a 540 MET cc_start: 0.9574 (tpp) cc_final: 0.9255 (tpt) REVERT: a 616 MET cc_start: 0.9065 (ttp) cc_final: 0.8773 (tmm) REVERT: a 636 ILE cc_start: 0.8905 (mm) cc_final: 0.8649 (tp) REVERT: a 637 GLN cc_start: 0.8607 (mt0) cc_final: 0.8298 (mt0) REVERT: a 642 VAL cc_start: 0.9212 (m) cc_final: 0.8504 (p) REVERT: a 645 MET cc_start: 0.8677 (ptt) cc_final: 0.8239 (ppp) REVERT: a 647 CYS cc_start: 0.9171 (m) cc_final: 0.8783 (m) REVERT: a 651 MET cc_start: 0.9043 (mmm) cc_final: 0.8459 (mmm) REVERT: a 721 GLN cc_start: 0.8827 (tp40) cc_final: 0.8389 (tp-100) REVERT: a 729 CYS cc_start: 0.8942 (m) cc_final: 0.8668 (p) REVERT: a 759 MET cc_start: 0.7845 (mmm) cc_final: 0.7283 (tmm) REVERT: a 801 LEU cc_start: 0.9413 (tt) cc_final: 0.9182 (tt) REVERT: b 19 MET cc_start: 0.8713 (mtp) cc_final: 0.8234 (mtm) REVERT: b 25 CYS cc_start: 0.9128 (m) cc_final: 0.8789 (t) REVERT: b 34 ARG cc_start: 0.8401 (mmm160) cc_final: 0.6361 (tpt170) REVERT: b 36 ASP cc_start: 0.7925 (t70) cc_final: 0.7428 (t0) REVERT: b 48 MET cc_start: 0.8942 (ttt) cc_final: 0.8474 (tmm) REVERT: b 52 LEU cc_start: 0.9501 (mt) cc_final: 0.9040 (mt) REVERT: b 70 TYR cc_start: 0.8975 (p90) cc_final: 0.8684 (p90) REVERT: b 71 ILE cc_start: 0.9428 (mm) cc_final: 0.9089 (mm) REVERT: b 74 SER cc_start: 0.9423 (m) cc_final: 0.9081 (t) REVERT: b 75 SER cc_start: 0.9718 (m) cc_final: 0.9414 (p) REVERT: b 82 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8536 (mmtp) REVERT: b 90 ASN cc_start: 0.8673 (m-40) cc_final: 0.8274 (m-40) REVERT: b 114 MET cc_start: 0.7876 (mtm) cc_final: 0.7380 (mtm) REVERT: b 130 ASN cc_start: 0.9048 (m-40) cc_final: 0.8748 (m-40) REVERT: b 137 MET cc_start: 0.9463 (ttt) cc_final: 0.9058 (tpp) REVERT: b 164 LEU cc_start: 0.9392 (mm) cc_final: 0.9089 (mt) REVERT: b 168 GLN cc_start: 0.9340 (mt0) cc_final: 0.9091 (mp10) REVERT: b 169 ASN cc_start: 0.8528 (t0) cc_final: 0.7816 (t0) REVERT: b 172 LEU cc_start: 0.8956 (mt) cc_final: 0.8213 (mt) REVERT: b 186 ILE cc_start: 0.9212 (mt) cc_final: 0.8972 (mt) REVERT: c 419 ILE cc_start: 0.8623 (mm) cc_final: 0.8277 (mm) REVERT: c 445 THR cc_start: 0.9094 (p) cc_final: 0.8749 (m) REVERT: c 448 ARG cc_start: 0.7498 (ptt-90) cc_final: 0.7284 (ptt-90) REVERT: d 23 LEU cc_start: 0.9066 (mm) cc_final: 0.8835 (mm) REVERT: d 76 GLU cc_start: 0.8405 (tt0) cc_final: 0.8034 (tp30) REVERT: d 98 ASP cc_start: 0.8793 (m-30) cc_final: 0.8137 (t0) REVERT: d 124 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8472 (mt-10) REVERT: d 128 LYS cc_start: 0.9184 (mmtt) cc_final: 0.8406 (mttt) REVERT: d 176 MET cc_start: 0.7799 (mtt) cc_final: 0.7520 (mtt) REVERT: d 179 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8448 (mm-30) REVERT: d 181 ILE cc_start: 0.9047 (mm) cc_final: 0.8847 (mm) REVERT: d 241 PHE cc_start: 0.8523 (m-10) cc_final: 0.8222 (m-80) REVERT: d 292 ASP cc_start: 0.8813 (m-30) cc_final: 0.7830 (t0) REVERT: d 297 HIS cc_start: 0.8550 (t-90) cc_final: 0.7995 (t-90) REVERT: d 308 ASN cc_start: 0.7599 (m-40) cc_final: 0.7298 (m-40) REVERT: d 335 CYS cc_start: 0.8688 (m) cc_final: 0.8252 (t) REVERT: e 9 PRO cc_start: 0.7449 (Cg_exo) cc_final: 0.6984 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7675 (m-80) cc_final: 0.7178 (m-80) REVERT: e 47 CYS cc_start: 0.7806 (p) cc_final: 0.7170 (p) REVERT: e 49 TYR cc_start: 0.8209 (t80) cc_final: 0.7950 (t80) REVERT: e 68 LEU cc_start: 0.8865 (tp) cc_final: 0.8565 (tp) REVERT: f 67 TYR cc_start: 0.8351 (m-80) cc_final: 0.8005 (m-80) REVERT: g 10 TYR cc_start: 0.6944 (m-80) cc_final: 0.6101 (m-80) REVERT: g 44 MET cc_start: 0.9223 (ppp) cc_final: 0.8794 (ppp) REVERT: g 45 SER cc_start: 0.9675 (p) cc_final: 0.9217 (p) REVERT: g 88 ARG cc_start: 0.8564 (mmm160) cc_final: 0.8241 (mmt180) REVERT: g 90 PHE cc_start: 0.8093 (m-80) cc_final: 0.7841 (m-80) REVERT: g 108 PHE cc_start: 0.9154 (m-80) cc_final: 0.8752 (m-80) REVERT: g 110 ILE cc_start: 0.9650 (mm) cc_final: 0.8736 (mm) REVERT: g 124 GLN cc_start: 0.8042 (tp-100) cc_final: 0.7670 (tm-30) REVERT: g 133 LEU cc_start: 0.9138 (mp) cc_final: 0.8927 (mp) REVERT: g 137 PHE cc_start: 0.8833 (m-10) cc_final: 0.8328 (m-80) REVERT: g 139 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7793 (mm-30) REVERT: g 141 LEU cc_start: 0.9410 (mt) cc_final: 0.8959 (mt) REVERT: g 144 TYR cc_start: 0.9132 (m-10) cc_final: 0.8762 (m-80) REVERT: g 152 LEU cc_start: 0.9496 (mt) cc_final: 0.9279 (mt) REVERT: h 10 TYR cc_start: 0.9078 (p90) cc_final: 0.8830 (p90) REVERT: h 13 PHE cc_start: 0.8351 (t80) cc_final: 0.8064 (t80) REVERT: h 17 MET cc_start: 0.8513 (mmm) cc_final: 0.7786 (mmm) REVERT: h 44 MET cc_start: 0.9055 (tmm) cc_final: 0.8805 (tmm) REVERT: h 78 ASN cc_start: 0.9043 (t0) cc_final: 0.8686 (p0) REVERT: h 84 ILE cc_start: 0.8465 (mt) cc_final: 0.8116 (pt) REVERT: i 47 MET cc_start: 0.8882 (mmp) cc_final: 0.7884 (mtt) REVERT: i 52 ILE cc_start: 0.9643 (tt) cc_final: 0.9304 (mm) REVERT: i 53 MET cc_start: 0.8669 (mmp) cc_final: 0.8341 (ptt) REVERT: i 61 MET cc_start: 0.9322 (mtm) cc_final: 0.8750 (ptp) REVERT: i 110 ILE cc_start: 0.9448 (mt) cc_final: 0.9015 (tt) REVERT: j 17 MET cc_start: 0.9286 (mmp) cc_final: 0.8685 (mmt) REVERT: j 41 ILE cc_start: 0.9159 (pt) cc_final: 0.8834 (pt) REVERT: j 44 MET cc_start: 0.8807 (ptt) cc_final: 0.8580 (ptt) REVERT: j 61 MET cc_start: 0.8852 (tpp) cc_final: 0.8542 (tpp) REVERT: j 68 TYR cc_start: 0.8931 (m-80) cc_final: 0.8633 (m-80) REVERT: j 70 LEU cc_start: 0.9593 (tp) cc_final: 0.9389 (tp) REVERT: j 84 ILE cc_start: 0.8571 (mm) cc_final: 0.7994 (mm) REVERT: j 127 LEU cc_start: 0.9009 (tt) cc_final: 0.8367 (tt) REVERT: j 131 MET cc_start: 0.9327 (ttt) cc_final: 0.9034 (ttt) REVERT: j 136 ILE cc_start: 0.9270 (mm) cc_final: 0.9019 (mm) REVERT: k 32 TYR cc_start: 0.8625 (t80) cc_final: 0.8182 (t80) REVERT: k 65 ILE cc_start: 0.9446 (mt) cc_final: 0.9244 (tp) REVERT: k 76 ILE cc_start: 0.9355 (mt) cc_final: 0.8409 (tt) REVERT: k 80 LEU cc_start: 0.9258 (mt) cc_final: 0.8918 (mt) REVERT: k 90 PHE cc_start: 0.8922 (m-80) cc_final: 0.8432 (m-80) REVERT: k 92 GLN cc_start: 0.9077 (mt0) cc_final: 0.8690 (mt0) REVERT: k 123 GLN cc_start: 0.8810 (tp40) cc_final: 0.8299 (tp40) REVERT: k 124 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8303 (tm-30) REVERT: k 133 LEU cc_start: 0.9270 (mt) cc_final: 0.8929 (mt) REVERT: k 137 PHE cc_start: 0.9051 (m-80) cc_final: 0.8547 (m-80) REVERT: k 143 LEU cc_start: 0.9395 (tp) cc_final: 0.9128 (mm) REVERT: k 147 ILE cc_start: 0.9454 (tp) cc_final: 0.9232 (tp) REVERT: k 150 LEU cc_start: 0.9009 (tt) cc_final: 0.8725 (mt) REVERT: l 54 LYS cc_start: 0.8565 (mttt) cc_final: 0.7938 (mmtt) REVERT: l 90 PHE cc_start: 0.8135 (m-10) cc_final: 0.7228 (m-80) REVERT: l 121 THR cc_start: 0.9068 (p) cc_final: 0.8835 (p) REVERT: l 123 GLN cc_start: 0.8892 (mp10) cc_final: 0.8645 (mp10) REVERT: l 152 LEU cc_start: 0.9439 (tp) cc_final: 0.8996 (tp) REVERT: m 17 MET cc_start: 0.9220 (mmm) cc_final: 0.8959 (mmm) REVERT: m 21 SER cc_start: 0.9179 (m) cc_final: 0.8585 (p) REVERT: m 24 VAL cc_start: 0.9622 (p) cc_final: 0.9367 (m) REVERT: m 25 PHE cc_start: 0.8398 (m-80) cc_final: 0.8005 (m-80) REVERT: m 47 MET cc_start: 0.8254 (tpp) cc_final: 0.7628 (tpp) REVERT: m 48 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.7799 (mmm-85) REVERT: m 53 MET cc_start: 0.9389 (tpp) cc_final: 0.9105 (tpp) REVERT: m 60 VAL cc_start: 0.9573 (m) cc_final: 0.9143 (m) REVERT: m 61 MET cc_start: 0.9579 (mmm) cc_final: 0.9149 (mmm) REVERT: m 139 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8301 (tm-30) REVERT: n 36 LYS cc_start: 0.8122 (mmtt) cc_final: 0.7694 (mttt) REVERT: n 60 VAL cc_start: 0.8830 (t) cc_final: 0.8612 (t) REVERT: n 80 LEU cc_start: 0.9106 (tp) cc_final: 0.8849 (tt) REVERT: n 90 PHE cc_start: 0.9626 (m-80) cc_final: 0.9273 (m-80) REVERT: n 121 THR cc_start: 0.9170 (p) cc_final: 0.8916 (p) REVERT: n 126 ARG cc_start: 0.8418 (mtt-85) cc_final: 0.7900 (mmm160) REVERT: n 127 LEU cc_start: 0.9459 (tp) cc_final: 0.9129 (tp) REVERT: n 137 PHE cc_start: 0.9480 (m-80) cc_final: 0.9257 (m-80) REVERT: n 141 LEU cc_start: 0.9312 (mt) cc_final: 0.8864 (mt) REVERT: n 144 TYR cc_start: 0.9069 (m-10) cc_final: 0.8626 (m-80) REVERT: o 23 MET cc_start: 0.9422 (tpp) cc_final: 0.9046 (tpp) REVERT: o 28 MET cc_start: 0.8759 (ttt) cc_final: 0.8007 (tpt) REVERT: o 32 TYR cc_start: 0.8276 (t80) cc_final: 0.8073 (t80) REVERT: o 44 MET cc_start: 0.8743 (ttp) cc_final: 0.8349 (ttp) REVERT: o 65 ILE cc_start: 0.9619 (mm) cc_final: 0.9397 (mm) REVERT: o 80 LEU cc_start: 0.9299 (mm) cc_final: 0.9071 (mm) REVERT: o 90 PHE cc_start: 0.8874 (m-10) cc_final: 0.8378 (m-10) REVERT: o 110 ILE cc_start: 0.9464 (mt) cc_final: 0.9263 (mt) REVERT: p 305 VAL cc_start: 0.9399 (t) cc_final: 0.9177 (p) REVERT: p 335 TYR cc_start: 0.7283 (m-80) cc_final: 0.7050 (m-10) REVERT: p 339 ILE cc_start: 0.7606 (mm) cc_final: 0.7121 (mt) REVERT: p 341 ARG cc_start: 0.8677 (ptm-80) cc_final: 0.8441 (ptm160) outliers start: 2 outliers final: 0 residues processed: 1126 average time/residue: 0.2946 time to fit residues: 528.4008 Evaluate side-chains 949 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 949 time to evaluate : 2.455 ------------------------------------------------------------------------------- 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: 0.8980 chunk 235 optimal weight: 0.8980 chunk 250 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 196 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 226 optimal weight: 2.9990 chunk 237 optimal weight: 0.9990 chunk 249 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 7 ASN m 92 GLN o 7 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.6428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21366 Z= 0.223 Angle : 0.700 15.821 28966 Z= 0.355 Chirality : 0.043 0.323 3430 Planarity : 0.004 0.054 3602 Dihedral : 4.140 20.726 2978 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.10 % Favored : 96.86 % Rotamer: Outliers : 0.09 % Allowed : 0.56 % Favored : 99.34 % 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: 1.61 (0.16), residues: 2771 helix: 1.75 (0.11), residues: 2065 sheet: -0.21 (1.23), residues: 18 loop : -1.00 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 67 HIS 0.004 0.001 HIS a 720 PHE 0.040 0.002 PHE c 431 TYR 0.037 0.002 TYR i 68 ARG 0.005 0.000 ARG l 48 *********************** 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 1123 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1121 time to evaluate : 2.410 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: H 56 MET cc_start: 0.9116 (tmm) cc_final: 0.8755 (tmm) REVERT: H 57 LEU cc_start: 0.9298 (tt) cc_final: 0.9052 (tt) REVERT: H 64 GLU cc_start: 0.8558 (tp30) cc_final: 0.8257 (tp30) REVERT: H 68 SER cc_start: 0.9280 (m) cc_final: 0.8739 (t) REVERT: H 91 GLN cc_start: 0.8408 (tt0) cc_final: 0.7871 (tt0) REVERT: H 134 LEU cc_start: 0.9054 (tp) cc_final: 0.8595 (tp) REVERT: H 137 ASN cc_start: 0.8916 (m110) cc_final: 0.8352 (m110) REVERT: H 151 LEU cc_start: 0.9047 (mm) cc_final: 0.8839 (mm) REVERT: L 6 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7724 (mmmm) REVERT: L 35 ASN cc_start: 0.9238 (p0) cc_final: 0.8635 (p0) REVERT: L 40 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8781 (mp0) REVERT: L 49 GLU cc_start: 0.8915 (pt0) cc_final: 0.8214 (pp20) REVERT: L 57 ASN cc_start: 0.8965 (m110) cc_final: 0.8744 (m110) REVERT: L 58 ARG cc_start: 0.7794 (mtt90) cc_final: 0.7577 (ttm-80) REVERT: L 73 MET cc_start: 0.8379 (mtm) cc_final: 0.7946 (ptp) REVERT: L 99 ASP cc_start: 0.5778 (t0) cc_final: 0.3779 (p0) REVERT: a 9 GLU cc_start: 0.7356 (mp0) cc_final: 0.6900 (pm20) REVERT: a 388 GLU cc_start: 0.8233 (tp30) cc_final: 0.7162 (tt0) REVERT: a 401 PHE cc_start: 0.9136 (t80) cc_final: 0.8589 (t80) REVERT: a 426 ARG cc_start: 0.6520 (mmt180) cc_final: 0.6312 (tpp-160) REVERT: a 449 ILE cc_start: 0.9539 (mt) cc_final: 0.9328 (mt) REVERT: a 467 CYS cc_start: 0.6465 (t) cc_final: 0.6091 (t) REVERT: a 519 ILE cc_start: 0.6958 (mp) cc_final: 0.6695 (mp) REVERT: a 540 MET cc_start: 0.9597 (tpp) cc_final: 0.9270 (tpt) REVERT: a 549 MET cc_start: 0.9376 (mmm) cc_final: 0.9003 (mmm) REVERT: a 580 MET cc_start: 0.8774 (mmm) cc_final: 0.8554 (mmm) REVERT: a 616 MET cc_start: 0.9060 (ttp) cc_final: 0.8833 (tmm) REVERT: a 636 ILE cc_start: 0.8960 (mm) cc_final: 0.8694 (tp) REVERT: a 637 GLN cc_start: 0.8628 (mt0) cc_final: 0.8277 (mt0) REVERT: a 642 VAL cc_start: 0.9239 (m) cc_final: 0.8597 (p) REVERT: a 645 MET cc_start: 0.8754 (ptt) cc_final: 0.8279 (ppp) REVERT: a 651 MET cc_start: 0.9046 (mmm) cc_final: 0.8487 (mmm) REVERT: a 721 GLN cc_start: 0.8840 (tp40) cc_final: 0.8316 (tp-100) REVERT: a 729 CYS cc_start: 0.8792 (m) cc_final: 0.8554 (p) REVERT: a 759 MET cc_start: 0.7853 (mmm) cc_final: 0.7290 (tmm) REVERT: a 801 LEU cc_start: 0.9407 (tt) cc_final: 0.9173 (tt) REVERT: b 4 LEU cc_start: 0.9193 (mt) cc_final: 0.8957 (mt) REVERT: b 8 TYR cc_start: 0.8808 (m-80) cc_final: 0.8114 (m-80) REVERT: b 19 MET cc_start: 0.8710 (mtp) cc_final: 0.8231 (mtm) REVERT: b 25 CYS cc_start: 0.9110 (m) cc_final: 0.8776 (t) REVERT: b 34 ARG cc_start: 0.8364 (mmm160) cc_final: 0.6467 (tpt170) REVERT: b 36 ASP cc_start: 0.8337 (t70) cc_final: 0.7966 (t0) REVERT: b 48 MET cc_start: 0.8961 (ttt) cc_final: 0.8469 (tmm) REVERT: b 52 LEU cc_start: 0.9504 (mt) cc_final: 0.9049 (mt) REVERT: b 70 TYR cc_start: 0.8999 (p90) cc_final: 0.8612 (p90) REVERT: b 71 ILE cc_start: 0.9482 (mm) cc_final: 0.9128 (mm) REVERT: b 74 SER cc_start: 0.9417 (m) cc_final: 0.9082 (t) REVERT: b 75 SER cc_start: 0.9713 (m) cc_final: 0.9343 (p) REVERT: b 82 LYS cc_start: 0.8942 (mmtt) cc_final: 0.8502 (mmtp) REVERT: b 85 ARG cc_start: 0.7231 (tpt170) cc_final: 0.7004 (tpt170) REVERT: b 88 THR cc_start: 0.8706 (t) cc_final: 0.8488 (t) REVERT: b 90 ASN cc_start: 0.8709 (m-40) cc_final: 0.8349 (m-40) REVERT: b 114 MET cc_start: 0.8027 (mtm) cc_final: 0.7476 (mtm) REVERT: b 137 MET cc_start: 0.9458 (ttt) cc_final: 0.9062 (tpp) REVERT: b 164 LEU cc_start: 0.9364 (mm) cc_final: 0.8955 (mt) REVERT: b 168 GLN cc_start: 0.9291 (mt0) cc_final: 0.9075 (mp10) REVERT: b 169 ASN cc_start: 0.8432 (t0) cc_final: 0.7669 (t0) REVERT: b 172 LEU cc_start: 0.8933 (mt) cc_final: 0.8189 (mt) REVERT: b 186 ILE cc_start: 0.9173 (mt) cc_final: 0.8948 (mt) REVERT: c 445 THR cc_start: 0.9089 (p) cc_final: 0.8771 (m) REVERT: d 76 GLU cc_start: 0.8363 (tt0) cc_final: 0.7987 (tp30) REVERT: d 98 ASP cc_start: 0.8804 (m-30) cc_final: 0.8138 (t0) REVERT: d 124 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8503 (mt-10) REVERT: d 128 LYS cc_start: 0.9202 (mmtt) cc_final: 0.8413 (mttt) REVERT: d 179 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8463 (mm-30) REVERT: d 181 ILE cc_start: 0.9048 (mm) cc_final: 0.8847 (mm) REVERT: d 241 PHE cc_start: 0.8514 (m-10) cc_final: 0.8204 (m-80) REVERT: d 257 ARG cc_start: 0.9505 (mmm-85) cc_final: 0.8875 (mtp-110) REVERT: d 292 ASP cc_start: 0.8816 (m-30) cc_final: 0.7830 (t0) REVERT: d 297 HIS cc_start: 0.8547 (t-90) cc_final: 0.7960 (t-90) REVERT: d 308 ASN cc_start: 0.7746 (m-40) cc_final: 0.7477 (m-40) REVERT: d 335 CYS cc_start: 0.8676 (m) cc_final: 0.8249 (t) REVERT: e 9 PRO cc_start: 0.7468 (Cg_exo) cc_final: 0.7037 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7746 (m-80) cc_final: 0.7233 (m-80) REVERT: e 47 CYS cc_start: 0.7833 (p) cc_final: 0.7261 (p) REVERT: e 49 TYR cc_start: 0.8175 (t80) cc_final: 0.7931 (t80) REVERT: e 68 LEU cc_start: 0.8801 (tp) cc_final: 0.8493 (tp) REVERT: f 67 TYR cc_start: 0.8379 (m-80) cc_final: 0.8038 (m-80) REVERT: g 10 TYR cc_start: 0.6909 (m-80) cc_final: 0.6064 (m-80) REVERT: g 44 MET cc_start: 0.9367 (ppp) cc_final: 0.8887 (ppp) REVERT: g 45 SER cc_start: 0.9676 (p) cc_final: 0.9054 (p) REVERT: g 61 MET cc_start: 0.8121 (mmm) cc_final: 0.7710 (mmm) REVERT: g 88 ARG cc_start: 0.8514 (mmm160) cc_final: 0.8075 (mmt180) REVERT: g 90 PHE cc_start: 0.8051 (m-80) cc_final: 0.7811 (m-80) REVERT: g 108 PHE cc_start: 0.9144 (m-80) cc_final: 0.8694 (m-80) REVERT: g 124 GLN cc_start: 0.8085 (tp-100) cc_final: 0.7714 (tm-30) REVERT: g 131 MET cc_start: 0.9423 (ttt) cc_final: 0.9084 (ttt) REVERT: g 141 LEU cc_start: 0.9237 (mt) cc_final: 0.8816 (mt) REVERT: g 144 TYR cc_start: 0.9172 (m-10) cc_final: 0.8660 (m-80) REVERT: g 152 LEU cc_start: 0.9503 (mt) cc_final: 0.9282 (mt) REVERT: h 10 TYR cc_start: 0.9071 (p90) cc_final: 0.8739 (p90) REVERT: h 13 PHE cc_start: 0.8336 (t80) cc_final: 0.8022 (t80) REVERT: h 17 MET cc_start: 0.8481 (mmm) cc_final: 0.7796 (mmm) REVERT: h 44 MET cc_start: 0.9060 (tmm) cc_final: 0.8815 (tmm) REVERT: h 54 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8304 (mmmt) REVERT: h 84 ILE cc_start: 0.8470 (mt) cc_final: 0.8119 (pt) REVERT: h 131 MET cc_start: 0.8692 (mmm) cc_final: 0.8477 (mmp) REVERT: i 6 ASN cc_start: 0.8639 (m-40) cc_final: 0.8209 (p0) REVERT: i 10 TYR cc_start: 0.5600 (m-80) cc_final: 0.5373 (m-80) REVERT: i 47 MET cc_start: 0.8869 (mmp) cc_final: 0.7859 (mtt) REVERT: i 52 ILE cc_start: 0.9647 (tt) cc_final: 0.9295 (mm) REVERT: i 53 MET cc_start: 0.8727 (mmp) cc_final: 0.8350 (ptt) REVERT: i 61 MET cc_start: 0.9314 (mtm) cc_final: 0.8852 (ptp) REVERT: i 90 PHE cc_start: 0.7480 (m-10) cc_final: 0.6850 (m-80) REVERT: i 110 ILE cc_start: 0.9465 (mt) cc_final: 0.9081 (tt) REVERT: j 17 MET cc_start: 0.9263 (mmp) cc_final: 0.8700 (mmt) REVERT: j 41 ILE cc_start: 0.8951 (pt) cc_final: 0.8637 (pt) REVERT: j 45 SER cc_start: 0.9021 (m) cc_final: 0.8093 (m) REVERT: j 61 MET cc_start: 0.8853 (tpp) cc_final: 0.8544 (tpp) REVERT: j 68 TYR cc_start: 0.8917 (m-80) cc_final: 0.8633 (m-80) REVERT: j 84 ILE cc_start: 0.8483 (mm) cc_final: 0.7894 (mm) REVERT: j 127 LEU cc_start: 0.9003 (tt) cc_final: 0.8387 (tt) REVERT: j 131 MET cc_start: 0.9317 (ttt) cc_final: 0.8982 (ttt) REVERT: j 136 ILE cc_start: 0.9260 (mm) cc_final: 0.8996 (mm) REVERT: k 32 TYR cc_start: 0.8594 (t80) cc_final: 0.8168 (t80) REVERT: k 57 ILE cc_start: 0.9181 (mm) cc_final: 0.8627 (mm) REVERT: k 61 MET cc_start: 0.9428 (mtm) cc_final: 0.9004 (mpp) REVERT: k 64 ILE cc_start: 0.9020 (mt) cc_final: 0.8809 (mt) REVERT: k 68 TYR cc_start: 0.8929 (m-80) cc_final: 0.8179 (m-80) REVERT: k 76 ILE cc_start: 0.9379 (mt) cc_final: 0.8442 (tt) REVERT: k 80 LEU cc_start: 0.9243 (mt) cc_final: 0.8931 (mt) REVERT: k 90 PHE cc_start: 0.8908 (m-80) cc_final: 0.8433 (m-80) REVERT: k 92 GLN cc_start: 0.9100 (mt0) cc_final: 0.8735 (mt0) REVERT: k 123 GLN cc_start: 0.8783 (tp40) cc_final: 0.8285 (tp40) REVERT: k 124 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8312 (tm-30) REVERT: k 133 LEU cc_start: 0.9268 (mt) cc_final: 0.8927 (mt) REVERT: k 137 PHE cc_start: 0.9075 (m-80) cc_final: 0.8490 (m-80) REVERT: k 143 LEU cc_start: 0.9357 (tp) cc_final: 0.9042 (mm) REVERT: k 147 ILE cc_start: 0.9417 (tp) cc_final: 0.9199 (tp) REVERT: k 150 LEU cc_start: 0.9006 (tt) cc_final: 0.8718 (mt) REVERT: l 32 TYR cc_start: 0.9177 (t80) cc_final: 0.8900 (t80) REVERT: l 54 LYS cc_start: 0.8521 (mttt) cc_final: 0.7902 (mmtt) REVERT: l 90 PHE cc_start: 0.8148 (m-10) cc_final: 0.7309 (m-80) REVERT: l 121 THR cc_start: 0.9230 (p) cc_final: 0.8884 (p) REVERT: l 127 LEU cc_start: 0.9266 (tp) cc_final: 0.8187 (tp) REVERT: l 152 LEU cc_start: 0.9426 (tp) cc_final: 0.9076 (tp) REVERT: m 17 MET cc_start: 0.9212 (mmm) cc_final: 0.8893 (mmm) REVERT: m 21 SER cc_start: 0.9101 (m) cc_final: 0.8492 (p) REVERT: m 24 VAL cc_start: 0.9645 (p) cc_final: 0.9391 (m) REVERT: m 25 PHE cc_start: 0.8368 (m-80) cc_final: 0.7963 (m-80) REVERT: m 47 MET cc_start: 0.8271 (tpp) cc_final: 0.7614 (tpp) REVERT: m 48 ARG cc_start: 0.8305 (mmm-85) cc_final: 0.7810 (mmm-85) REVERT: m 52 ILE cc_start: 0.8546 (mt) cc_final: 0.8301 (mt) REVERT: m 53 MET cc_start: 0.9442 (tpp) cc_final: 0.9142 (tpp) REVERT: m 60 VAL cc_start: 0.9568 (m) cc_final: 0.9146 (m) REVERT: m 61 MET cc_start: 0.9590 (mmm) cc_final: 0.9163 (mmm) REVERT: m 80 LEU cc_start: 0.9127 (mt) cc_final: 0.8885 (mt) REVERT: m 139 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8208 (tm-30) REVERT: n 36 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7725 (mmmt) REVERT: n 54 LYS cc_start: 0.8487 (mttt) cc_final: 0.8059 (ttmt) REVERT: n 57 ILE cc_start: 0.9241 (mm) cc_final: 0.8968 (mm) REVERT: n 61 MET cc_start: 0.8921 (mmp) cc_final: 0.8669 (mmp) REVERT: n 90 PHE cc_start: 0.9563 (m-80) cc_final: 0.9255 (m-80) REVERT: n 91 LEU cc_start: 0.9395 (mm) cc_final: 0.9117 (mp) REVERT: n 126 ARG cc_start: 0.8459 (mtt-85) cc_final: 0.7947 (mmm160) REVERT: n 141 LEU cc_start: 0.9311 (mt) cc_final: 0.8870 (mt) REVERT: n 144 TYR cc_start: 0.9042 (m-10) cc_final: 0.8576 (m-80) REVERT: o 23 MET cc_start: 0.9436 (tpp) cc_final: 0.9073 (tpp) REVERT: o 32 TYR cc_start: 0.8216 (t80) cc_final: 0.7949 (t80) REVERT: o 44 MET cc_start: 0.8738 (ttp) cc_final: 0.8351 (ttp) REVERT: o 80 LEU cc_start: 0.9319 (mm) cc_final: 0.8982 (mm) REVERT: p 305 VAL cc_start: 0.9397 (t) cc_final: 0.9177 (p) REVERT: p 338 ILE cc_start: 0.8588 (pt) cc_final: 0.8322 (pt) REVERT: p 339 ILE cc_start: 0.7628 (mm) cc_final: 0.7398 (mt) outliers start: 2 outliers final: 0 residues processed: 1122 average time/residue: 0.3064 time to fit residues: 548.1012 Evaluate side-chains 959 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 959 time to evaluate : 2.390 ------------------------------------------------------------------------------- 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: 0.0980 chunk 161 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 277 optimal weight: 0.6980 chunk 255 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 22 optimal weight: 0.0040 chunk 170 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 124 GLN m 7 ASN o 7 ASN p 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.6579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21366 Z= 0.237 Angle : 0.707 13.894 28966 Z= 0.361 Chirality : 0.042 0.212 3430 Planarity : 0.004 0.065 3602 Dihedral : 4.160 20.349 2978 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.72 % Rotamer: Outliers : 0.09 % Allowed : 0.23 % Favored : 99.67 % 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: 1.49 (0.16), residues: 2771 helix: 1.59 (0.11), residues: 2129 sheet: -0.03 (1.23), residues: 18 loop : -1.04 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 67 HIS 0.004 0.001 HIS a 548 PHE 0.031 0.002 PHE b 173 TYR 0.035 0.002 TYR i 68 ARG 0.005 0.000 ARG n 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 1099 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1097 time to evaluate : 2.379 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: H 56 MET cc_start: 0.9113 (tmm) cc_final: 0.8746 (tmm) REVERT: H 57 LEU cc_start: 0.9286 (tt) cc_final: 0.9035 (tt) REVERT: H 64 GLU cc_start: 0.8556 (tp30) cc_final: 0.8233 (tp30) REVERT: H 68 SER cc_start: 0.9287 (m) cc_final: 0.8729 (t) REVERT: H 91 GLN cc_start: 0.8429 (tt0) cc_final: 0.7952 (tt0) REVERT: H 134 LEU cc_start: 0.9045 (tp) cc_final: 0.8580 (tp) REVERT: H 137 ASN cc_start: 0.8899 (m110) cc_final: 0.8327 (m110) REVERT: H 151 LEU cc_start: 0.9052 (mm) cc_final: 0.8841 (mm) REVERT: L 6 LYS cc_start: 0.8197 (mmtt) cc_final: 0.7742 (mmmm) REVERT: L 35 ASN cc_start: 0.9275 (p0) cc_final: 0.7791 (p0) REVERT: L 40 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8801 (mp0) REVERT: L 49 GLU cc_start: 0.8912 (pt0) cc_final: 0.8210 (pp20) REVERT: L 57 ASN cc_start: 0.8973 (m110) cc_final: 0.8751 (m110) REVERT: L 58 ARG cc_start: 0.7792 (mtt90) cc_final: 0.7582 (ttm-80) REVERT: L 73 MET cc_start: 0.8404 (mtm) cc_final: 0.7941 (ptp) REVERT: L 99 ASP cc_start: 0.5807 (t0) cc_final: 0.3828 (p0) REVERT: a 9 GLU cc_start: 0.7404 (mp0) cc_final: 0.6923 (pm20) REVERT: a 388 GLU cc_start: 0.8250 (tp30) cc_final: 0.7243 (tt0) REVERT: a 401 PHE cc_start: 0.9137 (t80) cc_final: 0.8611 (t80) REVERT: a 423 MET cc_start: 0.9430 (mpp) cc_final: 0.8981 (mpp) REVERT: a 426 ARG cc_start: 0.6374 (mmt180) cc_final: 0.6092 (tpp-160) REVERT: a 467 CYS cc_start: 0.6572 (t) cc_final: 0.6090 (t) REVERT: a 538 MET cc_start: 0.7910 (ppp) cc_final: 0.7274 (ppp) REVERT: a 540 MET cc_start: 0.9561 (tpp) cc_final: 0.9334 (tpt) REVERT: a 549 MET cc_start: 0.9420 (mmm) cc_final: 0.9052 (mmm) REVERT: a 580 MET cc_start: 0.8779 (mmm) cc_final: 0.8531 (mmm) REVERT: a 616 MET cc_start: 0.9034 (ttp) cc_final: 0.8813 (tmm) REVERT: a 636 ILE cc_start: 0.8999 (mm) cc_final: 0.8715 (tp) REVERT: a 642 VAL cc_start: 0.9212 (m) cc_final: 0.8682 (m) REVERT: a 645 MET cc_start: 0.8750 (ptt) cc_final: 0.8303 (ppp) REVERT: a 651 MET cc_start: 0.9006 (mmm) cc_final: 0.8502 (mmm) REVERT: a 721 GLN cc_start: 0.8912 (tp40) cc_final: 0.8382 (tp-100) REVERT: a 725 THR cc_start: 0.9508 (m) cc_final: 0.9215 (m) REVERT: a 759 MET cc_start: 0.7862 (mmm) cc_final: 0.7315 (tmm) REVERT: a 801 LEU cc_start: 0.9418 (tt) cc_final: 0.9183 (tt) REVERT: b 25 CYS cc_start: 0.9093 (m) cc_final: 0.8783 (t) REVERT: b 34 ARG cc_start: 0.8475 (mmm160) cc_final: 0.6546 (tpt170) REVERT: b 36 ASP cc_start: 0.8070 (t70) cc_final: 0.7635 (t0) REVERT: b 48 MET cc_start: 0.8947 (ttt) cc_final: 0.8479 (tmm) REVERT: b 52 LEU cc_start: 0.9502 (mt) cc_final: 0.9031 (mt) REVERT: b 70 TYR cc_start: 0.8986 (p90) cc_final: 0.8572 (p90) REVERT: b 71 ILE cc_start: 0.9473 (mm) cc_final: 0.9108 (mm) REVERT: b 74 SER cc_start: 0.9447 (m) cc_final: 0.9142 (t) REVERT: b 75 SER cc_start: 0.9713 (m) cc_final: 0.9414 (p) REVERT: b 82 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8510 (mmtp) REVERT: b 90 ASN cc_start: 0.8741 (m-40) cc_final: 0.8216 (m-40) REVERT: b 96 PHE cc_start: 0.9183 (m-80) cc_final: 0.8677 (m-80) REVERT: b 114 MET cc_start: 0.8023 (mtm) cc_final: 0.7600 (mtm) REVERT: b 130 ASN cc_start: 0.9026 (m-40) cc_final: 0.8780 (m-40) REVERT: b 135 TYR cc_start: 0.8783 (m-80) cc_final: 0.8324 (m-80) REVERT: b 137 MET cc_start: 0.9464 (ttt) cc_final: 0.9076 (tpp) REVERT: b 164 LEU cc_start: 0.9377 (mm) cc_final: 0.9029 (mt) REVERT: b 168 GLN cc_start: 0.9274 (mt0) cc_final: 0.9063 (mp10) REVERT: b 169 ASN cc_start: 0.8445 (t0) cc_final: 0.7660 (t0) REVERT: b 172 LEU cc_start: 0.8954 (mt) cc_final: 0.8213 (mt) REVERT: b 186 ILE cc_start: 0.9197 (mt) cc_final: 0.8975 (mt) REVERT: c 419 ILE cc_start: 0.8692 (mm) cc_final: 0.8285 (mm) REVERT: c 439 MET cc_start: 0.9404 (mtp) cc_final: 0.9015 (mtm) REVERT: c 445 THR cc_start: 0.9166 (p) cc_final: 0.8827 (m) REVERT: d 76 GLU cc_start: 0.8354 (tt0) cc_final: 0.7961 (tp30) REVERT: d 98 ASP cc_start: 0.8768 (m-30) cc_final: 0.8131 (t0) REVERT: d 124 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8510 (mt-10) REVERT: d 128 LYS cc_start: 0.9210 (mmtt) cc_final: 0.8404 (mmmt) REVERT: d 179 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8467 (mm-30) REVERT: d 181 ILE cc_start: 0.9038 (mm) cc_final: 0.8807 (mm) REVERT: d 241 PHE cc_start: 0.8531 (m-10) cc_final: 0.8255 (m-80) REVERT: d 257 ARG cc_start: 0.9504 (mmm-85) cc_final: 0.8876 (mtp-110) REVERT: d 292 ASP cc_start: 0.8823 (m-30) cc_final: 0.7846 (t0) REVERT: d 308 ASN cc_start: 0.7716 (m-40) cc_final: 0.7426 (m-40) REVERT: d 335 CYS cc_start: 0.8672 (m) cc_final: 0.8257 (t) REVERT: e 9 PRO cc_start: 0.7501 (Cg_exo) cc_final: 0.7104 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7771 (m-80) cc_final: 0.7289 (m-80) REVERT: e 47 CYS cc_start: 0.7866 (p) cc_final: 0.7295 (p) REVERT: e 49 TYR cc_start: 0.8189 (t80) cc_final: 0.7949 (t80) REVERT: e 68 LEU cc_start: 0.8796 (tp) cc_final: 0.8476 (tp) REVERT: f 67 TYR cc_start: 0.8390 (m-80) cc_final: 0.8031 (m-80) REVERT: g 10 TYR cc_start: 0.6826 (m-80) cc_final: 0.5910 (m-80) REVERT: g 44 MET cc_start: 0.9393 (ppp) cc_final: 0.8918 (ppp) REVERT: g 45 SER cc_start: 0.9605 (p) cc_final: 0.9122 (p) REVERT: g 88 ARG cc_start: 0.8574 (mmm160) cc_final: 0.8203 (mmt180) REVERT: g 91 LEU cc_start: 0.8942 (mt) cc_final: 0.8721 (mt) REVERT: g 108 PHE cc_start: 0.9115 (m-80) cc_final: 0.8596 (m-80) REVERT: g 121 THR cc_start: 0.8656 (p) cc_final: 0.8449 (p) REVERT: g 124 GLN cc_start: 0.8085 (tp-100) cc_final: 0.7708 (tm-30) REVERT: g 131 MET cc_start: 0.9397 (ttt) cc_final: 0.9057 (ttt) REVERT: g 137 PHE cc_start: 0.8442 (m-80) cc_final: 0.8236 (m-80) REVERT: g 141 LEU cc_start: 0.9164 (mt) cc_final: 0.8708 (mt) REVERT: g 144 TYR cc_start: 0.9135 (m-10) cc_final: 0.8583 (m-80) REVERT: g 152 LEU cc_start: 0.9519 (mt) cc_final: 0.9301 (mt) REVERT: h 10 TYR cc_start: 0.9087 (p90) cc_final: 0.8766 (p90) REVERT: h 13 PHE cc_start: 0.8309 (t80) cc_final: 0.8091 (t80) REVERT: h 17 MET cc_start: 0.8454 (mmm) cc_final: 0.7791 (mmm) REVERT: h 41 ILE cc_start: 0.9417 (mt) cc_final: 0.9012 (mm) REVERT: h 54 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8304 (mmmt) REVERT: h 84 ILE cc_start: 0.8438 (mt) cc_final: 0.8064 (pt) REVERT: i 6 ASN cc_start: 0.8584 (m-40) cc_final: 0.8177 (p0) REVERT: i 14 PHE cc_start: 0.8923 (m-10) cc_final: 0.8428 (m-10) REVERT: i 47 MET cc_start: 0.8883 (mmp) cc_final: 0.7865 (mtt) REVERT: i 52 ILE cc_start: 0.9646 (tt) cc_final: 0.9293 (mm) REVERT: i 53 MET cc_start: 0.8769 (mmp) cc_final: 0.8363 (ptt) REVERT: i 61 MET cc_start: 0.9324 (mtm) cc_final: 0.8791 (ptm) REVERT: i 65 ILE cc_start: 0.9241 (mm) cc_final: 0.9033 (mm) REVERT: i 90 PHE cc_start: 0.7532 (m-10) cc_final: 0.6961 (m-80) REVERT: j 17 MET cc_start: 0.9235 (mmp) cc_final: 0.8643 (mmt) REVERT: j 48 ARG cc_start: 0.8358 (mpp80) cc_final: 0.7840 (mpt-90) REVERT: j 61 MET cc_start: 0.8832 (tpp) cc_final: 0.8535 (tpp) REVERT: j 70 LEU cc_start: 0.9542 (tp) cc_final: 0.9292 (tp) REVERT: j 118 VAL cc_start: 0.9468 (t) cc_final: 0.9242 (p) REVERT: j 127 LEU cc_start: 0.9005 (tt) cc_final: 0.8480 (tt) REVERT: j 131 MET cc_start: 0.9284 (ttt) cc_final: 0.8938 (ttt) REVERT: j 136 ILE cc_start: 0.9239 (mm) cc_final: 0.8976 (mm) REVERT: k 32 TYR cc_start: 0.8662 (t80) cc_final: 0.8239 (t80) REVERT: k 76 ILE cc_start: 0.9427 (mt) cc_final: 0.8496 (tt) REVERT: k 80 LEU cc_start: 0.9233 (mt) cc_final: 0.8894 (mt) REVERT: k 90 PHE cc_start: 0.8872 (m-80) cc_final: 0.8412 (m-80) REVERT: k 92 GLN cc_start: 0.9106 (mt0) cc_final: 0.8754 (mt0) REVERT: k 123 GLN cc_start: 0.8787 (tp40) cc_final: 0.8301 (tp40) REVERT: k 124 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8306 (tm-30) REVERT: k 133 LEU cc_start: 0.9269 (mt) cc_final: 0.8950 (mt) REVERT: k 137 PHE cc_start: 0.9127 (m-80) cc_final: 0.8546 (m-80) REVERT: k 143 LEU cc_start: 0.9348 (tp) cc_final: 0.9089 (mm) REVERT: l 32 TYR cc_start: 0.9169 (t80) cc_final: 0.8952 (t80) REVERT: l 54 LYS cc_start: 0.8512 (mttt) cc_final: 0.7882 (mmtt) REVERT: l 61 MET cc_start: 0.8984 (mmm) cc_final: 0.8238 (mmm) REVERT: l 90 PHE cc_start: 0.8228 (m-10) cc_final: 0.7347 (m-80) REVERT: l 91 LEU cc_start: 0.9416 (mt) cc_final: 0.9194 (mm) REVERT: l 108 PHE cc_start: 0.8813 (m-80) cc_final: 0.8002 (m-80) REVERT: l 123 GLN cc_start: 0.8770 (mp10) cc_final: 0.8526 (mp10) REVERT: l 152 LEU cc_start: 0.9474 (tp) cc_final: 0.9090 (tp) REVERT: m 17 MET cc_start: 0.9160 (mmm) cc_final: 0.8827 (mmm) REVERT: m 21 SER cc_start: 0.9080 (m) cc_final: 0.8425 (p) REVERT: m 24 VAL cc_start: 0.9667 (p) cc_final: 0.9421 (m) REVERT: m 25 PHE cc_start: 0.8429 (m-80) cc_final: 0.7999 (m-80) REVERT: m 47 MET cc_start: 0.8298 (tpp) cc_final: 0.7572 (tpp) REVERT: m 48 ARG cc_start: 0.8147 (mmm-85) cc_final: 0.7766 (mmm-85) REVERT: m 60 VAL cc_start: 0.9582 (m) cc_final: 0.9130 (m) REVERT: m 61 MET cc_start: 0.9584 (mmm) cc_final: 0.9146 (mmm) REVERT: m 139 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8133 (tm-30) REVERT: n 36 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7838 (mmtp) REVERT: n 54 LYS cc_start: 0.8379 (mttt) cc_final: 0.8014 (ttmm) REVERT: n 57 ILE cc_start: 0.9258 (mm) cc_final: 0.8989 (mm) REVERT: n 61 MET cc_start: 0.8970 (mmp) cc_final: 0.8708 (mmp) REVERT: n 81 THR cc_start: 0.9145 (t) cc_final: 0.8930 (t) REVERT: n 82 ASP cc_start: 0.9155 (p0) cc_final: 0.8793 (t70) REVERT: n 126 ARG cc_start: 0.8501 (mtt-85) cc_final: 0.7988 (mmm160) REVERT: n 141 LEU cc_start: 0.9315 (mt) cc_final: 0.8870 (mt) REVERT: n 144 TYR cc_start: 0.9053 (m-10) cc_final: 0.8589 (m-80) REVERT: o 23 MET cc_start: 0.9455 (tpp) cc_final: 0.9106 (tpp) REVERT: o 28 MET cc_start: 0.8754 (ttt) cc_final: 0.7994 (tpt) REVERT: o 32 TYR cc_start: 0.8138 (t80) cc_final: 0.7918 (t80) REVERT: o 44 MET cc_start: 0.8751 (ttp) cc_final: 0.8358 (ttp) REVERT: o 47 MET cc_start: 0.8865 (tpt) cc_final: 0.8663 (tpp) REVERT: o 61 MET cc_start: 0.7926 (mmp) cc_final: 0.7631 (mmp) REVERT: o 80 LEU cc_start: 0.9338 (mm) cc_final: 0.9089 (mm) REVERT: o 90 PHE cc_start: 0.8949 (m-10) cc_final: 0.8427 (m-10) REVERT: p 305 VAL cc_start: 0.9372 (t) cc_final: 0.9155 (p) REVERT: p 313 ILE cc_start: 0.9341 (mt) cc_final: 0.8997 (mt) REVERT: p 338 ILE cc_start: 0.8459 (pt) cc_final: 0.8232 (pt) REVERT: p 339 ILE cc_start: 0.7601 (mm) cc_final: 0.7338 (mt) outliers start: 2 outliers final: 0 residues processed: 1097 average time/residue: 0.2959 time to fit residues: 515.2105 Evaluate side-chains 943 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 943 time to evaluate : 2.483 ------------------------------------------------------------------------------- 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: 0.7980 chunk 67 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 227 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 194 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 297 HIS ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 7 ASN o 7 ASN p 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.086358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.074134 restraints weight = 72913.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076837 restraints weight = 41145.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.078735 restraints weight = 26533.695| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.6715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 21366 Z= 0.234 Angle : 0.715 13.055 28966 Z= 0.363 Chirality : 0.044 0.370 3430 Planarity : 0.004 0.054 3602 Dihedral : 4.162 19.843 2978 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.61 % Rotamer: Outliers : 0.09 % Allowed : 0.28 % Favored : 99.62 % 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: 1.45 (0.16), residues: 2771 helix: 1.57 (0.11), residues: 2123 sheet: 0.17 (1.24), residues: 18 loop : -1.06 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 743 HIS 0.010 0.001 HIS d 297 PHE 0.035 0.002 PHE h 128 TYR 0.055 0.002 TYR m 144 ARG 0.008 0.000 ARG n 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8046.60 seconds wall clock time: 145 minutes 8.33 seconds (8708.33 seconds total)