Starting phenix.real_space_refine on Sun Feb 18 05:26:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqc_21348/02_2024/6vqc_21348.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqc_21348/02_2024/6vqc_21348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqc_21348/02_2024/6vqc_21348.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqc_21348/02_2024/6vqc_21348.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqc_21348/02_2024/6vqc_21348.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqc_21348/02_2024/6vqc_21348.pdb" } resolution = 3.8 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= 0.069 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 135 5.16 5 C 13770 2.51 5 N 3384 2.21 5 O 3702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "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 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 475": "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 571": "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 800": "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 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 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 PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 76": "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 TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "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 PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 137": "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 TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 108": "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 "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 "p TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20991 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: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3495 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 18, 'TRANS': 422} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 46 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: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 621 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "f" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 480 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain breaks: 1 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 88 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: 10.93, per 1000 atoms: 0.52 Number of scatterers: 20991 At special positions: 0 Unit cell: (119.78, 125.08, 164.3, 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 135 16.00 O 3702 8.00 N 3384 7.00 C 13770 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: 8.98 Conformation dependent library (CDL) restraints added in 4.3 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: 117 helices and 3 sheets defined 81.1% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 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: 3.706A 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 75 through 81 removed outlier: 4.026A pdb=" N HIS L 81 " --> pdb=" O ALA L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 109 Processing helix chain 'a' and resid 370 through 380 removed outlier: 4.481A pdb=" N PHE a 374 " --> pdb=" O PHE a 370 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 407 removed outlier: 4.707A 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: 3.535A pdb=" N LEU a 452 " --> pdb=" O TYR a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 481 through 488 removed outlier: 3.559A pdb=" N ILE a 487 " --> pdb=" O PRO a 483 " (cutoff:3.500A) Processing helix chain 'a' and resid 495 through 500 Processing helix chain 'a' and resid 520 through 526 Processing helix chain 'a' and resid 528 through 563 removed outlier: 4.344A pdb=" N ASN a 534 " --> pdb=" O LEU a 530 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE a 536 " --> pdb=" O PHE a 532 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER a 556 " --> pdb=" O GLY a 552 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU a 557 " --> pdb=" O VAL a 553 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE a 558 " --> pdb=" O SER a 554 " (cutoff:3.500A) Processing helix chain 'a' and resid 565 through 571 removed outlier: 3.604A pdb=" N ILE a 569 " --> pdb=" O LYS a 565 " (cutoff:3.500A) Processing helix chain 'a' and resid 572 through 598 removed outlier: 4.398A pdb=" N TYR a 586 " --> pdb=" O SER a 582 " (cutoff:3.500A) removed outlier: 3.526A 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: 3.685A pdb=" N VAL a 648 " --> pdb=" O ALA a 644 " (cutoff:3.500A) Proline residue: a 649 - end of helix removed outlier: 5.906A 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: 4.234A pdb=" N TRP a 743 " --> pdb=" O TYR a 739 " (cutoff:3.500A) Processing helix chain 'a' and resid 761 through 765 Processing helix chain 'a' and resid 768 through 791 Processing helix chain 'a' and resid 793 through 810 Processing helix chain 'a' and resid 811 through 815 Processing helix chain 'b' and resid 3 through 29 Processing helix chain 'b' and resid 36 through 44 Processing helix chain 'b' and resid 45 through 80 removed outlier: 3.712A pdb=" N SER b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 3.569A 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: 4.228A pdb=" N LYS b 89 " --> pdb=" O ARG b 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 113 removed outlier: 3.748A pdb=" N GLY b 104 " --> pdb=" O VAL b 100 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 169 removed outlier: 3.883A pdb=" N GLN b 168 " --> pdb=" O LEU b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 172 through 198 removed outlier: 4.090A pdb=" N ILE b 178 " --> pdb=" O VAL b 174 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL b 179 " --> pdb=" O LYS b 175 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU b 180 " --> pdb=" O ILE b 176 " (cutoff:3.500A) removed outlier: 3.699A 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: 4.199A pdb=" N ASP d 12 " --> pdb=" O TYR d 8 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TYR d 15 " --> pdb=" O VAL d 11 " (cutoff:3.500A) removed outlier: 5.254A 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: 4.823A pdb=" N PHE d 96 " --> pdb=" O PRO d 92 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE d 100 " --> pdb=" O PHE d 96 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR d 114 " --> pdb=" O ILE d 110 " (cutoff:3.500A) removed outlier: 3.806A 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 158 Processing helix chain 'd' and resid 159 through 167 removed outlier: 4.179A 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 239 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: 4.408A pdb=" N LEU d 277 " --> pdb=" O GLU d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 305 Processing helix chain 'd' and resid 306 through 308 No H-bonds generated for 'chain 'd' and resid 306 through 308' Processing helix chain 'd' and resid 312 through 338 removed outlier: 3.710A 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: 4.094A pdb=" N ILE f 58 " --> pdb=" O GLY f 54 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 46 removed outlier: 3.726A pdb=" N PHE g 14 " --> pdb=" O TYR g 10 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER g 26 " --> pdb=" O ALA g 22 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL g 46 " --> pdb=" O ALA g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 52 Processing helix chain 'g' and resid 53 through 55 No H-bonds generated for 'chain 'g' and resid 53 through 55' Processing helix chain 'g' and resid 56 through 78 Processing helix chain 'g' and resid 86 through 124 Processing helix chain 'g' and resid 127 through 153 Processing helix chain 'h' and resid 11 through 46 removed outlier: 4.573A pdb=" N GLY h 15 " --> pdb=" O SER h 11 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET h 23 " --> pdb=" O ALA h 19 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL h 46 " --> pdb=" O ALA h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 52 Processing helix chain 'h' and resid 56 through 78 Processing helix chain 'h' and resid 86 through 124 Processing helix chain 'h' and resid 127 through 154 removed outlier: 3.531A pdb=" N GLY h 145 " --> pdb=" O LEU h 141 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR h 154 " --> pdb=" O LEU h 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 10 through 48 removed outlier: 4.120A pdb=" N PHE i 14 " --> pdb=" O TYR i 10 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY i 15 " --> pdb=" O SER i 11 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET i 23 " --> pdb=" O ALA i 19 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER i 26 " --> pdb=" O ALA i 22 " (cutoff:3.500A) removed outlier: 3.521A 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: 3.936A pdb=" N GLN i 123 " --> pdb=" O ARG i 119 " (cutoff:3.500A) Processing helix chain 'i' and resid 126 through 154 removed outlier: 4.643A pdb=" N GLY i 130 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY i 145 " --> pdb=" O LEU i 141 " (cutoff:3.500A) Processing helix chain 'j' and resid 11 through 45 removed outlier: 4.336A pdb=" N GLY j 15 " --> pdb=" O SER j 11 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET j 23 " --> pdb=" O ALA j 19 " (cutoff:3.500A) Processing helix chain 'j' and resid 48 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: 4.071A pdb=" N ILE j 64 " --> pdb=" O VAL j 60 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE j 65 " --> pdb=" O MET j 61 " (cutoff:3.500A) removed outlier: 4.206A 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: 4.661A pdb=" N GLY j 130 " --> pdb=" O ARG j 126 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY j 142 " --> pdb=" O ALA j 138 " (cutoff:3.500A) Processing helix chain 'k' and resid 10 through 48 removed outlier: 4.172A pdb=" N PHE k 14 " --> pdb=" O TYR k 10 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY k 15 " --> pdb=" O SER k 11 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET k 23 " --> pdb=" O ALA k 19 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL k 46 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 4.063A 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: 4.473A pdb=" N GLY l 15 " --> pdb=" O SER l 11 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL l 46 " --> pdb=" O ALA l 42 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET l 47 " --> pdb=" O ALA l 43 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 55 removed outlier: 3.925A pdb=" N MET l 53 " --> pdb=" O GLU l 50 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 80 Processing helix chain 'l' and resid 86 through 124 removed outlier: 3.932A pdb=" N GLN l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 126 through 155 removed outlier: 4.231A pdb=" N GLY l 130 " --> pdb=" O ARG l 126 " (cutoff:3.500A) Processing helix chain 'm' and resid 10 through 45 removed outlier: 4.068A pdb=" N PHE m 14 " --> pdb=" O TYR m 10 " (cutoff:3.500A) removed outlier: 3.629A 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: 4.799A 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: 3.986A pdb=" N GLN m 123 " --> pdb=" O ARG m 119 " (cutoff:3.500A) Processing helix chain 'm' and resid 126 through 154 removed outlier: 4.364A pdb=" N GLY m 130 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY m 145 " --> pdb=" O LEU m 141 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR m 154 " --> pdb=" O LEU m 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 10 through 46 removed outlier: 4.316A pdb=" N PHE n 14 " --> pdb=" O TYR n 10 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY n 15 " --> pdb=" O SER n 11 " (cutoff:3.500A) removed outlier: 4.021A 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: 3.624A pdb=" N ARG n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 126 through 154 removed outlier: 4.651A pdb=" N GLY n 130 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY n 145 " --> pdb=" O LEU n 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR n 154 " --> pdb=" O LEU n 150 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 48 removed outlier: 4.357A pdb=" N GLY o 15 " --> pdb=" O SER o 11 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET o 47 " --> pdb=" O ALA o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 51 through 56 Processing helix chain 'o' and resid 56 through 80 removed outlier: 3.503A pdb=" N VAL o 60 " --> pdb=" O ILE o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 86 through 124 Processing helix chain 'o' and resid 127 through 154 removed outlier: 3.577A pdb=" N GLY o 145 " --> pdb=" O LEU o 141 " (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: 8.520A pdb=" N LEU L 37 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL L 10 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA L 9 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ASN L 67 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE L 11 " --> pdb=" O ASN L 67 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE L 64 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE L 91 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE L 66 " --> pdb=" O ILE L 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'a' and resid 362 through 363 1747 hydrogen bonds defined for protein. 5121 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: 7.42 Time building geometry restraints manager: 9.61 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: 3288 1.30 - 1.43: 5515 1.43 - 1.55: 12361 1.55 - 1.68: 0 1.68 - 1.81: 250 Bond restraints: 21414 Sorted by residual: bond pdb=" C PRO H 107 " pdb=" O PRO H 107 " ideal model delta sigma weight residual 1.233 1.171 0.062 9.60e-03 1.09e+04 4.15e+01 bond pdb=" N PRO L 86 " pdb=" CD PRO L 86 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 2.04e+01 bond pdb=" CA ALA H 102 " pdb=" CB ALA H 102 " ideal model delta sigma weight residual 1.542 1.503 0.039 8.90e-03 1.26e+04 1.94e+01 bond pdb=" CA ALA L 109 " pdb=" CB ALA L 109 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.34e-02 5.57e+03 1.68e+01 bond pdb=" N PRO g 8 " pdb=" CD PRO g 8 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.67e+01 ... (remaining 21409 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.41: 563 106.41 - 113.27: 11718 113.27 - 120.14: 8419 120.14 - 127.01: 8152 127.01 - 133.88: 173 Bond angle restraints: 29025 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 111.28 102.54 8.74 1.09e+00 8.42e-01 6.43e+01 angle pdb=" C ARG L 108 " pdb=" N ALA L 109 " pdb=" CA ALA L 109 " ideal model delta sigma weight residual 122.77 112.35 10.42 1.33e+00 5.65e-01 6.14e+01 angle pdb=" N SER L 104 " pdb=" CA SER L 104 " pdb=" C SER L 104 " ideal model delta sigma weight residual 111.36 103.07 8.29 1.09e+00 8.42e-01 5.79e+01 angle pdb=" C ILE L 91 " pdb=" N PRO L 92 " pdb=" CA PRO L 92 " ideal model delta sigma weight residual 119.83 127.73 -7.90 1.08e+00 8.57e-01 5.35e+01 angle pdb=" C ASN m 7 " pdb=" N PRO m 8 " pdb=" CA PRO m 8 " ideal model delta sigma weight residual 119.90 127.30 -7.40 1.05e+00 9.07e-01 4.97e+01 ... (remaining 29020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11995 17.95 - 35.90: 331 35.90 - 53.85: 84 53.85 - 71.80: 21 71.80 - 89.75: 23 Dihedral angle restraints: 12454 sinusoidal: 4528 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 -159.91 -20.09 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA GLN d 119 " pdb=" C GLN d 119 " pdb=" N ARG d 120 " pdb=" CA ARG d 120 " ideal model delta harmonic sigma weight residual 180.00 160.21 19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLU l 50 " pdb=" C GLU l 50 " pdb=" N LEU l 51 " pdb=" CA LEU l 51 " ideal model delta harmonic sigma weight residual -180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 12451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2307 0.060 - 0.120: 917 0.120 - 0.180: 124 0.180 - 0.240: 75 0.240 - 0.300: 11 Chirality restraints: 3434 Sorted by residual: 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 2.25e+00 chirality pdb=" CA TYR g 144 " pdb=" N TYR g 144 " pdb=" C TYR g 144 " pdb=" CB TYR g 144 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.09e+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 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 3431 not shown) Planarity restraints: 3606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU o 86 " 0.023 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C LEU o 86 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU o 86 " 0.029 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 4.29e-02 1.84e+01 pdb=" C ASN k 7 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN k 7 " -0.028 2.00e-02 2.50e+03 pdb=" N PRO k 8 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU d 160 " 0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C LEU d 160 " -0.069 2.00e-02 2.50e+03 pdb=" O LEU d 160 " 0.026 2.00e-02 2.50e+03 pdb=" N ALA d 161 " 0.023 2.00e-02 2.50e+03 ... (remaining 3603 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6839 2.82 - 3.34: 23215 3.34 - 3.86: 35952 3.86 - 4.38: 43070 4.38 - 4.90: 69362 Nonbonded interactions: 178438 Sorted by model distance: nonbonded pdb=" OG SER b 136 " pdb=" O GLN b 197 " model vdw 2.305 2.440 nonbonded pdb=" NZ LYS H 55 " pdb=" OD2 ASP L 99 " model vdw 2.319 2.520 nonbonded pdb=" O GLU o 9 " pdb=" N SER o 11 " model vdw 2.372 2.520 nonbonded pdb=" O PRO i 8 " pdb=" OG SER i 11 " model vdw 2.373 2.440 nonbonded pdb=" O PRO d 249 " pdb=" NE2 GLN m 123 " model vdw 2.380 2.520 ... (remaining 178433 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: 0.010 Normalize map: mean=0, sd=1: 2.390 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: 9.440 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 56.650 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 0.063 21414 Z= 0.541 Angle : 0.964 10.419 29025 Z= 0.725 Chirality : 0.067 0.300 3434 Planarity : 0.005 0.046 3606 Dihedral : 11.016 89.754 7424 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.63 % Favored : 97.15 % Rotamer: Outliers : 0.61 % Allowed : 1.49 % Favored : 97.90 % 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: 0.62 (0.14), residues: 2771 helix: 1.05 (0.10), residues: 2047 sheet: -0.40 (1.07), residues: 18 loop : -1.34 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 743 HIS 0.001 0.000 HIS a 807 PHE 0.011 0.000 PHE i 128 TYR 0.011 0.001 TYR d 33 ARG 0.001 0.000 ARG l 126 *********************** 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 1256 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1243 time to evaluate : 2.347 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: H 67 PHE cc_start: 0.8545 (t80) cc_final: 0.8263 (t80) REVERT: H 99 ASP cc_start: 0.8706 (t0) cc_final: 0.8274 (t0) REVERT: H 110 GLU cc_start: 0.8464 (tt0) cc_final: 0.7869 (tt0) REVERT: L 51 THR cc_start: 0.9302 (m) cc_final: 0.9051 (p) REVERT: L 94 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8102 (ttpp) REVERT: L 97 PRO cc_start: 0.7834 (Cg_endo) cc_final: 0.7332 (Cg_exo) REVERT: L 107 ARG cc_start: 0.8134 (ttp80) cc_final: 0.7850 (ttp80) REVERT: a 385 THR cc_start: 0.8772 (m) cc_final: 0.8489 (p) REVERT: a 429 ARG cc_start: 0.7941 (mtt90) cc_final: 0.6898 (mtp180) REVERT: a 439 MET cc_start: 0.8384 (mmm) cc_final: 0.7785 (mmm) REVERT: a 576 GLU cc_start: 0.8535 (mt-10) cc_final: 0.7795 (mm-30) REVERT: a 580 MET cc_start: 0.8984 (ttm) cc_final: 0.8759 (ttm) REVERT: a 616 MET cc_start: 0.8256 (ttp) cc_final: 0.7702 (tpp) REVERT: a 634 LYS cc_start: 0.8534 (mttt) cc_final: 0.8016 (ptmt) REVERT: a 637 GLN cc_start: 0.8738 (mt0) cc_final: 0.7218 (mm-40) REVERT: a 651 MET cc_start: 0.8065 (ptp) cc_final: 0.7659 (mtm) REVERT: a 768 ARG cc_start: 0.6494 (mtp180) cc_final: 0.5931 (mtt180) REVERT: a 790 ILE cc_start: 0.9473 (mp) cc_final: 0.9204 (mm) REVERT: a 792 LEU cc_start: 0.8977 (tp) cc_final: 0.8703 (mt) REVERT: a 794 MET cc_start: 0.8866 (tmm) cc_final: 0.8339 (tmm) REVERT: a 832 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7059 (mmm-85) REVERT: b 25 CYS cc_start: 0.9041 (m) cc_final: 0.8533 (t) REVERT: b 26 TYR cc_start: 0.8287 (m-10) cc_final: 0.8061 (m-80) REVERT: b 35 PHE cc_start: 0.7923 (t80) cc_final: 0.7606 (t80) REVERT: b 39 TRP cc_start: 0.7600 (t60) cc_final: 0.7366 (t60) REVERT: b 61 SER cc_start: 0.9389 (m) cc_final: 0.9109 (t) REVERT: b 75 SER cc_start: 0.9169 (m) cc_final: 0.8944 (p) REVERT: b 137 MET cc_start: 0.9256 (mtp) cc_final: 0.8999 (mtp) REVERT: b 148 ASN cc_start: 0.9455 (m-40) cc_final: 0.9158 (m110) REVERT: b 169 ASN cc_start: 0.8623 (t0) cc_final: 0.8228 (t0) REVERT: b 195 ILE cc_start: 0.9437 (mt) cc_final: 0.9152 (mm) REVERT: c 419 ILE cc_start: 0.8853 (mt) cc_final: 0.8546 (mt) REVERT: c 426 THR cc_start: 0.9479 (m) cc_final: 0.9216 (p) REVERT: c 435 TYR cc_start: 0.9019 (t80) cc_final: 0.8420 (t80) REVERT: c 449 PHE cc_start: 0.7950 (m-80) cc_final: 0.7470 (m-80) REVERT: d 3 PHE cc_start: 0.6795 (m-80) cc_final: 0.5116 (m-80) REVERT: d 17 GLU cc_start: 0.8325 (tp30) cc_final: 0.7998 (tp30) REVERT: d 76 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7577 (mm-30) REVERT: d 121 SER cc_start: 0.8676 (t) cc_final: 0.7884 (m) REVERT: d 129 CYS cc_start: 0.8114 (m) cc_final: 0.7821 (m) REVERT: d 152 ASN cc_start: 0.8667 (m-40) cc_final: 0.8418 (t0) REVERT: d 208 MET cc_start: 0.8772 (tpt) cc_final: 0.8309 (tpp) REVERT: d 214 PHE cc_start: 0.8599 (t80) cc_final: 0.8336 (t80) REVERT: d 250 GLU cc_start: 0.6852 (tt0) cc_final: 0.6377 (tt0) REVERT: e 51 PHE cc_start: 0.8562 (t80) cc_final: 0.8330 (t80) REVERT: e 68 LEU cc_start: 0.8771 (mt) cc_final: 0.8534 (mm) REVERT: e 78 PHE cc_start: 0.8857 (m-80) cc_final: 0.8469 (m-10) REVERT: g 10 TYR cc_start: 0.5443 (m-80) cc_final: 0.5227 (m-80) REVERT: g 88 ARG cc_start: 0.8454 (mmm160) cc_final: 0.7935 (tpp80) REVERT: g 101 LEU cc_start: 0.9403 (tp) cc_final: 0.9154 (tp) REVERT: g 104 LEU cc_start: 0.9214 (tp) cc_final: 0.8747 (tp) REVERT: g 108 PHE cc_start: 0.8936 (m-80) cc_final: 0.8661 (m-80) REVERT: g 126 ARG cc_start: 0.8797 (mtp180) cc_final: 0.8570 (mtp85) REVERT: h 61 MET cc_start: 0.8297 (mtt) cc_final: 0.7658 (mtm) REVERT: h 64 ILE cc_start: 0.8930 (mt) cc_final: 0.8583 (mt) REVERT: h 68 TYR cc_start: 0.8349 (m-10) cc_final: 0.8096 (m-10) REVERT: h 89 SER cc_start: 0.9303 (m) cc_final: 0.8853 (t) REVERT: h 90 PHE cc_start: 0.9135 (m-80) cc_final: 0.8557 (m-80) REVERT: h 92 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8606 (mm-40) REVERT: h 124 GLN cc_start: 0.8443 (tp-100) cc_final: 0.8008 (tm-30) REVERT: h 139 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8181 (tp30) REVERT: h 140 VAL cc_start: 0.9227 (t) cc_final: 0.8153 (t) REVERT: j 14 PHE cc_start: 0.7597 (m-80) cc_final: 0.7394 (m-80) REVERT: j 53 MET cc_start: 0.8667 (tmm) cc_final: 0.8130 (tmm) REVERT: k 26 SER cc_start: 0.9153 (m) cc_final: 0.8912 (p) REVERT: k 37 SER cc_start: 0.9465 (m) cc_final: 0.9202 (p) REVERT: k 41 ILE cc_start: 0.9434 (mt) cc_final: 0.9231 (mm) REVERT: k 48 ARG cc_start: 0.8421 (mtt-85) cc_final: 0.7953 (mmt90) REVERT: k 50 GLU cc_start: 0.8236 (pm20) cc_final: 0.7921 (pm20) REVERT: k 53 MET cc_start: 0.7706 (mtp) cc_final: 0.6915 (mtt) REVERT: k 70 LEU cc_start: 0.8946 (tp) cc_final: 0.8733 (tt) REVERT: k 75 LEU cc_start: 0.8562 (mt) cc_final: 0.8261 (tp) REVERT: k 98 SER cc_start: 0.9640 (t) cc_final: 0.9379 (m) REVERT: k 131 MET cc_start: 0.8306 (ttp) cc_final: 0.8027 (ttp) REVERT: l 37 SER cc_start: 0.8642 (m) cc_final: 0.8346 (p) REVERT: l 53 MET cc_start: 0.8394 (tmm) cc_final: 0.8168 (mtt) REVERT: l 131 MET cc_start: 0.8296 (ttp) cc_final: 0.8043 (ttp) REVERT: l 135 LEU cc_start: 0.9201 (mt) cc_final: 0.8958 (mt) REVERT: l 151 ILE cc_start: 0.9369 (mt) cc_final: 0.9126 (tp) REVERT: m 21 SER cc_start: 0.9429 (m) cc_final: 0.9088 (p) REVERT: m 46 VAL cc_start: 0.9324 (t) cc_final: 0.9105 (m) REVERT: m 84 ILE cc_start: 0.8081 (mt) cc_final: 0.7470 (mt) REVERT: m 97 LEU cc_start: 0.9240 (mt) cc_final: 0.8640 (mm) REVERT: m 119 ARG cc_start: 0.8335 (mtt-85) cc_final: 0.7917 (ttm170) REVERT: n 23 MET cc_start: 0.8893 (tpt) cc_final: 0.8683 (tpp) REVERT: n 36 LYS cc_start: 0.8507 (mmmt) cc_final: 0.7913 (tppp) REVERT: n 70 LEU cc_start: 0.8890 (tp) cc_final: 0.8548 (tp) REVERT: n 84 ILE cc_start: 0.8091 (tt) cc_final: 0.7824 (tt) REVERT: n 132 ILE cc_start: 0.8835 (mm) cc_final: 0.8594 (mm) REVERT: o 17 MET cc_start: 0.9397 (mmp) cc_final: 0.9182 (tpp) REVERT: o 21 SER cc_start: 0.9076 (m) cc_final: 0.8741 (p) REVERT: o 37 SER cc_start: 0.9044 (m) cc_final: 0.8304 (t) REVERT: o 87 TYR cc_start: 0.8488 (t80) cc_final: 0.8272 (t80) REVERT: o 89 SER cc_start: 0.8195 (m) cc_final: 0.7681 (t) REVERT: o 90 PHE cc_start: 0.8201 (m-80) cc_final: 0.7869 (m-80) REVERT: o 119 ARG cc_start: 0.8235 (mtm-85) cc_final: 0.7999 (mtm-85) REVERT: o 124 GLN cc_start: 0.8326 (tp-100) cc_final: 0.7512 (tm-30) REVERT: o 133 LEU cc_start: 0.9241 (mt) cc_final: 0.9037 (tp) REVERT: p 294 ASN cc_start: 0.8083 (m-40) cc_final: 0.7816 (p0) REVERT: p 298 LYS cc_start: 0.8792 (mttt) cc_final: 0.8243 (mmtt) REVERT: p 301 LEU cc_start: 0.5675 (mt) cc_final: 0.4683 (mp) outliers start: 13 outliers final: 3 residues processed: 1249 average time/residue: 0.3104 time to fit residues: 607.1697 Evaluate side-chains 768 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 764 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain h residue 139 GLU Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 139 GLU 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: 0.8980 chunk 117 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 253 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 33 HIS L 96 HIS a 433 GLN a 548 HIS ** a 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS d 50 GLN d 119 GLN d 297 HIS d 309 GLN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 6 ASN j 78 ASN ** k 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 7 ASN m 78 ASN n 6 ASN p 330 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 21414 Z= 0.253 Angle : 0.690 10.323 29025 Z= 0.363 Chirality : 0.042 0.230 3434 Planarity : 0.005 0.040 3606 Dihedral : 4.491 53.797 2988 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.56 % Favored : 97.40 % Rotamer: Outliers : 5.74 % Allowed : 17.41 % Favored : 76.85 % 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: 2.16 (0.15), residues: 2771 helix: 2.16 (0.10), residues: 2082 sheet: -0.76 (1.09), residues: 18 loop : -0.85 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP e 74 HIS 0.005 0.001 HIS b 132 PHE 0.038 0.002 PHE e 6 TYR 0.031 0.002 TYR h 144 ARG 0.006 0.001 ARG L 32 *********************** 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 988 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 865 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 83 VAL cc_start: 0.9310 (t) cc_final: 0.9097 (t) REVERT: H 86 ASN cc_start: 0.9104 (t0) cc_final: 0.8834 (t0) REVERT: H 98 LYS cc_start: 0.8563 (pttt) cc_final: 0.8077 (pttp) REVERT: H 99 ASP cc_start: 0.8690 (t0) cc_final: 0.8336 (t0) REVERT: L 68 GLN cc_start: 0.7938 (tp40) cc_final: 0.7730 (tp40) REVERT: L 72 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8331 (mm-30) REVERT: L 94 LYS cc_start: 0.8261 (ttpt) cc_final: 0.7990 (ttpp) REVERT: a 10 MET cc_start: 0.7568 (mmt) cc_final: 0.7048 (mmm) REVERT: a 375 GLN cc_start: 0.8133 (tp40) cc_final: 0.7717 (tp40) REVERT: a 406 MET cc_start: 0.8562 (mtt) cc_final: 0.8328 (mtt) REVERT: a 429 ARG cc_start: 0.7614 (mtt90) cc_final: 0.6588 (mtp180) REVERT: a 439 MET cc_start: 0.8302 (mmm) cc_final: 0.7566 (mmm) REVERT: a 502 GLN cc_start: 0.6688 (tm-30) cc_final: 0.6459 (tm-30) REVERT: a 576 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8192 (mt-10) REVERT: a 582 SER cc_start: 0.9230 (OUTLIER) cc_final: 0.8913 (t) REVERT: a 640 LEU cc_start: 0.8942 (mt) cc_final: 0.8628 (mt) REVERT: a 651 MET cc_start: 0.8136 (ptp) cc_final: 0.7559 (mtm) REVERT: a 660 ARG cc_start: 0.6183 (ttt-90) cc_final: 0.5473 (tmt170) REVERT: a 759 MET cc_start: 0.8125 (mmp) cc_final: 0.6686 (tpt) REVERT: a 768 ARG cc_start: 0.6495 (mtp180) cc_final: 0.5709 (mtt180) REVERT: a 792 LEU cc_start: 0.9014 (tp) cc_final: 0.8481 (mt) REVERT: a 832 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7105 (mmm-85) REVERT: b 25 CYS cc_start: 0.9051 (m) cc_final: 0.8492 (t) REVERT: b 47 PHE cc_start: 0.8374 (m-10) cc_final: 0.7809 (m-10) REVERT: b 52 LEU cc_start: 0.8873 (tp) cc_final: 0.8639 (tt) REVERT: b 61 SER cc_start: 0.9318 (m) cc_final: 0.9111 (t) REVERT: b 75 SER cc_start: 0.9219 (m) cc_final: 0.8895 (p) REVERT: b 107 MET cc_start: 0.8995 (mmm) cc_final: 0.8572 (mmm) REVERT: b 137 MET cc_start: 0.9212 (mtp) cc_final: 0.8971 (mtp) REVERT: b 169 ASN cc_start: 0.8469 (t0) cc_final: 0.7814 (t0) REVERT: c 419 ILE cc_start: 0.8864 (mt) cc_final: 0.8554 (mt) REVERT: c 426 THR cc_start: 0.9333 (m) cc_final: 0.9115 (p) REVERT: c 435 TYR cc_start: 0.8969 (t80) cc_final: 0.8659 (t80) REVERT: d 40 GLU cc_start: 0.8185 (tt0) cc_final: 0.7715 (tp30) REVERT: d 76 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7517 (mm-30) REVERT: d 121 SER cc_start: 0.8317 (t) cc_final: 0.7793 (m) REVERT: d 124 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8155 (mp0) REVERT: d 129 CYS cc_start: 0.8186 (m) cc_final: 0.7875 (m) REVERT: d 171 GLN cc_start: 0.8662 (tt0) cc_final: 0.8286 (pm20) REVERT: d 175 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8277 (mt-10) REVERT: d 176 MET cc_start: 0.7244 (mtt) cc_final: 0.6861 (mtt) REVERT: d 208 MET cc_start: 0.8955 (tpt) cc_final: 0.8617 (tpp) REVERT: d 339 ARG cc_start: 0.7130 (mpt180) cc_final: 0.6775 (mmt90) REVERT: e 47 CYS cc_start: 0.9091 (m) cc_final: 0.8732 (m) REVERT: e 78 PHE cc_start: 0.9058 (m-80) cc_final: 0.8561 (m-80) REVERT: g 13 PHE cc_start: 0.7601 (t80) cc_final: 0.7259 (t80) REVERT: g 44 MET cc_start: 0.8920 (tmm) cc_final: 0.8576 (tmm) REVERT: g 47 MET cc_start: 0.7821 (tpt) cc_final: 0.7613 (tpt) REVERT: g 87 TYR cc_start: 0.8626 (t80) cc_final: 0.8237 (t80) REVERT: g 126 ARG cc_start: 0.8962 (mtp180) cc_final: 0.8637 (mtp85) REVERT: h 10 TYR cc_start: 0.9013 (p90) cc_final: 0.8740 (p90) REVERT: h 36 LYS cc_start: 0.9077 (mmmm) cc_final: 0.8632 (tppt) REVERT: h 48 ARG cc_start: 0.7937 (mtp180) cc_final: 0.7672 (mtt180) REVERT: h 64 ILE cc_start: 0.8834 (mt) cc_final: 0.8402 (mt) REVERT: h 65 ILE cc_start: 0.8362 (mp) cc_final: 0.7901 (tp) REVERT: h 68 TYR cc_start: 0.8569 (m-10) cc_final: 0.7530 (m-10) REVERT: h 90 PHE cc_start: 0.8977 (m-80) cc_final: 0.8647 (m-80) REVERT: h 92 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8593 (mm-40) REVERT: h 124 GLN cc_start: 0.8350 (tp-100) cc_final: 0.7854 (tm-30) REVERT: h 140 VAL cc_start: 0.9449 (t) cc_final: 0.9157 (p) REVERT: i 61 MET cc_start: 0.8774 (tpp) cc_final: 0.8537 (mmm) REVERT: i 92 GLN cc_start: 0.8705 (mt0) cc_final: 0.8382 (mt0) REVERT: i 115 ASP cc_start: 0.8490 (t70) cc_final: 0.8102 (t0) REVERT: i 144 TYR cc_start: 0.9057 (m-10) cc_final: 0.8776 (m-80) REVERT: j 17 MET cc_start: 0.9142 (mmm) cc_final: 0.8912 (mmm) REVERT: j 32 TYR cc_start: 0.8829 (t80) cc_final: 0.8628 (t80) REVERT: j 47 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8101 (mtm) REVERT: j 53 MET cc_start: 0.8699 (tmm) cc_final: 0.8374 (tmm) REVERT: j 87 TYR cc_start: 0.8611 (t80) cc_final: 0.8235 (t80) REVERT: j 91 LEU cc_start: 0.9252 (mp) cc_final: 0.9025 (mt) REVERT: j 139 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7634 (tm-30) REVERT: k 26 SER cc_start: 0.9237 (m) cc_final: 0.8942 (p) REVERT: k 37 SER cc_start: 0.9412 (m) cc_final: 0.9165 (p) REVERT: k 53 MET cc_start: 0.7783 (mtp) cc_final: 0.7456 (mtt) REVERT: k 70 LEU cc_start: 0.9180 (tp) cc_final: 0.8944 (tp) REVERT: k 92 GLN cc_start: 0.8688 (mm-40) cc_final: 0.7835 (mm-40) REVERT: k 123 GLN cc_start: 0.8389 (mt0) cc_final: 0.8096 (mt0) REVERT: k 124 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7665 (tm-30) REVERT: k 127 LEU cc_start: 0.8797 (mp) cc_final: 0.8247 (mp) REVERT: k 131 MET cc_start: 0.8385 (ttp) cc_final: 0.7976 (ttp) REVERT: l 17 MET cc_start: 0.8673 (tpp) cc_final: 0.8349 (tpp) REVERT: l 34 THR cc_start: 0.9267 (m) cc_final: 0.8996 (p) REVERT: l 37 SER cc_start: 0.8602 (m) cc_final: 0.8156 (p) REVERT: l 48 ARG cc_start: 0.8043 (ptm-80) cc_final: 0.7581 (ptm-80) REVERT: l 68 TYR cc_start: 0.8760 (m-10) cc_final: 0.8436 (m-80) REVERT: l 131 MET cc_start: 0.8233 (ttp) cc_final: 0.7993 (ttp) REVERT: l 139 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8492 (mm-30) REVERT: m 78 ASN cc_start: 0.8495 (m-40) cc_final: 0.8268 (m110) REVERT: m 92 GLN cc_start: 0.9337 (mt0) cc_final: 0.8995 (mt0) REVERT: n 13 PHE cc_start: 0.8414 (t80) cc_final: 0.8093 (t80) REVERT: n 23 MET cc_start: 0.9078 (tpt) cc_final: 0.8744 (tpt) REVERT: n 36 LYS cc_start: 0.8459 (mmmt) cc_final: 0.8036 (tppt) REVERT: n 47 MET cc_start: 0.8445 (tpp) cc_final: 0.7870 (tpt) REVERT: n 84 ILE cc_start: 0.7876 (tt) cc_final: 0.7566 (tt) REVERT: n 115 ASP cc_start: 0.8063 (t0) cc_final: 0.7842 (t0) REVERT: n 124 GLN cc_start: 0.7885 (tp-100) cc_final: 0.7619 (tp-100) REVERT: o 17 MET cc_start: 0.9385 (mmp) cc_final: 0.9121 (mmm) REVERT: o 21 SER cc_start: 0.8831 (m) cc_final: 0.8535 (p) REVERT: o 37 SER cc_start: 0.8952 (m) cc_final: 0.8480 (t) REVERT: o 76 ILE cc_start: 0.9330 (mt) cc_final: 0.9108 (mm) REVERT: o 90 PHE cc_start: 0.8265 (m-80) cc_final: 0.7957 (m-80) REVERT: o 92 GLN cc_start: 0.9108 (mm-40) cc_final: 0.8712 (mm-40) REVERT: o 124 GLN cc_start: 0.8038 (tp-100) cc_final: 0.7027 (tm-30) REVERT: o 131 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7795 (ttp) REVERT: p 294 ASN cc_start: 0.8049 (m-40) cc_final: 0.7841 (p0) REVERT: p 298 LYS cc_start: 0.8747 (mttt) cc_final: 0.8131 (mmtt) outliers start: 123 outliers final: 68 residues processed: 913 average time/residue: 0.3095 time to fit residues: 445.0898 Evaluate side-chains 788 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 717 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain a residue 363 THR Chi-restraints excluded: chain a residue 378 VAL Chi-restraints excluded: chain a residue 458 ILE Chi-restraints excluded: chain a residue 533 LEU Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 582 SER Chi-restraints excluded: chain a residue 599 ASP Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 136 SER Chi-restraints excluded: chain b residue 154 CYS Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain c residue 440 ILE Chi-restraints excluded: chain d residue 51 SER Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 66 THR Chi-restraints excluded: chain d residue 68 SER Chi-restraints excluded: chain d residue 101 THR Chi-restraints excluded: chain d residue 114 THR Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain g residue 17 MET Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 52 ILE Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 153 SER Chi-restraints excluded: chain i residue 21 SER Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain j residue 47 MET Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 102 SER Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain k residue 11 SER Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain l residue 7 ASN Chi-restraints excluded: chain l residue 81 THR Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain m residue 11 SER Chi-restraints excluded: chain m residue 12 SER Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain m residue 45 SER Chi-restraints excluded: chain m residue 139 GLU Chi-restraints excluded: chain n residue 20 SER Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 82 ASP Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 98 SER Chi-restraints excluded: chain o residue 20 SER Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 85 THR Chi-restraints excluded: chain o residue 112 ILE Chi-restraints excluded: chain o residue 131 MET Chi-restraints excluded: chain p residue 321 VAL Chi-restraints excluded: chain p residue 325 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 140 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 253 optimal weight: 0.8980 chunk 274 optimal weight: 0.0050 chunk 226 optimal weight: 1.9990 chunk 251 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 203 optimal weight: 6.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 96 HIS a 433 GLN ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 ASN ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 302 ASN d 309 GLN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 78 ASN ** k 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 21414 Z= 0.217 Angle : 0.638 9.612 29025 Z= 0.331 Chirality : 0.041 0.207 3434 Planarity : 0.004 0.045 3606 Dihedral : 4.012 28.034 2980 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.60 % Favored : 97.37 % Rotamer: Outliers : 4.43 % Allowed : 21.93 % Favored : 73.64 % 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: 2.12 (0.15), residues: 2771 helix: 2.10 (0.11), residues: 2093 sheet: -0.93 (1.07), residues: 18 loop : -0.81 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP e 74 HIS 0.005 0.001 HIS b 132 PHE 0.038 0.002 PHE j 108 TYR 0.031 0.002 TYR n 144 ARG 0.004 0.000 ARG l 119 *********************** 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 867 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 772 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASN cc_start: 0.9130 (t0) cc_final: 0.8822 (t0) REVERT: H 98 LYS cc_start: 0.8575 (pttt) cc_final: 0.8073 (pttp) REVERT: H 99 ASP cc_start: 0.8730 (t0) cc_final: 0.8442 (t0) REVERT: L 22 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8988 (mp) REVERT: L 49 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7705 (tm-30) REVERT: L 94 LYS cc_start: 0.8251 (ttpt) cc_final: 0.7993 (ttpp) REVERT: a 10 MET cc_start: 0.7590 (mmt) cc_final: 0.7079 (mmm) REVERT: a 375 GLN cc_start: 0.8155 (tp40) cc_final: 0.7747 (tp40) REVERT: a 399 PHE cc_start: 0.8844 (t80) cc_final: 0.8593 (t80) REVERT: a 406 MET cc_start: 0.8613 (mtt) cc_final: 0.8384 (mtt) REVERT: a 423 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8150 (mtm) REVERT: a 429 ARG cc_start: 0.7600 (mtt90) cc_final: 0.6600 (mtp180) REVERT: a 439 MET cc_start: 0.8254 (mmm) cc_final: 0.7724 (mmm) REVERT: a 459 TYR cc_start: 0.8636 (t80) cc_final: 0.8346 (t80) REVERT: a 502 GLN cc_start: 0.6730 (tm-30) cc_final: 0.6465 (tm-30) REVERT: a 628 MET cc_start: 0.7953 (mmm) cc_final: 0.7627 (mtt) REVERT: a 660 ARG cc_start: 0.6087 (ttt-90) cc_final: 0.5400 (tmt170) REVERT: a 759 MET cc_start: 0.8054 (mmp) cc_final: 0.6581 (tpt) REVERT: a 768 ARG cc_start: 0.6468 (mtp180) cc_final: 0.5674 (mtt180) REVERT: a 792 LEU cc_start: 0.8960 (tp) cc_final: 0.8425 (mt) REVERT: a 832 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7077 (mmm-85) REVERT: b 25 CYS cc_start: 0.8995 (m) cc_final: 0.8428 (t) REVERT: b 36 ASP cc_start: 0.7240 (t0) cc_final: 0.6999 (t0) REVERT: b 39 TRP cc_start: 0.7673 (t60) cc_final: 0.7267 (t60) REVERT: b 98 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7284 (mm-30) REVERT: b 107 MET cc_start: 0.9098 (mmm) cc_final: 0.8874 (mmm) REVERT: b 116 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7866 (mm-30) REVERT: c 419 ILE cc_start: 0.8808 (mt) cc_final: 0.8493 (mm) REVERT: c 426 THR cc_start: 0.9401 (m) cc_final: 0.9183 (p) REVERT: c 435 TYR cc_start: 0.9114 (t80) cc_final: 0.8883 (t80) REVERT: d 40 GLU cc_start: 0.8170 (tt0) cc_final: 0.7763 (tp30) REVERT: d 65 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8936 (mm) REVERT: d 76 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7461 (mm-30) REVERT: d 129 CYS cc_start: 0.8246 (m) cc_final: 0.7961 (m) REVERT: d 171 GLN cc_start: 0.8643 (tt0) cc_final: 0.8153 (mm-40) REVERT: d 175 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8449 (mm-30) REVERT: d 176 MET cc_start: 0.7173 (mtt) cc_final: 0.6932 (mtt) REVERT: d 213 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.6950 (tp30) REVERT: d 215 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: d 325 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8100 (tt0) REVERT: d 339 ARG cc_start: 0.7150 (mpt180) cc_final: 0.6695 (mmt90) REVERT: d 340 HIS cc_start: 0.7974 (m-70) cc_final: 0.7748 (m170) REVERT: e 47 CYS cc_start: 0.9102 (m) cc_final: 0.8814 (m) REVERT: e 66 PRO cc_start: 0.8800 (Cg_endo) cc_final: 0.8531 (Cg_exo) REVERT: e 78 PHE cc_start: 0.9167 (m-80) cc_final: 0.8849 (m-80) REVERT: g 13 PHE cc_start: 0.7547 (t80) cc_final: 0.7248 (t80) REVERT: g 44 MET cc_start: 0.9023 (tmm) cc_final: 0.8595 (tmm) REVERT: g 47 MET cc_start: 0.7952 (tpt) cc_final: 0.7723 (tpt) REVERT: g 76 ILE cc_start: 0.9662 (mt) cc_final: 0.9344 (tt) REVERT: g 87 TYR cc_start: 0.8592 (t80) cc_final: 0.8165 (t80) REVERT: g 88 ARG cc_start: 0.7856 (mmm160) cc_final: 0.7576 (mmm160) REVERT: h 10 TYR cc_start: 0.8986 (p90) cc_final: 0.8681 (p90) REVERT: h 23 MET cc_start: 0.9165 (tpp) cc_final: 0.8794 (ttm) REVERT: h 48 ARG cc_start: 0.7887 (mtp180) cc_final: 0.7604 (mtt-85) REVERT: h 64 ILE cc_start: 0.8976 (mt) cc_final: 0.8690 (mt) REVERT: h 65 ILE cc_start: 0.8475 (mp) cc_final: 0.8090 (tp) REVERT: h 68 TYR cc_start: 0.8715 (m-10) cc_final: 0.7887 (m-10) REVERT: h 76 ILE cc_start: 0.9522 (mt) cc_final: 0.9279 (mp) REVERT: h 90 PHE cc_start: 0.9020 (m-80) cc_final: 0.8628 (m-80) REVERT: h 92 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8620 (mm-40) REVERT: h 123 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8638 (mm110) REVERT: h 124 GLN cc_start: 0.8091 (tp-100) cc_final: 0.7658 (tm-30) REVERT: h 131 MET cc_start: 0.8516 (ttp) cc_final: 0.8113 (ttp) REVERT: h 140 VAL cc_start: 0.9510 (t) cc_final: 0.9279 (p) REVERT: h 144 TYR cc_start: 0.8889 (m-80) cc_final: 0.8675 (m-80) REVERT: i 61 MET cc_start: 0.8745 (tpp) cc_final: 0.8240 (mmm) REVERT: i 76 ILE cc_start: 0.9599 (mt) cc_final: 0.9105 (tt) REVERT: i 81 THR cc_start: 0.8785 (t) cc_final: 0.8579 (t) REVERT: i 115 ASP cc_start: 0.8652 (t70) cc_final: 0.8425 (t0) REVERT: i 144 TYR cc_start: 0.8826 (m-10) cc_final: 0.8542 (m-80) REVERT: j 17 MET cc_start: 0.9068 (mmm) cc_final: 0.8674 (mmm) REVERT: j 44 MET cc_start: 0.9255 (tmm) cc_final: 0.8935 (tmm) REVERT: j 48 ARG cc_start: 0.8854 (mmt90) cc_final: 0.8348 (mmt90) REVERT: j 53 MET cc_start: 0.8673 (tmm) cc_final: 0.8302 (tmm) REVERT: j 87 TYR cc_start: 0.8609 (t80) cc_final: 0.8131 (t80) REVERT: j 91 LEU cc_start: 0.9238 (mp) cc_final: 0.8981 (mt) REVERT: j 108 PHE cc_start: 0.9079 (m-80) cc_final: 0.8869 (m-80) REVERT: k 26 SER cc_start: 0.9246 (m) cc_final: 0.8990 (p) REVERT: k 37 SER cc_start: 0.9362 (m) cc_final: 0.9140 (p) REVERT: k 53 MET cc_start: 0.8018 (mtp) cc_final: 0.7761 (mtt) REVERT: k 124 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7903 (tm-30) REVERT: k 127 LEU cc_start: 0.8894 (mp) cc_final: 0.8393 (mp) REVERT: k 131 MET cc_start: 0.8264 (ttp) cc_final: 0.7963 (ttp) REVERT: l 34 THR cc_start: 0.9282 (m) cc_final: 0.9030 (p) REVERT: l 37 SER cc_start: 0.8615 (m) cc_final: 0.8224 (p) REVERT: l 48 ARG cc_start: 0.7971 (ptm-80) cc_final: 0.7678 (ptp-170) REVERT: l 131 MET cc_start: 0.8244 (ttp) cc_final: 0.7843 (ttp) REVERT: m 78 ASN cc_start: 0.8477 (m-40) cc_final: 0.8219 (m110) REVERT: m 92 GLN cc_start: 0.9313 (mt0) cc_final: 0.8897 (mt0) REVERT: m 155 LYS cc_start: 0.7243 (tptm) cc_final: 0.6927 (tptm) REVERT: n 17 MET cc_start: 0.8274 (mtp) cc_final: 0.7947 (tpp) REVERT: n 23 MET cc_start: 0.9084 (tpt) cc_final: 0.8730 (tpt) REVERT: o 17 MET cc_start: 0.9257 (mmp) cc_final: 0.9024 (mmm) REVERT: o 37 SER cc_start: 0.8823 (m) cc_final: 0.8386 (t) REVERT: o 90 PHE cc_start: 0.8347 (m-80) cc_final: 0.8131 (m-80) REVERT: o 124 GLN cc_start: 0.8097 (tp-100) cc_final: 0.7426 (tm-30) REVERT: p 294 ASN cc_start: 0.8227 (m-40) cc_final: 0.7904 (p0) REVERT: p 298 LYS cc_start: 0.8888 (mttt) cc_final: 0.8267 (mmtt) REVERT: p 303 TYR cc_start: 0.8615 (t80) cc_final: 0.8356 (t80) REVERT: p 308 ASN cc_start: 0.7978 (t0) cc_final: 0.7707 (t0) REVERT: p 330 ASN cc_start: 0.9181 (m110) cc_final: 0.8848 (m-40) outliers start: 95 outliers final: 57 residues processed: 819 average time/residue: 0.3039 time to fit residues: 394.2171 Evaluate side-chains 755 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 693 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain a residue 363 THR Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 458 ILE Chi-restraints excluded: chain a residue 533 LEU Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 599 ASP Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 154 CYS Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain c residue 423 LEU Chi-restraints excluded: chain c residue 440 ILE Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 66 THR Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain d residue 213 GLU Chi-restraints excluded: chain d residue 215 GLU Chi-restraints excluded: chain d residue 230 THR Chi-restraints excluded: chain d residue 309 GLN Chi-restraints excluded: chain e residue 19 LEU Chi-restraints excluded: chain g residue 17 MET Chi-restraints excluded: chain g residue 21 SER Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 80 LEU Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 93 LEU Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain j residue 7 ASN Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 102 SER Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain k residue 10 TYR Chi-restraints excluded: chain k residue 11 SER Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain l residue 81 THR Chi-restraints excluded: chain m residue 11 SER Chi-restraints excluded: chain m residue 12 SER Chi-restraints excluded: chain m residue 45 SER Chi-restraints excluded: chain n residue 20 SER Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 82 ASP Chi-restraints excluded: chain n residue 98 SER Chi-restraints excluded: chain o residue 20 SER Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 85 THR Chi-restraints excluded: chain p residue 314 MET Chi-restraints excluded: chain p residue 325 SER Chi-restraints excluded: chain p residue 336 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 250 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 254 optimal weight: 0.9990 chunk 269 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 241 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 113 HIS a 433 GLN ** a 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 309 GLN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 92 GLN k 7 ASN ** k 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21414 Z= 0.216 Angle : 0.637 9.876 29025 Z= 0.329 Chirality : 0.040 0.216 3434 Planarity : 0.004 0.046 3606 Dihedral : 4.003 29.094 2980 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.76 % Allowed : 23.24 % Favored : 72.00 % 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: 2.01 (0.15), residues: 2771 helix: 2.03 (0.11), residues: 2115 sheet: -0.97 (1.22), residues: 18 loop : -0.99 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP e 74 HIS 0.007 0.001 HIS b 132 PHE 0.028 0.002 PHE j 108 TYR 0.041 0.002 TYR n 144 ARG 0.010 0.000 ARG l 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 758 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASN cc_start: 0.9134 (t0) cc_final: 0.8816 (t0) REVERT: H 99 ASP cc_start: 0.8686 (t0) cc_final: 0.8364 (t0) REVERT: L 22 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8974 (mp) REVERT: L 49 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7650 (tm-30) REVERT: L 94 LYS cc_start: 0.8331 (ttpt) cc_final: 0.8075 (ttpp) REVERT: a 10 MET cc_start: 0.7518 (mmt) cc_final: 0.7120 (mmm) REVERT: a 399 PHE cc_start: 0.8774 (t80) cc_final: 0.8548 (t80) REVERT: a 406 MET cc_start: 0.8647 (mtt) cc_final: 0.8429 (mtt) REVERT: a 423 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8222 (mtm) REVERT: a 429 ARG cc_start: 0.7559 (mtt90) cc_final: 0.6595 (mtp180) REVERT: a 439 MET cc_start: 0.8244 (mmm) cc_final: 0.7871 (mmm) REVERT: a 459 TYR cc_start: 0.8847 (t80) cc_final: 0.8444 (t80) REVERT: a 502 GLN cc_start: 0.6701 (tm-30) cc_final: 0.6335 (tm-30) REVERT: a 538 MET cc_start: 0.8105 (ttp) cc_final: 0.7884 (mtp) REVERT: a 576 GLU cc_start: 0.8552 (mt-10) cc_final: 0.7999 (mm-30) REVERT: a 628 MET cc_start: 0.7882 (mmm) cc_final: 0.7623 (mtt) REVERT: a 637 GLN cc_start: 0.9100 (mt0) cc_final: 0.8604 (mt0) REVERT: a 660 ARG cc_start: 0.6104 (ttt-90) cc_final: 0.5394 (tmt170) REVERT: a 662 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7614 (mm-40) REVERT: a 726 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8298 (tp) REVERT: a 768 ARG cc_start: 0.6400 (mtp180) cc_final: 0.5675 (mtt180) REVERT: a 792 LEU cc_start: 0.8922 (tp) cc_final: 0.8365 (mt) REVERT: a 832 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7101 (mmm-85) REVERT: b 19 MET cc_start: 0.8682 (mmm) cc_final: 0.8360 (mmm) REVERT: b 25 CYS cc_start: 0.9017 (m) cc_final: 0.8562 (m) REVERT: b 39 TRP cc_start: 0.7644 (t60) cc_final: 0.7359 (t60) REVERT: b 47 PHE cc_start: 0.8363 (m-10) cc_final: 0.7872 (m-80) REVERT: b 98 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7362 (mm-30) REVERT: b 103 TYR cc_start: 0.7902 (m-80) cc_final: 0.7516 (m-80) REVERT: b 116 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7872 (mp0) REVERT: b 132 HIS cc_start: 0.9250 (t70) cc_final: 0.9030 (t-90) REVERT: b 137 MET cc_start: 0.9177 (mtp) cc_final: 0.8865 (mtp) REVERT: b 188 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9117 (mm) REVERT: c 419 ILE cc_start: 0.8825 (mt) cc_final: 0.8491 (mm) REVERT: c 421 MET cc_start: 0.8214 (mtm) cc_final: 0.7847 (ttm) REVERT: c 435 TYR cc_start: 0.9119 (t80) cc_final: 0.8842 (t80) REVERT: d 40 GLU cc_start: 0.8121 (tt0) cc_final: 0.7737 (tp30) REVERT: d 65 LEU cc_start: 0.9240 (mm) cc_final: 0.8980 (mm) REVERT: d 76 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7511 (mm-30) REVERT: d 129 CYS cc_start: 0.8229 (m) cc_final: 0.7975 (m) REVERT: d 171 GLN cc_start: 0.8650 (tt0) cc_final: 0.8184 (mm-40) REVERT: d 176 MET cc_start: 0.7128 (mtt) cc_final: 0.6883 (mtt) REVERT: d 213 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7123 (mm-30) REVERT: d 215 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: d 250 GLU cc_start: 0.6584 (tt0) cc_final: 0.6278 (tt0) REVERT: d 269 ASP cc_start: 0.8288 (t0) cc_final: 0.8023 (m-30) REVERT: d 343 LYS cc_start: 0.8359 (mmtt) cc_final: 0.8151 (mttp) REVERT: e 47 CYS cc_start: 0.9013 (m) cc_final: 0.8659 (m) REVERT: g 13 PHE cc_start: 0.7355 (t80) cc_final: 0.7139 (t80) REVERT: g 44 MET cc_start: 0.9035 (tmm) cc_final: 0.8523 (tmm) REVERT: g 87 TYR cc_start: 0.8445 (t80) cc_final: 0.7447 (t80) REVERT: h 10 TYR cc_start: 0.8991 (p90) cc_final: 0.8739 (p90) REVERT: h 23 MET cc_start: 0.9170 (tpp) cc_final: 0.8885 (ttm) REVERT: h 64 ILE cc_start: 0.8984 (mt) cc_final: 0.8644 (mt) REVERT: h 65 ILE cc_start: 0.8690 (mp) cc_final: 0.8288 (tp) REVERT: h 68 TYR cc_start: 0.8853 (m-10) cc_final: 0.8071 (m-10) REVERT: h 90 PHE cc_start: 0.8953 (m-10) cc_final: 0.8686 (m-80) REVERT: h 123 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8631 (mm110) REVERT: h 124 GLN cc_start: 0.7978 (tp-100) cc_final: 0.7561 (tm-30) REVERT: h 131 MET cc_start: 0.8330 (ttp) cc_final: 0.8096 (ttp) REVERT: h 140 VAL cc_start: 0.9520 (t) cc_final: 0.9199 (p) REVERT: h 144 TYR cc_start: 0.8920 (m-80) cc_final: 0.8533 (m-80) REVERT: i 61 MET cc_start: 0.8748 (tpp) cc_final: 0.8256 (mmm) REVERT: i 76 ILE cc_start: 0.9642 (mt) cc_final: 0.9197 (tt) REVERT: i 115 ASP cc_start: 0.8701 (t70) cc_final: 0.8467 (t0) REVERT: i 144 TYR cc_start: 0.8809 (m-10) cc_final: 0.8569 (m-10) REVERT: j 17 MET cc_start: 0.9010 (mmm) cc_final: 0.8546 (mmm) REVERT: j 44 MET cc_start: 0.9261 (tmm) cc_final: 0.9040 (tmm) REVERT: j 53 MET cc_start: 0.8594 (tmm) cc_final: 0.8201 (tmm) REVERT: j 87 TYR cc_start: 0.8546 (t80) cc_final: 0.8099 (t80) REVERT: j 91 LEU cc_start: 0.9198 (mp) cc_final: 0.8992 (mt) REVERT: k 26 SER cc_start: 0.9214 (m) cc_final: 0.8993 (p) REVERT: k 37 SER cc_start: 0.9353 (m) cc_final: 0.9109 (p) REVERT: k 53 MET cc_start: 0.8112 (mtp) cc_final: 0.7857 (mtt) REVERT: k 70 LEU cc_start: 0.9324 (tp) cc_final: 0.9005 (mt) REVERT: k 124 GLN cc_start: 0.8350 (tm-30) cc_final: 0.7831 (tm-30) REVERT: k 127 LEU cc_start: 0.8862 (mp) cc_final: 0.8516 (mp) REVERT: k 131 MET cc_start: 0.8259 (ttp) cc_final: 0.8013 (ttp) REVERT: l 23 MET cc_start: 0.9056 (mmm) cc_final: 0.8674 (mmm) REVERT: l 34 THR cc_start: 0.9299 (m) cc_final: 0.9057 (p) REVERT: l 37 SER cc_start: 0.8575 (m) cc_final: 0.8170 (p) REVERT: l 68 TYR cc_start: 0.8768 (m-80) cc_final: 0.8548 (m-80) REVERT: l 97 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9159 (mm) REVERT: l 139 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8710 (mm-30) REVERT: m 78 ASN cc_start: 0.8489 (m-40) cc_final: 0.8211 (m110) REVERT: m 92 GLN cc_start: 0.9214 (mt0) cc_final: 0.8849 (mt0) REVERT: m 155 LYS cc_start: 0.7441 (tptm) cc_final: 0.7092 (tptm) REVERT: n 17 MET cc_start: 0.8175 (mtp) cc_final: 0.7913 (tpp) REVERT: n 23 MET cc_start: 0.9095 (tpt) cc_final: 0.8751 (tpt) REVERT: n 48 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.8279 (mmt90) REVERT: n 87 TYR cc_start: 0.7877 (t80) cc_final: 0.7643 (t80) REVERT: n 139 GLU cc_start: 0.8573 (tp30) cc_final: 0.8317 (tp30) REVERT: o 17 MET cc_start: 0.9219 (mmp) cc_final: 0.8994 (mmm) REVERT: o 37 SER cc_start: 0.8819 (m) cc_final: 0.8381 (t) REVERT: o 82 ASP cc_start: 0.7624 (t0) cc_final: 0.6898 (t70) REVERT: o 87 TYR cc_start: 0.8725 (t80) cc_final: 0.8436 (t80) REVERT: o 92 GLN cc_start: 0.9133 (mm-40) cc_final: 0.8825 (mt0) REVERT: o 124 GLN cc_start: 0.8150 (tp-100) cc_final: 0.7540 (tm-30) REVERT: p 294 ASN cc_start: 0.8298 (m-40) cc_final: 0.7988 (p0) REVERT: p 298 LYS cc_start: 0.8861 (mttt) cc_final: 0.8238 (mmtt) REVERT: p 308 ASN cc_start: 0.8011 (t0) cc_final: 0.7699 (t0) REVERT: p 330 ASN cc_start: 0.9117 (m110) cc_final: 0.8811 (m-40) outliers start: 102 outliers final: 67 residues processed: 806 average time/residue: 0.2955 time to fit residues: 379.2360 Evaluate side-chains 776 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 702 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain a residue 363 THR Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 541 SER Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 567 LEU Chi-restraints excluded: chain a residue 591 ILE Chi-restraints excluded: chain a residue 599 ASP Chi-restraints excluded: chain a residue 726 ILE Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 114 MET Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 154 CYS Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain c residue 423 LEU Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 440 ILE Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 66 THR Chi-restraints excluded: chain d residue 213 GLU Chi-restraints excluded: chain d residue 215 GLU Chi-restraints excluded: chain d residue 230 THR Chi-restraints excluded: chain e residue 19 LEU Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain g residue 17 MET Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 75 LEU Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain h residue 134 ILE Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain i residue 45 SER Chi-restraints excluded: chain j residue 7 ASN Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 102 SER Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain k residue 10 TYR Chi-restraints excluded: chain k residue 11 SER Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain l residue 81 THR Chi-restraints excluded: chain l residue 97 LEU Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain m residue 11 SER Chi-restraints excluded: chain m residue 12 SER Chi-restraints excluded: chain m residue 36 LYS Chi-restraints excluded: chain m residue 45 SER Chi-restraints excluded: chain m residue 108 PHE Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 82 ASP Chi-restraints excluded: chain n residue 98 SER Chi-restraints excluded: chain o residue 20 SER Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 85 THR Chi-restraints excluded: chain o residue 137 PHE Chi-restraints excluded: chain p residue 314 MET Chi-restraints excluded: chain p residue 325 SER Chi-restraints excluded: chain p residue 336 ASP Chi-restraints excluded: chain p residue 343 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 224 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 186 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 242 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 433 GLN ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 735 ASN a 812 GLN ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 168 GLN d 13 ASN d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 78 ASN ** k 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 92 GLN ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21414 Z= 0.222 Angle : 0.634 12.444 29025 Z= 0.325 Chirality : 0.040 0.283 3434 Planarity : 0.004 0.049 3606 Dihedral : 3.964 29.658 2980 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.27 % Allowed : 24.08 % Favored : 70.65 % 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: 2.11 (0.16), residues: 2771 helix: 2.11 (0.11), residues: 2093 sheet: -1.13 (1.25), residues: 18 loop : -0.89 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP e 74 HIS 0.006 0.001 HIS L 81 PHE 0.032 0.002 PHE o 90 TYR 0.041 0.002 TYR g 68 ARG 0.007 0.000 ARG l 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 762 time to evaluate : 2.633 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: H 86 ASN cc_start: 0.9117 (t0) cc_final: 0.8795 (t0) REVERT: H 98 LYS cc_start: 0.8492 (pttt) cc_final: 0.8040 (pttp) REVERT: H 99 ASP cc_start: 0.8632 (t0) cc_final: 0.8306 (t0) REVERT: L 49 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7597 (tm-30) REVERT: L 60 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8095 (t0) REVERT: L 94 LYS cc_start: 0.8334 (ttpt) cc_final: 0.8101 (ttpp) REVERT: a 10 MET cc_start: 0.7318 (mmt) cc_final: 0.6835 (mmm) REVERT: a 399 PHE cc_start: 0.8846 (t80) cc_final: 0.8643 (t80) REVERT: a 423 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8156 (mtm) REVERT: a 429 ARG cc_start: 0.7592 (mtt90) cc_final: 0.6723 (mtp180) REVERT: a 439 MET cc_start: 0.8245 (mmm) cc_final: 0.7957 (mmm) REVERT: a 442 MET cc_start: 0.8314 (ttm) cc_final: 0.8075 (ttm) REVERT: a 453 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8356 (ttp) REVERT: a 532 PHE cc_start: 0.8625 (t80) cc_final: 0.8361 (t80) REVERT: a 538 MET cc_start: 0.8136 (ttp) cc_final: 0.7931 (mtp) REVERT: a 576 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7840 (mm-30) REVERT: a 628 MET cc_start: 0.7982 (mmm) cc_final: 0.7634 (mtt) REVERT: a 660 ARG cc_start: 0.6071 (ttt-90) cc_final: 0.5357 (tmt170) REVERT: a 662 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7658 (mm-40) REVERT: a 759 MET cc_start: 0.7966 (mmp) cc_final: 0.6582 (tpt) REVERT: a 768 ARG cc_start: 0.6283 (mtp180) cc_final: 0.5555 (mtt180) REVERT: a 792 LEU cc_start: 0.8954 (tp) cc_final: 0.8702 (mt) REVERT: a 832 ARG cc_start: 0.7957 (mtm-85) cc_final: 0.7071 (mmm-85) REVERT: b 25 CYS cc_start: 0.9061 (m) cc_final: 0.8596 (m) REVERT: b 47 PHE cc_start: 0.8449 (m-10) cc_final: 0.7890 (m-80) REVERT: b 98 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7258 (mm-30) REVERT: b 103 TYR cc_start: 0.8024 (m-80) cc_final: 0.7560 (m-80) REVERT: b 107 MET cc_start: 0.9275 (mmm) cc_final: 0.8809 (mmm) REVERT: b 116 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7961 (mp0) REVERT: b 137 MET cc_start: 0.9273 (mtp) cc_final: 0.8955 (mtp) REVERT: b 188 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9054 (mm) REVERT: b 200 ARG cc_start: 0.7507 (mtm-85) cc_final: 0.6673 (ptt-90) REVERT: c 419 ILE cc_start: 0.8734 (mt) cc_final: 0.8456 (mm) REVERT: c 421 MET cc_start: 0.8228 (mtm) cc_final: 0.7857 (ttm) REVERT: c 424 LEU cc_start: 0.9283 (mm) cc_final: 0.9032 (mm) REVERT: c 435 TYR cc_start: 0.9137 (t80) cc_final: 0.8901 (t80) REVERT: d 3 PHE cc_start: 0.7667 (m-80) cc_final: 0.7211 (m-80) REVERT: d 40 GLU cc_start: 0.8130 (tt0) cc_final: 0.7816 (tp30) REVERT: d 65 LEU cc_start: 0.9260 (mm) cc_final: 0.9026 (mm) REVERT: d 91 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7616 (tp30) REVERT: d 129 CYS cc_start: 0.8184 (m) cc_final: 0.7928 (m) REVERT: d 213 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7208 (mm-30) REVERT: d 215 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: d 231 GLU cc_start: 0.8251 (pp20) cc_final: 0.7762 (pp20) REVERT: e 47 CYS cc_start: 0.9060 (m) cc_final: 0.8782 (m) REVERT: g 44 MET cc_start: 0.9097 (tmm) cc_final: 0.8888 (tmm) REVERT: g 87 TYR cc_start: 0.8280 (t80) cc_final: 0.7015 (t80) REVERT: h 10 TYR cc_start: 0.8994 (p90) cc_final: 0.8707 (p90) REVERT: h 23 MET cc_start: 0.9136 (tpp) cc_final: 0.8867 (ttm) REVERT: h 64 ILE cc_start: 0.9117 (mt) cc_final: 0.8757 (mt) REVERT: h 65 ILE cc_start: 0.8781 (mt) cc_final: 0.8461 (tp) REVERT: h 68 TYR cc_start: 0.8887 (m-10) cc_final: 0.8243 (m-10) REVERT: h 92 GLN cc_start: 0.9286 (mt0) cc_final: 0.9049 (mm-40) REVERT: h 123 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8728 (mm110) REVERT: h 124 GLN cc_start: 0.7975 (tp-100) cc_final: 0.7586 (tm-30) REVERT: h 151 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8970 (tp) REVERT: i 10 TYR cc_start: 0.5962 (m-80) cc_final: 0.5053 (m-80) REVERT: i 76 ILE cc_start: 0.9621 (mt) cc_final: 0.9249 (tt) REVERT: i 115 ASP cc_start: 0.8600 (t70) cc_final: 0.8293 (t0) REVERT: i 144 TYR cc_start: 0.8801 (m-10) cc_final: 0.8588 (m-10) REVERT: j 10 TYR cc_start: 0.8178 (p90) cc_final: 0.7470 (p90) REVERT: j 17 MET cc_start: 0.9010 (mmm) cc_final: 0.8652 (mmm) REVERT: j 44 MET cc_start: 0.9282 (tmm) cc_final: 0.8990 (tmm) REVERT: j 48 ARG cc_start: 0.8985 (mtp85) cc_final: 0.8751 (mtp85) REVERT: j 53 MET cc_start: 0.8591 (tmm) cc_final: 0.8202 (tmm) REVERT: j 87 TYR cc_start: 0.8539 (t80) cc_final: 0.8044 (t80) REVERT: j 91 LEU cc_start: 0.9241 (mp) cc_final: 0.8982 (mt) REVERT: k 53 MET cc_start: 0.8149 (mtp) cc_final: 0.7805 (mtt) REVERT: k 68 TYR cc_start: 0.8428 (m-10) cc_final: 0.7919 (m-80) REVERT: k 123 GLN cc_start: 0.8548 (mt0) cc_final: 0.8099 (tp40) REVERT: k 124 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8041 (tm-30) REVERT: k 127 LEU cc_start: 0.9008 (mp) cc_final: 0.8766 (mp) REVERT: k 131 MET cc_start: 0.8340 (ttp) cc_final: 0.8060 (ttp) REVERT: l 34 THR cc_start: 0.9306 (m) cc_final: 0.9068 (p) REVERT: l 37 SER cc_start: 0.8593 (m) cc_final: 0.8156 (p) REVERT: l 97 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9122 (mm) REVERT: l 108 PHE cc_start: 0.8826 (m-80) cc_final: 0.8543 (m-80) REVERT: l 136 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8920 (tp) REVERT: m 26 SER cc_start: 0.9512 (OUTLIER) cc_final: 0.9261 (p) REVERT: m 78 ASN cc_start: 0.8536 (m-40) cc_final: 0.8239 (m110) REVERT: m 92 GLN cc_start: 0.9204 (mt0) cc_final: 0.8970 (mt0) REVERT: m 123 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7523 (mp-120) REVERT: m 155 LYS cc_start: 0.7397 (tptm) cc_final: 0.7058 (tptm) REVERT: n 23 MET cc_start: 0.9156 (tpt) cc_final: 0.8857 (tpt) REVERT: n 28 MET cc_start: 0.8614 (mmm) cc_final: 0.8368 (mmm) REVERT: n 32 TYR cc_start: 0.7869 (t80) cc_final: 0.7480 (t80) REVERT: n 47 MET cc_start: 0.8631 (tpp) cc_final: 0.8361 (mmm) REVERT: n 48 ARG cc_start: 0.8739 (mmm-85) cc_final: 0.8490 (mmt90) REVERT: n 87 TYR cc_start: 0.7897 (t80) cc_final: 0.7658 (t80) REVERT: o 37 SER cc_start: 0.8877 (m) cc_final: 0.8440 (t) REVERT: o 61 MET cc_start: 0.8796 (mmt) cc_final: 0.7966 (mmt) REVERT: o 82 ASP cc_start: 0.7555 (t0) cc_final: 0.6857 (t70) REVERT: o 124 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7620 (tm-30) REVERT: p 294 ASN cc_start: 0.8308 (m-40) cc_final: 0.7994 (p0) REVERT: p 298 LYS cc_start: 0.8953 (mttt) cc_final: 0.8281 (mmtt) REVERT: p 308 ASN cc_start: 0.7890 (t0) cc_final: 0.7561 (t0) REVERT: p 330 ASN cc_start: 0.9125 (m110) cc_final: 0.8903 (m-40) outliers start: 113 outliers final: 70 residues processed: 816 average time/residue: 0.2989 time to fit residues: 390.7648 Evaluate side-chains 769 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 688 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain a residue 363 THR Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 458 ILE Chi-restraints excluded: chain a residue 530 LEU Chi-restraints excluded: chain a residue 541 SER Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 785 THR Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 114 MET Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 154 CYS Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 440 ILE Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 66 THR Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 213 GLU Chi-restraints excluded: chain d residue 215 GLU Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain g residue 17 MET Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 80 LEU Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 134 ILE Chi-restraints excluded: chain h residue 151 ILE Chi-restraints excluded: chain h residue 153 SER Chi-restraints excluded: chain i residue 21 SER Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain i residue 45 SER Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain j residue 7 ASN Chi-restraints excluded: chain j residue 9 GLU Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 102 SER Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain j residue 147 ILE Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain l residue 81 THR Chi-restraints excluded: chain l residue 97 LEU Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 137 PHE Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 11 SER Chi-restraints excluded: chain m residue 12 SER Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain m residue 36 LYS Chi-restraints excluded: chain m residue 45 SER Chi-restraints excluded: chain m residue 108 PHE Chi-restraints excluded: chain m residue 123 GLN Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 82 ASP Chi-restraints excluded: chain n residue 98 SER Chi-restraints excluded: chain n residue 121 THR Chi-restraints excluded: chain o residue 20 SER Chi-restraints excluded: chain o residue 85 THR Chi-restraints excluded: chain o residue 133 LEU Chi-restraints excluded: chain o residue 137 PHE Chi-restraints excluded: chain p residue 314 MET Chi-restraints excluded: chain p residue 325 SER Chi-restraints excluded: chain p residue 336 ASP Chi-restraints excluded: chain p residue 343 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 90 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 269 optimal weight: 0.9990 chunk 224 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 33 HIS L 82 GLN ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 433 GLN ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 812 GLN ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 346 ASN ** k 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21414 Z= 0.247 Angle : 0.662 11.736 29025 Z= 0.340 Chirality : 0.041 0.266 3434 Planarity : 0.004 0.048 3606 Dihedral : 4.002 30.865 2980 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.46 % Allowed : 25.24 % Favored : 69.30 % 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: 2.01 (0.16), residues: 2771 helix: 2.04 (0.11), residues: 2096 sheet: -1.28 (1.26), residues: 18 loop : -0.92 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 479 HIS 0.006 0.001 HIS L 81 PHE 0.041 0.002 PHE h 90 TYR 0.032 0.002 TYR g 68 ARG 0.005 0.000 ARG i 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 731 time to evaluate : 2.519 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: H 86 ASN cc_start: 0.9143 (t0) cc_final: 0.8844 (t0) REVERT: H 99 ASP cc_start: 0.8663 (t0) cc_final: 0.8362 (t0) REVERT: L 49 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7647 (tm-30) REVERT: L 60 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8184 (t0) REVERT: L 63 ILE cc_start: 0.8421 (mt) cc_final: 0.8083 (tt) REVERT: L 94 LYS cc_start: 0.8378 (ttpt) cc_final: 0.8171 (ttpp) REVERT: a 10 MET cc_start: 0.7265 (mmt) cc_final: 0.6774 (mmm) REVERT: a 399 PHE cc_start: 0.8943 (t80) cc_final: 0.8718 (t80) REVERT: a 401 PHE cc_start: 0.8580 (t80) cc_final: 0.8326 (t80) REVERT: a 423 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8164 (mtm) REVERT: a 429 ARG cc_start: 0.7683 (mtt90) cc_final: 0.6584 (mtp180) REVERT: a 439 MET cc_start: 0.8284 (mmm) cc_final: 0.8015 (mmm) REVERT: a 453 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8241 (ttp) REVERT: a 538 MET cc_start: 0.8186 (ttp) cc_final: 0.7984 (mtp) REVERT: a 544 LEU cc_start: 0.8913 (tp) cc_final: 0.8690 (tp) REVERT: a 576 GLU cc_start: 0.8545 (mt-10) cc_final: 0.7712 (mm-30) REVERT: a 580 MET cc_start: 0.8796 (ttm) cc_final: 0.8529 (tpp) REVERT: a 628 MET cc_start: 0.8184 (mmm) cc_final: 0.7179 (mtt) REVERT: a 660 ARG cc_start: 0.6069 (ttt-90) cc_final: 0.5366 (tmt170) REVERT: a 662 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7699 (mm-40) REVERT: a 751 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8879 (mm-40) REVERT: a 759 MET cc_start: 0.8032 (mmp) cc_final: 0.6681 (tpt) REVERT: a 768 ARG cc_start: 0.6336 (mtp180) cc_final: 0.5683 (mtt180) REVERT: a 792 LEU cc_start: 0.8985 (tp) cc_final: 0.8746 (mt) REVERT: a 832 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7127 (mmm-85) REVERT: b 25 CYS cc_start: 0.9030 (m) cc_final: 0.8566 (m) REVERT: b 30 ASP cc_start: 0.8551 (t70) cc_final: 0.8289 (t70) REVERT: b 47 PHE cc_start: 0.8452 (m-10) cc_final: 0.7845 (m-80) REVERT: b 98 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7330 (mm-30) REVERT: b 103 TYR cc_start: 0.7942 (m-80) cc_final: 0.7596 (m-80) REVERT: b 107 MET cc_start: 0.9253 (mmm) cc_final: 0.8969 (mmm) REVERT: b 116 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7925 (mp0) REVERT: b 132 HIS cc_start: 0.9288 (t-90) cc_final: 0.8911 (t-90) REVERT: b 137 MET cc_start: 0.9279 (mtp) cc_final: 0.9026 (mtp) REVERT: b 188 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9031 (mm) REVERT: b 200 ARG cc_start: 0.7754 (mtm-85) cc_final: 0.6944 (ptt-90) REVERT: c 419 ILE cc_start: 0.8762 (mt) cc_final: 0.8475 (mm) REVERT: c 421 MET cc_start: 0.8238 (mtm) cc_final: 0.7819 (ttm) REVERT: c 424 LEU cc_start: 0.9212 (mm) cc_final: 0.8907 (mm) REVERT: c 435 TYR cc_start: 0.9175 (t80) cc_final: 0.8938 (t80) REVERT: d 40 GLU cc_start: 0.8174 (tt0) cc_final: 0.7908 (tp30) REVERT: d 65 LEU cc_start: 0.9253 (mm) cc_final: 0.9041 (mm) REVERT: d 91 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7662 (tp30) REVERT: d 129 CYS cc_start: 0.8165 (m) cc_final: 0.7926 (m) REVERT: d 138 MET cc_start: 0.8161 (tpp) cc_final: 0.7925 (tpp) REVERT: d 213 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7135 (mm-30) REVERT: d 215 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8323 (tt0) REVERT: e 47 CYS cc_start: 0.9124 (m) cc_final: 0.8811 (m) REVERT: g 13 PHE cc_start: 0.7796 (t80) cc_final: 0.7316 (t80) REVERT: g 44 MET cc_start: 0.9109 (tmm) cc_final: 0.8853 (tmm) REVERT: g 87 TYR cc_start: 0.8347 (t80) cc_final: 0.6953 (t80) REVERT: h 10 TYR cc_start: 0.9035 (p90) cc_final: 0.8780 (p90) REVERT: h 17 MET cc_start: 0.8954 (tpp) cc_final: 0.8597 (tpp) REVERT: h 23 MET cc_start: 0.9131 (tpp) cc_final: 0.8880 (ttm) REVERT: h 64 ILE cc_start: 0.9249 (mt) cc_final: 0.8942 (mt) REVERT: h 68 TYR cc_start: 0.8977 (m-10) cc_final: 0.8409 (m-10) REVERT: h 90 PHE cc_start: 0.9104 (m-80) cc_final: 0.8657 (m-80) REVERT: h 92 GLN cc_start: 0.9284 (mt0) cc_final: 0.9001 (mm-40) REVERT: h 123 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8740 (mm110) REVERT: h 124 GLN cc_start: 0.8023 (tp-100) cc_final: 0.7665 (tm-30) REVERT: h 131 MET cc_start: 0.8444 (ttp) cc_final: 0.8231 (ttp) REVERT: h 144 TYR cc_start: 0.8953 (m-80) cc_final: 0.8593 (m-80) REVERT: h 151 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8997 (tp) REVERT: i 10 TYR cc_start: 0.5953 (m-80) cc_final: 0.5078 (m-80) REVERT: i 76 ILE cc_start: 0.9627 (mt) cc_final: 0.9303 (tt) REVERT: i 108 PHE cc_start: 0.8447 (m-10) cc_final: 0.8247 (m-80) REVERT: i 115 ASP cc_start: 0.8666 (t70) cc_final: 0.8325 (t0) REVERT: i 124 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8351 (tm-30) REVERT: j 10 TYR cc_start: 0.8235 (p90) cc_final: 0.7466 (p90) REVERT: j 17 MET cc_start: 0.9035 (mmm) cc_final: 0.8503 (mmm) REVERT: j 44 MET cc_start: 0.9288 (tmm) cc_final: 0.9002 (tmm) REVERT: j 48 ARG cc_start: 0.9007 (mtp85) cc_final: 0.8802 (mtp85) REVERT: j 53 MET cc_start: 0.8475 (tmm) cc_final: 0.8076 (tmm) REVERT: j 87 TYR cc_start: 0.8484 (t80) cc_final: 0.8096 (t80) REVERT: j 91 LEU cc_start: 0.9249 (mp) cc_final: 0.8936 (mt) REVERT: k 53 MET cc_start: 0.8180 (mtp) cc_final: 0.7835 (mtt) REVERT: k 68 TYR cc_start: 0.8472 (m-10) cc_final: 0.7944 (m-80) REVERT: k 123 GLN cc_start: 0.8575 (mt0) cc_final: 0.8129 (tp40) REVERT: k 124 GLN cc_start: 0.8461 (tm-30) cc_final: 0.7912 (tm-30) REVERT: k 127 LEU cc_start: 0.9015 (mp) cc_final: 0.8579 (mp) REVERT: k 131 MET cc_start: 0.8371 (ttp) cc_final: 0.8094 (ttp) REVERT: k 143 LEU cc_start: 0.9390 (tp) cc_final: 0.9134 (tt) REVERT: l 34 THR cc_start: 0.9311 (m) cc_final: 0.9029 (p) REVERT: l 37 SER cc_start: 0.8625 (m) cc_final: 0.8194 (p) REVERT: l 97 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9084 (mm) REVERT: l 136 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8893 (tp) REVERT: m 26 SER cc_start: 0.9511 (OUTLIER) cc_final: 0.9260 (p) REVERT: m 54 LYS cc_start: 0.7393 (mptt) cc_final: 0.7172 (mppt) REVERT: m 78 ASN cc_start: 0.8657 (m-40) cc_final: 0.8357 (m110) REVERT: m 92 GLN cc_start: 0.9191 (mt0) cc_final: 0.8987 (mt0) REVERT: m 123 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7497 (mp-120) REVERT: n 17 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7839 (mtp) REVERT: n 23 MET cc_start: 0.9197 (tpt) cc_final: 0.8889 (tpt) REVERT: n 28 MET cc_start: 0.8632 (mmm) cc_final: 0.8393 (mmm) REVERT: n 47 MET cc_start: 0.8635 (tpp) cc_final: 0.8371 (mmm) REVERT: n 48 ARG cc_start: 0.8810 (mmm-85) cc_final: 0.8551 (mmt90) REVERT: n 144 TYR cc_start: 0.9031 (m-80) cc_final: 0.8820 (m-80) REVERT: o 37 SER cc_start: 0.8892 (m) cc_final: 0.8439 (t) REVERT: o 61 MET cc_start: 0.8881 (mmt) cc_final: 0.8076 (mmt) REVERT: o 124 GLN cc_start: 0.8245 (tp-100) cc_final: 0.7682 (tm-30) REVERT: o 135 LEU cc_start: 0.9187 (mm) cc_final: 0.8833 (mm) REVERT: p 294 ASN cc_start: 0.8320 (m-40) cc_final: 0.8000 (p0) REVERT: p 298 LYS cc_start: 0.9006 (mttt) cc_final: 0.8342 (mmtt) REVERT: p 308 ASN cc_start: 0.7765 (t0) cc_final: 0.7421 (t0) REVERT: p 330 ASN cc_start: 0.9154 (m110) cc_final: 0.8945 (m-40) outliers start: 117 outliers final: 78 residues processed: 787 average time/residue: 0.3034 time to fit residues: 381.1275 Evaluate side-chains 785 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 695 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 82 GLN Chi-restraints excluded: chain a residue 363 THR Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 530 LEU Chi-restraints excluded: chain a residue 541 SER Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 813 ASN Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 70 TYR Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 154 CYS Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain c residue 440 ILE Chi-restraints excluded: chain c residue 442 SER Chi-restraints excluded: chain d residue 11 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 66 THR Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 213 GLU Chi-restraints excluded: chain d residue 215 GLU Chi-restraints excluded: chain d residue 230 THR Chi-restraints excluded: chain e residue 19 LEU Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 80 LEU Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 102 SER Chi-restraints excluded: chain h residue 134 ILE Chi-restraints excluded: chain h residue 151 ILE Chi-restraints excluded: chain i residue 21 SER Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain i residue 45 SER Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain j residue 7 ASN Chi-restraints excluded: chain j residue 9 GLU Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 102 SER Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain j residue 147 ILE Chi-restraints excluded: chain k residue 11 SER Chi-restraints excluded: chain k residue 20 SER Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain l residue 81 THR Chi-restraints excluded: chain l residue 97 LEU Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 137 PHE Chi-restraints excluded: chain m residue 11 SER Chi-restraints excluded: chain m residue 12 SER Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain m residue 36 LYS Chi-restraints excluded: chain m residue 45 SER Chi-restraints excluded: chain m residue 108 PHE Chi-restraints excluded: chain m residue 123 GLN Chi-restraints excluded: chain n residue 17 MET Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 82 ASP Chi-restraints excluded: chain n residue 98 SER Chi-restraints excluded: chain n residue 121 THR Chi-restraints excluded: chain o residue 20 SER Chi-restraints excluded: chain o residue 85 THR Chi-restraints excluded: chain o residue 133 LEU Chi-restraints excluded: chain o residue 136 ILE Chi-restraints excluded: chain o residue 137 PHE Chi-restraints excluded: chain p residue 314 MET Chi-restraints excluded: chain p residue 325 SER Chi-restraints excluded: chain p residue 336 ASP Chi-restraints excluded: chain p residue 343 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 260 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 152 optimal weight: 0.7980 chunk 227 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 268 optimal weight: 0.6980 chunk 168 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 33 HIS ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 812 GLN ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21414 Z= 0.214 Angle : 0.670 11.097 29025 Z= 0.339 Chirality : 0.041 0.294 3434 Planarity : 0.004 0.049 3606 Dihedral : 3.985 32.180 2980 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.99 % Allowed : 26.55 % Favored : 68.46 % 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: 1.98 (0.16), residues: 2771 helix: 2.01 (0.11), residues: 2098 sheet: -1.11 (1.28), residues: 18 loop : -0.92 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP e 74 HIS 0.006 0.001 HIS L 81 PHE 0.039 0.002 PHE h 90 TYR 0.034 0.002 TYR g 68 ARG 0.006 0.000 ARG j 126 *********************** 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 845 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 738 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASN cc_start: 0.9238 (t0) cc_final: 0.8954 (t0) REVERT: H 99 ASP cc_start: 0.8739 (t0) cc_final: 0.8363 (t0) REVERT: L 49 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7627 (tm-30) REVERT: L 60 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8133 (t0) REVERT: L 63 ILE cc_start: 0.8346 (mt) cc_final: 0.8017 (tt) REVERT: L 94 LYS cc_start: 0.8342 (ttpt) cc_final: 0.8137 (ttpp) REVERT: a 10 MET cc_start: 0.7156 (mmt) cc_final: 0.6676 (mmm) REVERT: a 399 PHE cc_start: 0.8900 (t80) cc_final: 0.8679 (t80) REVERT: a 401 PHE cc_start: 0.8552 (t80) cc_final: 0.8305 (t80) REVERT: a 423 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8197 (mtm) REVERT: a 429 ARG cc_start: 0.7697 (mtt90) cc_final: 0.6574 (mtp180) REVERT: a 439 MET cc_start: 0.8279 (mmm) cc_final: 0.8042 (mmm) REVERT: a 453 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8208 (ttp) REVERT: a 479 TRP cc_start: 0.6719 (t-100) cc_final: 0.6504 (t-100) REVERT: a 538 MET cc_start: 0.8024 (ttp) cc_final: 0.7822 (mtp) REVERT: a 544 LEU cc_start: 0.8917 (tp) cc_final: 0.8690 (tp) REVERT: a 576 GLU cc_start: 0.8536 (mt-10) cc_final: 0.7945 (mm-30) REVERT: a 580 MET cc_start: 0.8706 (ttm) cc_final: 0.8482 (tpp) REVERT: a 660 ARG cc_start: 0.6051 (ttt-90) cc_final: 0.5391 (tmt170) REVERT: a 662 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7488 (mm110) REVERT: a 759 MET cc_start: 0.8057 (mmp) cc_final: 0.6699 (tpt) REVERT: a 768 ARG cc_start: 0.6290 (mtp180) cc_final: 0.5692 (mtt180) REVERT: a 792 LEU cc_start: 0.8997 (tp) cc_final: 0.8763 (mt) REVERT: a 832 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.7124 (mmm-85) REVERT: b 25 CYS cc_start: 0.9057 (m) cc_final: 0.8576 (m) REVERT: b 47 PHE cc_start: 0.8427 (m-10) cc_final: 0.7806 (m-80) REVERT: b 89 LYS cc_start: 0.6250 (mtpp) cc_final: 0.5990 (mtpp) REVERT: b 98 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7268 (mm-30) REVERT: b 103 TYR cc_start: 0.7993 (m-80) cc_final: 0.7706 (m-80) REVERT: b 116 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8107 (mp0) REVERT: b 132 HIS cc_start: 0.9311 (t-90) cc_final: 0.8767 (t-90) REVERT: b 188 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9015 (mm) REVERT: b 200 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.6914 (ptt-90) REVERT: c 419 ILE cc_start: 0.8756 (mt) cc_final: 0.8466 (mm) REVERT: c 421 MET cc_start: 0.8295 (mtm) cc_final: 0.7851 (ttm) REVERT: c 424 LEU cc_start: 0.9217 (mm) cc_final: 0.8888 (mm) REVERT: d 91 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7654 (tp30) REVERT: d 105 MET cc_start: 0.8079 (ttp) cc_final: 0.7662 (ttm) REVERT: d 129 CYS cc_start: 0.8126 (m) cc_final: 0.7894 (m) REVERT: d 138 MET cc_start: 0.8335 (tpp) cc_final: 0.8085 (tpp) REVERT: d 213 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7091 (mm-30) REVERT: d 215 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8277 (tt0) REVERT: d 325 GLU cc_start: 0.7827 (tt0) cc_final: 0.7498 (tm-30) REVERT: e 4 HIS cc_start: 0.7902 (m-70) cc_final: 0.7635 (m-70) REVERT: e 47 CYS cc_start: 0.9097 (m) cc_final: 0.8795 (m) REVERT: g 44 MET cc_start: 0.9122 (tmm) cc_final: 0.8873 (tmm) REVERT: g 87 TYR cc_start: 0.8337 (t80) cc_final: 0.6958 (t80) REVERT: h 10 TYR cc_start: 0.8961 (p90) cc_final: 0.8718 (p90) REVERT: h 23 MET cc_start: 0.9169 (tpp) cc_final: 0.8648 (ttm) REVERT: h 64 ILE cc_start: 0.9246 (mt) cc_final: 0.8898 (mt) REVERT: h 65 ILE cc_start: 0.8665 (mt) cc_final: 0.8314 (tp) REVERT: h 68 TYR cc_start: 0.8978 (m-10) cc_final: 0.8325 (m-10) REVERT: h 90 PHE cc_start: 0.9029 (m-80) cc_final: 0.8402 (m-80) REVERT: h 92 GLN cc_start: 0.9294 (mt0) cc_final: 0.8974 (mm-40) REVERT: h 123 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8736 (mm110) REVERT: h 124 GLN cc_start: 0.7980 (tp-100) cc_final: 0.7611 (tm-30) REVERT: h 144 TYR cc_start: 0.8930 (m-80) cc_final: 0.8579 (m-80) REVERT: h 151 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8981 (tp) REVERT: i 10 TYR cc_start: 0.5950 (m-80) cc_final: 0.5081 (m-80) REVERT: i 76 ILE cc_start: 0.9608 (mt) cc_final: 0.9331 (tt) REVERT: i 115 ASP cc_start: 0.8628 (t70) cc_final: 0.8342 (t0) REVERT: i 144 TYR cc_start: 0.8828 (m-10) cc_final: 0.8555 (m-80) REVERT: j 10 TYR cc_start: 0.8215 (p90) cc_final: 0.7581 (p90) REVERT: j 17 MET cc_start: 0.8996 (mmm) cc_final: 0.8610 (mmm) REVERT: j 44 MET cc_start: 0.9290 (tmm) cc_final: 0.8974 (tmm) REVERT: j 48 ARG cc_start: 0.9000 (mtp85) cc_final: 0.8786 (mtp85) REVERT: j 53 MET cc_start: 0.8407 (tmm) cc_final: 0.8036 (tmm) REVERT: j 87 TYR cc_start: 0.8442 (t80) cc_final: 0.8062 (t80) REVERT: j 91 LEU cc_start: 0.9239 (mp) cc_final: 0.8921 (mt) REVERT: j 134 ILE cc_start: 0.9071 (mm) cc_final: 0.8685 (mm) REVERT: k 13 PHE cc_start: 0.8761 (t80) cc_final: 0.8476 (t80) REVERT: k 53 MET cc_start: 0.8236 (mtp) cc_final: 0.7898 (mtt) REVERT: k 68 TYR cc_start: 0.8439 (m-10) cc_final: 0.7817 (m-80) REVERT: k 92 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8056 (mt0) REVERT: k 123 GLN cc_start: 0.8531 (mt0) cc_final: 0.8177 (tp40) REVERT: k 124 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8076 (tm-30) REVERT: k 127 LEU cc_start: 0.8991 (mp) cc_final: 0.8718 (mp) REVERT: k 131 MET cc_start: 0.8349 (ttp) cc_final: 0.8035 (ttp) REVERT: k 143 LEU cc_start: 0.9354 (tp) cc_final: 0.8723 (tp) REVERT: l 34 THR cc_start: 0.9308 (m) cc_final: 0.9040 (p) REVERT: l 37 SER cc_start: 0.8588 (m) cc_final: 0.8160 (p) REVERT: l 97 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9052 (mm) REVERT: l 108 PHE cc_start: 0.8847 (m-80) cc_final: 0.8512 (m-80) REVERT: l 136 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8834 (tp) REVERT: m 7 ASN cc_start: 0.8881 (m-40) cc_final: 0.8567 (m-40) REVERT: m 26 SER cc_start: 0.9501 (OUTLIER) cc_final: 0.9239 (p) REVERT: m 54 LYS cc_start: 0.7364 (mptt) cc_final: 0.7154 (mppt) REVERT: m 78 ASN cc_start: 0.8662 (m-40) cc_final: 0.8356 (m110) REVERT: m 123 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7438 (mp-120) REVERT: m 155 LYS cc_start: 0.7387 (tptm) cc_final: 0.7048 (tptm) REVERT: n 17 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7804 (mtp) REVERT: n 23 MET cc_start: 0.9184 (tpt) cc_final: 0.8878 (tpt) REVERT: n 28 MET cc_start: 0.8630 (mmm) cc_final: 0.8403 (mmm) REVERT: n 47 MET cc_start: 0.8611 (tpp) cc_final: 0.8337 (mmm) REVERT: n 48 ARG cc_start: 0.8765 (mmm-85) cc_final: 0.8555 (mmt90) REVERT: n 87 TYR cc_start: 0.7896 (t80) cc_final: 0.7660 (t80) REVERT: n 97 LEU cc_start: 0.8887 (mm) cc_final: 0.8646 (mm) REVERT: o 25 PHE cc_start: 0.8671 (m-80) cc_final: 0.8242 (m-80) REVERT: o 37 SER cc_start: 0.8805 (m) cc_final: 0.8360 (t) REVERT: o 61 MET cc_start: 0.8864 (mmt) cc_final: 0.8041 (mmt) REVERT: o 82 ASP cc_start: 0.7651 (t0) cc_final: 0.7050 (t70) REVERT: o 124 GLN cc_start: 0.8239 (tp-100) cc_final: 0.7667 (tm-30) REVERT: p 294 ASN cc_start: 0.8465 (m-40) cc_final: 0.8065 (p0) REVERT: p 298 LYS cc_start: 0.8986 (mttt) cc_final: 0.8338 (mmtt) REVERT: p 308 ASN cc_start: 0.7752 (t0) cc_final: 0.7422 (t0) outliers start: 107 outliers final: 77 residues processed: 789 average time/residue: 0.2924 time to fit residues: 367.7044 Evaluate side-chains 782 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 693 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 82 GLN Chi-restraints excluded: chain a residue 363 THR Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 530 LEU Chi-restraints excluded: chain a residue 541 SER Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 813 ASN Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 70 TYR Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 154 CYS Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain c residue 426 THR Chi-restraints excluded: chain c residue 440 ILE Chi-restraints excluded: chain d residue 11 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 66 THR Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 166 ASP Chi-restraints excluded: chain d residue 213 GLU Chi-restraints excluded: chain d residue 215 GLU Chi-restraints excluded: chain d residue 230 THR Chi-restraints excluded: chain e residue 19 LEU Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain e residue 76 VAL Chi-restraints excluded: chain g residue 21 SER Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 80 LEU Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain h residue 102 SER Chi-restraints excluded: chain h residue 134 ILE Chi-restraints excluded: chain h residue 151 ILE Chi-restraints excluded: chain i residue 21 SER Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain i residue 45 SER Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain j residue 7 ASN Chi-restraints excluded: chain j residue 9 GLU Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 102 SER Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain j residue 147 ILE Chi-restraints excluded: chain k residue 11 SER Chi-restraints excluded: chain k residue 20 SER Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain l residue 81 THR Chi-restraints excluded: chain l residue 97 LEU Chi-restraints excluded: chain l residue 102 SER Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 137 PHE Chi-restraints excluded: chain m residue 11 SER Chi-restraints excluded: chain m residue 12 SER Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain m residue 36 LYS Chi-restraints excluded: chain m residue 45 SER Chi-restraints excluded: chain m residue 108 PHE Chi-restraints excluded: chain m residue 123 GLN Chi-restraints excluded: chain n residue 17 MET Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 82 ASP Chi-restraints excluded: chain n residue 98 SER Chi-restraints excluded: chain n residue 121 THR Chi-restraints excluded: chain o residue 20 SER Chi-restraints excluded: chain o residue 85 THR Chi-restraints excluded: chain o residue 133 LEU Chi-restraints excluded: chain o residue 136 ILE Chi-restraints excluded: chain o residue 137 PHE Chi-restraints excluded: chain p residue 314 MET Chi-restraints excluded: chain p residue 325 SER Chi-restraints excluded: chain p residue 343 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 166 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 81 optimal weight: 0.0050 chunk 52 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 183 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 244 optimal weight: 0.0030 overall best weight: 0.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 33 HIS L 82 GLN ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 338 GLN ** m 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 6 ASN n 92 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21414 Z= 0.206 Angle : 0.681 12.143 29025 Z= 0.342 Chirality : 0.041 0.361 3434 Planarity : 0.004 0.045 3606 Dihedral : 4.002 32.816 2980 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.83 % Allowed : 28.56 % Favored : 67.62 % 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: 1.97 (0.16), residues: 2771 helix: 1.99 (0.11), residues: 2097 sheet: -1.28 (1.27), residues: 18 loop : -0.86 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP e 74 HIS 0.004 0.001 HIS L 81 PHE 0.033 0.002 PHE h 90 TYR 0.035 0.002 TYR g 68 ARG 0.007 0.000 ARG d 219 *********************** 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 813 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 731 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASN cc_start: 0.9242 (t0) cc_final: 0.8956 (t0) REVERT: H 92 VAL cc_start: 0.9297 (t) cc_final: 0.8919 (m) REVERT: H 99 ASP cc_start: 0.8709 (t0) cc_final: 0.8259 (t0) REVERT: L 27 GLU cc_start: 0.8259 (pt0) cc_final: 0.7953 (tt0) REVERT: L 49 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7597 (tm-30) REVERT: L 60 ASP cc_start: 0.8446 (m-30) cc_final: 0.8013 (t0) REVERT: L 63 ILE cc_start: 0.8296 (mt) cc_final: 0.7954 (tt) REVERT: L 94 LYS cc_start: 0.8363 (ttpt) cc_final: 0.8146 (ttpp) REVERT: L 110 LYS cc_start: 0.8042 (ttmt) cc_final: 0.7614 (tmtt) REVERT: a 10 MET cc_start: 0.7011 (mmt) cc_final: 0.6507 (mmm) REVERT: a 399 PHE cc_start: 0.8857 (t80) cc_final: 0.8648 (t80) REVERT: a 401 PHE cc_start: 0.8547 (t80) cc_final: 0.8286 (t80) REVERT: a 423 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8166 (mtm) REVERT: a 429 ARG cc_start: 0.7750 (mtt90) cc_final: 0.6550 (mtp180) REVERT: a 453 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8107 (ttp) REVERT: a 576 GLU cc_start: 0.8505 (mt-10) cc_final: 0.7974 (mm-30) REVERT: a 660 ARG cc_start: 0.6015 (ttt-90) cc_final: 0.5373 (tmt170) REVERT: a 662 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7461 (mm110) REVERT: a 759 MET cc_start: 0.8086 (mmp) cc_final: 0.6667 (tpt) REVERT: a 768 ARG cc_start: 0.6267 (mtp180) cc_final: 0.5678 (mtt180) REVERT: a 792 LEU cc_start: 0.8960 (tp) cc_final: 0.8734 (mt) REVERT: a 832 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7168 (mmm-85) REVERT: b 25 CYS cc_start: 0.8969 (m) cc_final: 0.8477 (m) REVERT: b 47 PHE cc_start: 0.8335 (m-10) cc_final: 0.7826 (m-80) REVERT: b 98 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7194 (mm-30) REVERT: b 103 TYR cc_start: 0.8042 (m-80) cc_final: 0.7763 (m-80) REVERT: b 116 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8063 (mp0) REVERT: b 132 HIS cc_start: 0.9253 (t-90) cc_final: 0.8710 (t-90) REVERT: b 188 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8997 (mm) REVERT: b 200 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.6805 (ptt-90) REVERT: c 419 ILE cc_start: 0.8767 (mt) cc_final: 0.8497 (mm) REVERT: c 421 MET cc_start: 0.8264 (mtm) cc_final: 0.7856 (ttm) REVERT: c 424 LEU cc_start: 0.9223 (mm) cc_final: 0.8857 (mm) REVERT: c 429 MET cc_start: 0.8810 (ptm) cc_final: 0.8579 (ptm) REVERT: d 28 LEU cc_start: 0.9099 (mt) cc_final: 0.8800 (mp) REVERT: d 88 HIS cc_start: 0.7761 (m170) cc_final: 0.7395 (m170) REVERT: d 91 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7746 (tp30) REVERT: d 105 MET cc_start: 0.7987 (ttp) cc_final: 0.7616 (ttm) REVERT: d 129 CYS cc_start: 0.8087 (m) cc_final: 0.7838 (m) REVERT: d 138 MET cc_start: 0.8400 (tpp) cc_final: 0.8143 (tpp) REVERT: d 208 MET cc_start: 0.8848 (tpp) cc_final: 0.8037 (tpp) REVERT: d 213 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7104 (mm-30) REVERT: d 215 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: d 325 GLU cc_start: 0.7755 (tt0) cc_final: 0.7439 (tm-30) REVERT: e 47 CYS cc_start: 0.9066 (m) cc_final: 0.8780 (m) REVERT: g 44 MET cc_start: 0.9111 (tmm) cc_final: 0.8842 (tmm) REVERT: g 87 TYR cc_start: 0.8337 (t80) cc_final: 0.6921 (t80) REVERT: h 17 MET cc_start: 0.8936 (tpp) cc_final: 0.8565 (tpp) REVERT: h 23 MET cc_start: 0.9152 (tpp) cc_final: 0.8895 (ttm) REVERT: h 64 ILE cc_start: 0.9260 (mt) cc_final: 0.8938 (mt) REVERT: h 65 ILE cc_start: 0.8563 (mt) cc_final: 0.8214 (tp) REVERT: h 68 TYR cc_start: 0.8935 (m-10) cc_final: 0.8343 (m-10) REVERT: h 90 PHE cc_start: 0.8936 (m-80) cc_final: 0.8240 (m-80) REVERT: h 92 GLN cc_start: 0.9270 (mt0) cc_final: 0.8915 (mm-40) REVERT: h 123 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8748 (mm110) REVERT: h 124 GLN cc_start: 0.7959 (tp-100) cc_final: 0.7628 (tm-30) REVERT: h 144 TYR cc_start: 0.8930 (m-80) cc_final: 0.8610 (m-80) REVERT: h 151 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.9012 (tp) REVERT: i 10 TYR cc_start: 0.5966 (m-80) cc_final: 0.5105 (m-80) REVERT: i 76 ILE cc_start: 0.9600 (mt) cc_final: 0.9333 (tt) REVERT: i 115 ASP cc_start: 0.8568 (t70) cc_final: 0.8290 (t0) REVERT: i 144 TYR cc_start: 0.8783 (m-10) cc_final: 0.8534 (m-80) REVERT: j 10 TYR cc_start: 0.8083 (p90) cc_final: 0.7403 (p90) REVERT: j 17 MET cc_start: 0.9037 (mmm) cc_final: 0.8517 (mmm) REVERT: j 44 MET cc_start: 0.9284 (tmm) cc_final: 0.8962 (tmm) REVERT: j 53 MET cc_start: 0.8396 (tmm) cc_final: 0.8026 (tmm) REVERT: j 87 TYR cc_start: 0.8426 (t80) cc_final: 0.8023 (t80) REVERT: j 91 LEU cc_start: 0.9226 (mp) cc_final: 0.8897 (mt) REVERT: k 13 PHE cc_start: 0.8727 (t80) cc_final: 0.8498 (t80) REVERT: k 53 MET cc_start: 0.8195 (mtp) cc_final: 0.7859 (mtt) REVERT: k 68 TYR cc_start: 0.8441 (m-10) cc_final: 0.7819 (m-80) REVERT: k 76 ILE cc_start: 0.9355 (mt) cc_final: 0.9046 (tt) REVERT: k 123 GLN cc_start: 0.8535 (mt0) cc_final: 0.8141 (tp40) REVERT: k 124 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7959 (tm-30) REVERT: k 127 LEU cc_start: 0.8975 (mp) cc_final: 0.8754 (mp) REVERT: k 131 MET cc_start: 0.8308 (ttp) cc_final: 0.8007 (ttp) REVERT: k 143 LEU cc_start: 0.9331 (tp) cc_final: 0.8814 (tp) REVERT: l 25 PHE cc_start: 0.8816 (m-80) cc_final: 0.8565 (m-80) REVERT: l 34 THR cc_start: 0.9319 (m) cc_final: 0.9053 (p) REVERT: l 37 SER cc_start: 0.8572 (m) cc_final: 0.8131 (p) REVERT: l 97 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9026 (mm) REVERT: l 136 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8771 (tp) REVERT: m 7 ASN cc_start: 0.8922 (m-40) cc_final: 0.8615 (m-40) REVERT: m 26 SER cc_start: 0.9464 (OUTLIER) cc_final: 0.9216 (p) REVERT: m 78 ASN cc_start: 0.8684 (m-40) cc_final: 0.8397 (m110) REVERT: m 87 TYR cc_start: 0.7632 (t80) cc_final: 0.7376 (t80) REVERT: m 123 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7308 (mp-120) REVERT: m 155 LYS cc_start: 0.7480 (tptm) cc_final: 0.7152 (tptm) REVERT: n 17 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7718 (mpp) REVERT: n 23 MET cc_start: 0.9148 (tpt) cc_final: 0.8842 (tpt) REVERT: n 28 MET cc_start: 0.8626 (mmm) cc_final: 0.8395 (mmm) REVERT: n 36 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8116 (tppt) REVERT: n 47 MET cc_start: 0.8606 (tpp) cc_final: 0.8334 (mmm) REVERT: n 48 ARG cc_start: 0.8682 (mmm-85) cc_final: 0.8470 (mmt90) REVERT: n 87 TYR cc_start: 0.7957 (t80) cc_final: 0.7627 (t80) REVERT: o 17 MET cc_start: 0.8315 (mmm) cc_final: 0.8036 (mmt) REVERT: o 25 PHE cc_start: 0.8617 (m-80) cc_final: 0.8251 (m-80) REVERT: o 37 SER cc_start: 0.8724 (m) cc_final: 0.8264 (t) REVERT: o 61 MET cc_start: 0.8879 (mmt) cc_final: 0.8085 (mmt) REVERT: o 82 ASP cc_start: 0.7594 (t0) cc_final: 0.7180 (t70) REVERT: o 92 GLN cc_start: 0.9374 (mm-40) cc_final: 0.9148 (mm-40) REVERT: o 124 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7646 (tm-30) REVERT: p 294 ASN cc_start: 0.8448 (m-40) cc_final: 0.8054 (p0) REVERT: p 298 LYS cc_start: 0.9001 (mttt) cc_final: 0.8362 (mmtt) REVERT: p 308 ASN cc_start: 0.7873 (t0) cc_final: 0.7569 (t0) outliers start: 82 outliers final: 57 residues processed: 770 average time/residue: 0.2904 time to fit residues: 356.3186 Evaluate side-chains 756 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 688 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 82 GLN Chi-restraints excluded: chain a residue 363 THR Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 530 LEU Chi-restraints excluded: chain a residue 541 SER Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 813 ASN Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 70 TYR Chi-restraints excluded: chain b residue 154 CYS Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 440 ILE Chi-restraints excluded: chain c residue 442 SER Chi-restraints excluded: chain d residue 11 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 66 THR Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 166 ASP Chi-restraints excluded: chain d residue 213 GLU Chi-restraints excluded: chain d residue 215 GLU Chi-restraints excluded: chain e residue 19 LEU Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain g residue 133 LEU Chi-restraints excluded: chain h residue 151 ILE Chi-restraints excluded: chain i residue 45 SER Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain j residue 7 ASN Chi-restraints excluded: chain j residue 9 GLU Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 102 SER Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain j residue 147 ILE Chi-restraints excluded: chain k residue 20 SER Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain l residue 81 THR Chi-restraints excluded: chain l residue 97 LEU Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 137 PHE Chi-restraints excluded: chain m residue 11 SER Chi-restraints excluded: chain m residue 12 SER Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain m residue 36 LYS Chi-restraints excluded: chain m residue 45 SER Chi-restraints excluded: chain m residue 123 GLN Chi-restraints excluded: chain n residue 17 MET Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 82 ASP Chi-restraints excluded: chain n residue 98 SER Chi-restraints excluded: chain o residue 85 THR Chi-restraints excluded: chain o residue 137 PHE Chi-restraints excluded: chain p residue 314 MET Chi-restraints excluded: chain p residue 343 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 257 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 237 optimal weight: 0.6980 chunk 249 optimal weight: 0.0060 chunk 164 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 82 GLN ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 HIS ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21414 Z= 0.213 Angle : 0.709 12.797 29025 Z= 0.353 Chirality : 0.042 0.403 3434 Planarity : 0.004 0.046 3606 Dihedral : 4.018 34.060 2980 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.64 % Allowed : 29.82 % Favored : 66.54 % 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: 1.97 (0.16), residues: 2771 helix: 1.99 (0.11), residues: 2091 sheet: -1.36 (1.21), residues: 18 loop : -0.84 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP a 479 HIS 0.009 0.001 HIS L 81 PHE 0.038 0.002 PHE L 52 TYR 0.035 0.002 TYR g 68 ARG 0.010 0.001 ARG j 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 717 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 85 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8484 (tt0) REVERT: H 86 ASN cc_start: 0.9253 (t0) cc_final: 0.8951 (t0) REVERT: H 92 VAL cc_start: 0.9305 (t) cc_final: 0.8939 (m) REVERT: H 99 ASP cc_start: 0.8686 (t0) cc_final: 0.8231 (t0) REVERT: L 49 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7592 (tm-30) REVERT: L 60 ASP cc_start: 0.8376 (m-30) cc_final: 0.7906 (t0) REVERT: L 63 ILE cc_start: 0.8373 (mt) cc_final: 0.7983 (tt) REVERT: L 94 LYS cc_start: 0.8387 (ttpt) cc_final: 0.8177 (ttpp) REVERT: L 110 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7646 (tmtt) REVERT: a 10 MET cc_start: 0.7046 (mmt) cc_final: 0.6493 (mmm) REVERT: a 399 PHE cc_start: 0.8838 (t80) cc_final: 0.8619 (t80) REVERT: a 401 PHE cc_start: 0.8541 (t80) cc_final: 0.8289 (t80) REVERT: a 423 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7718 (tpp) REVERT: a 429 ARG cc_start: 0.7779 (mtt90) cc_final: 0.6522 (mtp180) REVERT: a 453 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8114 (ttp) REVERT: a 576 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8012 (mm-30) REVERT: a 616 MET cc_start: 0.8728 (tmm) cc_final: 0.8024 (tmm) REVERT: a 633 GLN cc_start: 0.8371 (tp40) cc_final: 0.8092 (tp-100) REVERT: a 660 ARG cc_start: 0.6191 (ttt-90) cc_final: 0.5358 (tmt170) REVERT: a 662 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7471 (mm110) REVERT: a 759 MET cc_start: 0.8084 (mmp) cc_final: 0.6671 (tpt) REVERT: a 768 ARG cc_start: 0.6318 (mtp180) cc_final: 0.5719 (mtt180) REVERT: a 792 LEU cc_start: 0.8949 (tp) cc_final: 0.8725 (mt) REVERT: a 832 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7167 (mmm-85) REVERT: b 25 CYS cc_start: 0.8964 (m) cc_final: 0.8476 (m) REVERT: b 30 ASP cc_start: 0.8150 (t70) cc_final: 0.7906 (t70) REVERT: b 47 PHE cc_start: 0.8299 (m-80) cc_final: 0.7691 (m-80) REVERT: b 98 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7209 (mm-30) REVERT: b 103 TYR cc_start: 0.7967 (m-80) cc_final: 0.7691 (m-80) REVERT: b 107 MET cc_start: 0.9221 (mmm) cc_final: 0.9004 (mmm) REVERT: b 116 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8001 (mp0) REVERT: b 132 HIS cc_start: 0.9233 (t-90) cc_final: 0.8703 (t-90) REVERT: b 188 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8950 (mm) REVERT: b 200 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.6878 (ptt-90) REVERT: c 419 ILE cc_start: 0.8781 (mt) cc_final: 0.8529 (mm) REVERT: c 421 MET cc_start: 0.8254 (mtm) cc_final: 0.7825 (ttm) REVERT: c 424 LEU cc_start: 0.9254 (mm) cc_final: 0.8898 (mm) REVERT: d 6 GLU cc_start: 0.9189 (pt0) cc_final: 0.8986 (pt0) REVERT: d 28 LEU cc_start: 0.9094 (mt) cc_final: 0.8789 (mp) REVERT: d 91 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7701 (tp30) REVERT: d 105 MET cc_start: 0.7976 (ttp) cc_final: 0.7622 (ttm) REVERT: d 129 CYS cc_start: 0.7996 (m) cc_final: 0.7681 (m) REVERT: d 138 MET cc_start: 0.8420 (tpp) cc_final: 0.8178 (tpp) REVERT: d 213 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7175 (mm-30) REVERT: d 325 GLU cc_start: 0.7679 (tt0) cc_final: 0.7347 (tm-30) REVERT: e 47 CYS cc_start: 0.9056 (m) cc_final: 0.8777 (m) REVERT: g 13 PHE cc_start: 0.6700 (t80) cc_final: 0.6445 (t80) REVERT: g 17 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.8005 (tpp) REVERT: g 44 MET cc_start: 0.9071 (tmm) cc_final: 0.8792 (tmm) REVERT: g 87 TYR cc_start: 0.8418 (t80) cc_final: 0.6946 (t80) REVERT: h 23 MET cc_start: 0.9155 (tpp) cc_final: 0.8675 (ttm) REVERT: h 64 ILE cc_start: 0.9245 (mt) cc_final: 0.8898 (mt) REVERT: h 68 TYR cc_start: 0.8946 (m-10) cc_final: 0.8441 (m-10) REVERT: h 90 PHE cc_start: 0.8938 (m-80) cc_final: 0.8275 (m-80) REVERT: h 123 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8698 (mm110) REVERT: h 124 GLN cc_start: 0.7988 (tp-100) cc_final: 0.7642 (tm-30) REVERT: h 144 TYR cc_start: 0.8985 (m-80) cc_final: 0.8624 (m-80) REVERT: h 151 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.9015 (tp) REVERT: i 10 TYR cc_start: 0.5961 (m-80) cc_final: 0.5075 (m-80) REVERT: i 76 ILE cc_start: 0.9593 (mt) cc_final: 0.9377 (tt) REVERT: i 92 GLN cc_start: 0.8642 (mt0) cc_final: 0.8284 (mp10) REVERT: i 115 ASP cc_start: 0.8611 (t70) cc_final: 0.8310 (t0) REVERT: i 144 TYR cc_start: 0.8770 (m-10) cc_final: 0.8544 (m-80) REVERT: i 152 LEU cc_start: 0.9197 (tp) cc_final: 0.8943 (tp) REVERT: j 10 TYR cc_start: 0.8073 (p90) cc_final: 0.7420 (p90) REVERT: j 17 MET cc_start: 0.9023 (mmm) cc_final: 0.8537 (mmm) REVERT: j 25 PHE cc_start: 0.8887 (m-80) cc_final: 0.8619 (m-80) REVERT: j 36 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7657 (mmmt) REVERT: j 44 MET cc_start: 0.9289 (tmm) cc_final: 0.8958 (tmm) REVERT: j 53 MET cc_start: 0.8330 (tmm) cc_final: 0.8034 (tmm) REVERT: j 87 TYR cc_start: 0.8539 (t80) cc_final: 0.8182 (t80) REVERT: j 91 LEU cc_start: 0.9245 (mp) cc_final: 0.8962 (mt) REVERT: k 13 PHE cc_start: 0.8768 (t80) cc_final: 0.8477 (t80) REVERT: k 53 MET cc_start: 0.8244 (mtp) cc_final: 0.7903 (mtt) REVERT: k 68 TYR cc_start: 0.8414 (m-10) cc_final: 0.7815 (m-80) REVERT: k 123 GLN cc_start: 0.8545 (mt0) cc_final: 0.8152 (tp40) REVERT: k 124 GLN cc_start: 0.8383 (tm-30) cc_final: 0.8027 (tm-30) REVERT: k 127 LEU cc_start: 0.8979 (mp) cc_final: 0.8776 (mp) REVERT: k 131 MET cc_start: 0.8295 (ttp) cc_final: 0.7989 (ttp) REVERT: k 143 LEU cc_start: 0.9323 (tp) cc_final: 0.8709 (tp) REVERT: l 25 PHE cc_start: 0.8792 (m-80) cc_final: 0.8510 (m-80) REVERT: l 34 THR cc_start: 0.9314 (m) cc_final: 0.9054 (p) REVERT: l 37 SER cc_start: 0.8556 (m) cc_final: 0.8112 (p) REVERT: l 97 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9010 (mm) REVERT: l 131 MET cc_start: 0.8305 (ttp) cc_final: 0.7983 (ttt) REVERT: l 136 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8740 (tp) REVERT: m 7 ASN cc_start: 0.8955 (m-40) cc_final: 0.8645 (m-40) REVERT: m 26 SER cc_start: 0.9466 (OUTLIER) cc_final: 0.9229 (p) REVERT: m 78 ASN cc_start: 0.8741 (m-40) cc_final: 0.8467 (m110) REVERT: m 123 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7315 (mp-120) REVERT: m 155 LYS cc_start: 0.7544 (tptm) cc_final: 0.7309 (tptm) REVERT: n 17 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7708 (mpp) REVERT: n 23 MET cc_start: 0.9144 (tpt) cc_final: 0.8848 (tpt) REVERT: n 28 MET cc_start: 0.8640 (mmm) cc_final: 0.8405 (mmm) REVERT: n 36 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8107 (tppt) REVERT: n 47 MET cc_start: 0.8553 (tpp) cc_final: 0.8352 (mmm) REVERT: n 87 TYR cc_start: 0.7970 (t80) cc_final: 0.7684 (t80) REVERT: o 25 PHE cc_start: 0.8609 (m-80) cc_final: 0.8276 (m-80) REVERT: o 37 SER cc_start: 0.8703 (m) cc_final: 0.8226 (t) REVERT: o 61 MET cc_start: 0.8900 (mmt) cc_final: 0.8106 (mmt) REVERT: o 82 ASP cc_start: 0.7604 (t0) cc_final: 0.7129 (t70) REVERT: o 92 GLN cc_start: 0.9401 (mm-40) cc_final: 0.8732 (mm-40) REVERT: o 124 GLN cc_start: 0.8163 (tp-100) cc_final: 0.7112 (tm-30) REVERT: p 294 ASN cc_start: 0.8451 (m-40) cc_final: 0.8056 (p0) REVERT: p 298 LYS cc_start: 0.9034 (mttt) cc_final: 0.8364 (mmtt) REVERT: p 308 ASN cc_start: 0.7891 (t0) cc_final: 0.7578 (t0) outliers start: 78 outliers final: 55 residues processed: 755 average time/residue: 0.3148 time to fit residues: 381.7012 Evaluate side-chains 755 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 688 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 82 GLN Chi-restraints excluded: chain a residue 363 THR Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 544 LEU Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 813 ASN Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 70 TYR Chi-restraints excluded: chain b residue 154 CYS Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain c residue 434 THR Chi-restraints excluded: chain c residue 440 ILE Chi-restraints excluded: chain d residue 11 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 66 THR Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 166 ASP Chi-restraints excluded: chain d residue 213 GLU Chi-restraints excluded: chain e residue 19 LEU Chi-restraints excluded: chain e residue 40 MET Chi-restraints excluded: chain g residue 17 MET Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain g residue 110 ILE Chi-restraints excluded: chain h residue 102 SER Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain h residue 151 ILE Chi-restraints excluded: chain i residue 45 SER Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain j residue 7 ASN Chi-restraints excluded: chain j residue 9 GLU Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 102 SER Chi-restraints excluded: chain j residue 129 VAL Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain k residue 11 SER Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain l residue 81 THR Chi-restraints excluded: chain l residue 97 LEU Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 137 PHE Chi-restraints excluded: chain m residue 11 SER Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain m residue 36 LYS Chi-restraints excluded: chain m residue 45 SER Chi-restraints excluded: chain m residue 123 GLN Chi-restraints excluded: chain n residue 17 MET Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 82 ASP Chi-restraints excluded: chain n residue 98 SER Chi-restraints excluded: chain o residue 85 THR Chi-restraints excluded: chain o residue 137 PHE Chi-restraints excluded: chain p residue 314 MET Chi-restraints excluded: chain p residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 264 optimal weight: 0.0040 chunk 161 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 277 optimal weight: 0.8980 chunk 255 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 33 HIS L 82 GLN ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 433 GLN a 633 GLN ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 309 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 21414 Z= 0.261 Angle : 0.734 12.937 29025 Z= 0.368 Chirality : 0.044 0.413 3434 Planarity : 0.004 0.046 3606 Dihedral : 4.048 37.540 2980 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.73 % Allowed : 30.66 % Favored : 65.61 % 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: 1.90 (0.16), residues: 2771 helix: 1.95 (0.11), residues: 2096 sheet: -1.57 (1.18), residues: 18 loop : -0.91 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP e 74 HIS 0.012 0.001 HIS L 81 PHE 0.031 0.002 PHE a 571 TYR 0.039 0.002 TYR l 68 ARG 0.007 0.001 ARG H 136 ********************** 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 780 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 700 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 85 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8560 (tt0) REVERT: H 86 ASN cc_start: 0.9295 (t0) cc_final: 0.8984 (t0) REVERT: H 92 VAL cc_start: 0.9334 (t) cc_final: 0.8979 (p) REVERT: H 99 ASP cc_start: 0.8756 (t0) cc_final: 0.8268 (t0) REVERT: L 49 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7626 (tm-30) REVERT: L 60 ASP cc_start: 0.8405 (m-30) cc_final: 0.8031 (t0) REVERT: L 73 MET cc_start: 0.8546 (mmp) cc_final: 0.7979 (mtt) REVERT: L 110 LYS cc_start: 0.8281 (ttmt) cc_final: 0.7779 (tmtt) REVERT: a 10 MET cc_start: 0.7098 (mmt) cc_final: 0.6512 (mmm) REVERT: a 399 PHE cc_start: 0.8843 (t80) cc_final: 0.8640 (t80) REVERT: a 423 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7786 (tpp) REVERT: a 429 ARG cc_start: 0.7702 (mtt90) cc_final: 0.6546 (mtp180) REVERT: a 453 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8224 (ttp) REVERT: a 479 TRP cc_start: 0.6758 (t-100) cc_final: 0.6541 (t-100) REVERT: a 576 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7992 (mm-30) REVERT: a 580 MET cc_start: 0.8713 (tpp) cc_final: 0.8328 (tpp) REVERT: a 616 MET cc_start: 0.8706 (tmm) cc_final: 0.8005 (tmm) REVERT: a 633 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8122 (tp-100) REVERT: a 660 ARG cc_start: 0.6351 (ttt-90) cc_final: 0.5463 (tmt170) REVERT: a 662 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7495 (mm110) REVERT: a 751 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8946 (mm-40) REVERT: a 759 MET cc_start: 0.8145 (mmp) cc_final: 0.6725 (tpt) REVERT: a 768 ARG cc_start: 0.6306 (mtp180) cc_final: 0.5731 (mtt180) REVERT: a 792 LEU cc_start: 0.8941 (tp) cc_final: 0.8736 (mt) REVERT: a 832 ARG cc_start: 0.7927 (mtm-85) cc_final: 0.7100 (mmm-85) REVERT: b 25 CYS cc_start: 0.8946 (m) cc_final: 0.8426 (m) REVERT: b 47 PHE cc_start: 0.8467 (m-80) cc_final: 0.7810 (m-80) REVERT: b 98 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7231 (mm-30) REVERT: b 116 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7962 (mp0) REVERT: b 132 HIS cc_start: 0.9218 (t-90) cc_final: 0.8615 (t-90) REVERT: b 137 MET cc_start: 0.9228 (mtp) cc_final: 0.8800 (mtm) REVERT: b 188 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8934 (mm) REVERT: b 200 ARG cc_start: 0.7864 (mtm-85) cc_final: 0.6903 (ptt-90) REVERT: c 419 ILE cc_start: 0.8827 (mt) cc_final: 0.8575 (mm) REVERT: c 421 MET cc_start: 0.8258 (mtm) cc_final: 0.7805 (ttm) REVERT: c 424 LEU cc_start: 0.9264 (mm) cc_final: 0.8914 (mm) REVERT: d 88 HIS cc_start: 0.7692 (m170) cc_final: 0.7423 (m170) REVERT: d 91 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7636 (tp30) REVERT: d 105 MET cc_start: 0.8014 (ttp) cc_final: 0.7656 (ttm) REVERT: d 129 CYS cc_start: 0.8022 (m) cc_final: 0.7722 (m) REVERT: d 208 MET cc_start: 0.8867 (tpp) cc_final: 0.8093 (tpp) REVERT: d 213 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7227 (mm-30) REVERT: d 215 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: d 310 PHE cc_start: 0.9096 (m-80) cc_final: 0.8323 (m-10) REVERT: d 325 GLU cc_start: 0.7803 (tt0) cc_final: 0.7413 (tm-30) REVERT: e 47 CYS cc_start: 0.9102 (m) cc_final: 0.8750 (m) REVERT: g 44 MET cc_start: 0.9035 (tmm) cc_final: 0.8736 (tmm) REVERT: g 87 TYR cc_start: 0.8549 (t80) cc_final: 0.7032 (t80) REVERT: h 17 MET cc_start: 0.8955 (tpp) cc_final: 0.8498 (tpp) REVERT: h 23 MET cc_start: 0.9177 (tpp) cc_final: 0.8698 (ttm) REVERT: h 64 ILE cc_start: 0.9280 (mt) cc_final: 0.8940 (mt) REVERT: h 68 TYR cc_start: 0.8938 (m-10) cc_final: 0.8451 (m-10) REVERT: h 90 PHE cc_start: 0.8968 (m-80) cc_final: 0.8387 (m-80) REVERT: h 124 GLN cc_start: 0.8065 (tp-100) cc_final: 0.7737 (tm-30) REVERT: h 144 TYR cc_start: 0.9045 (m-80) cc_final: 0.8665 (m-80) REVERT: h 151 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8996 (tp) REVERT: i 10 TYR cc_start: 0.5935 (m-80) cc_final: 0.4916 (m-80) REVERT: i 92 GLN cc_start: 0.8696 (mt0) cc_final: 0.8331 (mp10) REVERT: i 144 TYR cc_start: 0.8783 (m-10) cc_final: 0.8534 (m-80) REVERT: i 152 LEU cc_start: 0.9201 (tp) cc_final: 0.8981 (tp) REVERT: j 10 TYR cc_start: 0.8228 (p90) cc_final: 0.7469 (p90) REVERT: j 17 MET cc_start: 0.8980 (mmm) cc_final: 0.8531 (mmm) REVERT: j 25 PHE cc_start: 0.8975 (m-80) cc_final: 0.8705 (m-80) REVERT: j 36 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7653 (mmmt) REVERT: j 44 MET cc_start: 0.9255 (tmm) cc_final: 0.8919 (tmm) REVERT: j 53 MET cc_start: 0.8329 (tmm) cc_final: 0.8023 (tmm) REVERT: j 87 TYR cc_start: 0.8548 (t80) cc_final: 0.8077 (t80) REVERT: k 13 PHE cc_start: 0.8833 (t80) cc_final: 0.8423 (t80) REVERT: k 53 MET cc_start: 0.8333 (mtp) cc_final: 0.7989 (mtt) REVERT: k 68 TYR cc_start: 0.8352 (m-10) cc_final: 0.7775 (m-80) REVERT: k 123 GLN cc_start: 0.8565 (mt0) cc_final: 0.8162 (tp40) REVERT: k 124 GLN cc_start: 0.8439 (tm-30) cc_final: 0.7910 (tm-30) REVERT: k 127 LEU cc_start: 0.9024 (mp) cc_final: 0.8622 (mp) REVERT: k 131 MET cc_start: 0.8354 (ttp) cc_final: 0.8045 (ttp) REVERT: k 143 LEU cc_start: 0.9346 (tp) cc_final: 0.8743 (tp) REVERT: l 25 PHE cc_start: 0.8836 (m-80) cc_final: 0.8568 (m-80) REVERT: l 37 SER cc_start: 0.8581 (m) cc_final: 0.8137 (p) REVERT: l 97 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9007 (mm) REVERT: l 131 MET cc_start: 0.8235 (ttp) cc_final: 0.7921 (ttt) REVERT: l 136 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8753 (tp) REVERT: m 7 ASN cc_start: 0.8953 (m-40) cc_final: 0.8638 (m-40) REVERT: m 26 SER cc_start: 0.9508 (OUTLIER) cc_final: 0.9264 (p) REVERT: m 78 ASN cc_start: 0.8770 (m-40) cc_final: 0.8495 (m110) REVERT: m 123 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7356 (mp-120) REVERT: m 155 LYS cc_start: 0.7566 (tptm) cc_final: 0.7359 (tptm) REVERT: n 17 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7766 (mtp) REVERT: n 23 MET cc_start: 0.9169 (tpt) cc_final: 0.8892 (tpt) REVERT: n 28 MET cc_start: 0.8596 (mmm) cc_final: 0.8369 (mmm) REVERT: n 36 LYS cc_start: 0.8615 (mmmt) cc_final: 0.8171 (tppt) REVERT: n 47 MET cc_start: 0.8704 (tpp) cc_final: 0.8384 (mmm) REVERT: n 87 TYR cc_start: 0.7996 (t80) cc_final: 0.7694 (t80) REVERT: n 144 TYR cc_start: 0.9010 (m-80) cc_final: 0.8676 (m-80) REVERT: o 25 PHE cc_start: 0.8746 (m-80) cc_final: 0.8438 (m-80) REVERT: o 37 SER cc_start: 0.8745 (m) cc_final: 0.8262 (t) REVERT: o 61 MET cc_start: 0.8912 (mmt) cc_final: 0.8113 (mmt) REVERT: o 82 ASP cc_start: 0.7613 (t0) cc_final: 0.7124 (t0) REVERT: o 92 GLN cc_start: 0.9322 (mm-40) cc_final: 0.8881 (mm-40) REVERT: o 124 GLN cc_start: 0.8256 (tp-100) cc_final: 0.7679 (tm-30) REVERT: p 294 ASN cc_start: 0.8472 (m-40) cc_final: 0.8070 (p0) REVERT: p 298 LYS cc_start: 0.9012 (mttt) cc_final: 0.8350 (mmtt) REVERT: p 308 ASN cc_start: 0.8033 (t0) cc_final: 0.7723 (t0) outliers start: 80 outliers final: 56 residues processed: 740 average time/residue: 0.2971 time to fit residues: 351.5857 Evaluate side-chains 754 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 685 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 82 GLN Chi-restraints excluded: chain a residue 363 THR Chi-restraints excluded: chain a residue 423 MET Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 530 LEU Chi-restraints excluded: chain a residue 541 SER Chi-restraints excluded: chain a residue 544 LEU Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 633 GLN Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 813 ASN Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 70 TYR Chi-restraints excluded: chain b residue 154 CYS Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain c residue 440 ILE Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 51 SER Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 66 THR Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 166 ASP Chi-restraints excluded: chain d residue 213 GLU Chi-restraints excluded: chain d residue 215 GLU Chi-restraints excluded: chain e residue 19 LEU Chi-restraints excluded: chain e residue 39 THR Chi-restraints excluded: chain e residue 76 VAL Chi-restraints excluded: chain g residue 26 SER Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 151 ILE Chi-restraints excluded: chain i residue 21 SER Chi-restraints excluded: chain i residue 45 SER Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain j residue 7 ASN Chi-restraints excluded: chain j residue 9 GLU Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 102 SER Chi-restraints excluded: chain j residue 136 ILE Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain l residue 47 MET Chi-restraints excluded: chain l residue 81 THR Chi-restraints excluded: chain l residue 97 LEU Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain m residue 11 SER Chi-restraints excluded: chain m residue 26 SER Chi-restraints excluded: chain m residue 36 LYS Chi-restraints excluded: chain m residue 45 SER Chi-restraints excluded: chain m residue 123 GLN Chi-restraints excluded: chain n residue 17 MET Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 82 ASP Chi-restraints excluded: chain n residue 98 SER Chi-restraints excluded: chain o residue 85 THR Chi-restraints excluded: chain o residue 137 PHE Chi-restraints excluded: chain p residue 314 MET Chi-restraints excluded: chain p residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 204 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 227 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 194 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 33 HIS ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 633 GLN ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 309 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.104710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.091556 restraints weight = 51285.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.094469 restraints weight = 24061.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.096367 restraints weight = 13708.609| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.169 21414 Z= 0.348 Angle : 0.877 59.087 29025 Z= 0.469 Chirality : 0.047 1.106 3434 Planarity : 0.005 0.133 3606 Dihedral : 4.051 37.561 2980 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.87 % Allowed : 31.22 % Favored : 64.91 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.16), residues: 2771 helix: 1.94 (0.11), residues: 2096 sheet: -1.60 (1.18), residues: 18 loop : -0.91 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP e 74 HIS 0.008 0.001 HIS L 81 PHE 0.062 0.002 PHE i 13 TYR 0.038 0.002 TYR l 68 ARG 0.005 0.000 ARG d 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6325.04 seconds wall clock time: 114 minutes 3.70 seconds (6843.70 seconds total)