Starting phenix.real_space_refine on Sat Feb 17 17:42:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnl_26013/02_2024/7tnl_26013_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnl_26013/02_2024/7tnl_26013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnl_26013/02_2024/7tnl_26013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnl_26013/02_2024/7tnl_26013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnl_26013/02_2024/7tnl_26013_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnl_26013/02_2024/7tnl_26013_updated.pdb" } resolution = 3.59 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 136 5.16 5 Cl 4 4.86 5 C 12558 2.51 5 N 3144 2.21 5 O 3592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 453": "NH1" <-> "NH2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 1036": "NH1" <-> "NH2" Residue "B ARG 1203": "NH1" <-> "NH2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 819": "NH1" <-> "NH2" Residue "C ARG 1036": "NH1" <-> "NH2" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 1036": "NH1" <-> "NH2" Residue "D ARG 1203": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19434 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4831 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "B" Number of atoms: 4828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4828 Classifications: {'peptide': 621} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 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: "C" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4831 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "D" Number of atoms: 4828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4828 Classifications: {'peptide': 621} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 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: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.72, per 1000 atoms: 0.55 Number of scatterers: 19434 At special positions: 0 Unit cell: (123.67, 115.37, 131.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 136 16.00 O 3592 8.00 N 3144 7.00 C 12558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.04 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.04 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.01 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.02 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.04 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.02 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.04 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.01 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.36 Conformation dependent library (CDL) restraints added in 4.1 seconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 24 sheets defined 49.9% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 417 through 420 removed outlier: 3.956A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.870A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 525 through 544 Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 596 through 624 removed outlier: 3.583A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 654 through 661 removed outlier: 3.511A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 676 removed outlier: 3.666A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 694 Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.607A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 755 Processing helix chain 'A' and resid 758 through 768 removed outlier: 3.725A pdb=" N TYR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 793 through 819 Processing helix chain 'A' and resid 1005 through 1028 Processing helix chain 'A' and resid 1051 through 1053 No H-bonds generated for 'chain 'A' and resid 1051 through 1053' Processing helix chain 'A' and resid 1092 through 1103 Processing helix chain 'A' and resid 1105 through 1125 removed outlier: 4.661A pdb=" N GLU A1125 " --> pdb=" O ILE A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1158 removed outlier: 3.542A pdb=" N VAL A1154 " --> pdb=" O ILE A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1208 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 516 through 519 Processing helix chain 'B' and resid 523 through 544 removed outlier: 3.527A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.607A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 618 removed outlier: 3.739A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 624 removed outlier: 3.597A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 620 through 624' Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 654 through 660 removed outlier: 3.612A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 686 through 695 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 741 through 755 removed outlier: 3.829A pdb=" N THR B 744 " --> pdb=" O SER B 741 " (cutoff:3.500A) Proline residue: B 745 - end of helix removed outlier: 3.685A pdb=" N SER B 754 " --> pdb=" O LEU B 751 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU B 755 " --> pdb=" O LYS B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 766 Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 793 through 818 Processing helix chain 'B' and resid 1005 through 1028 Processing helix chain 'B' and resid 1092 through 1103 Processing helix chain 'B' and resid 1105 through 1125 removed outlier: 3.543A pdb=" N LEU B1114 " --> pdb=" O SER B1110 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU B1125 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1160 removed outlier: 3.515A pdb=" N ILE B1150 " --> pdb=" O LEU B1146 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA B1160 " --> pdb=" O ILE B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1208 removed outlier: 3.549A pdb=" N VAL B1197 " --> pdb=" O GLY B1193 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS B1204 " --> pdb=" O PHE B1200 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 removed outlier: 3.956A pdb=" N ARG C 420 " --> pdb=" O GLY C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 483 through 488 removed outlier: 3.870A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 525 through 544 Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 596 through 624 removed outlier: 3.583A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 654 through 661 removed outlier: 3.511A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 676 removed outlier: 3.665A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 694 Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.607A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 755 Processing helix chain 'C' and resid 758 through 768 removed outlier: 3.725A pdb=" N TYR C 768 " --> pdb=" O ASN C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 791 No H-bonds generated for 'chain 'C' and resid 789 through 791' Processing helix chain 'C' and resid 793 through 819 Processing helix chain 'C' and resid 1005 through 1028 Processing helix chain 'C' and resid 1051 through 1053 No H-bonds generated for 'chain 'C' and resid 1051 through 1053' Processing helix chain 'C' and resid 1092 through 1103 Processing helix chain 'C' and resid 1105 through 1125 removed outlier: 4.660A pdb=" N GLU C1125 " --> pdb=" O ILE C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1133 through 1158 removed outlier: 3.543A pdb=" N VAL C1154 " --> pdb=" O ILE C1150 " (cutoff:3.500A) Processing helix chain 'C' and resid 1177 through 1208 Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 516 through 519 Processing helix chain 'D' and resid 523 through 544 removed outlier: 3.528A pdb=" N MET D 527 " --> pdb=" O TYR D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 568 No H-bonds generated for 'chain 'D' and resid 566 through 568' Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.607A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 618 removed outlier: 3.740A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 618 " --> pdb=" O SER D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 624 removed outlier: 3.598A pdb=" N LEU D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 620 through 624' Processing helix chain 'D' and resid 636 through 640 Processing helix chain 'D' and resid 654 through 660 removed outlier: 3.613A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 741 through 755 removed outlier: 3.828A pdb=" N THR D 744 " --> pdb=" O SER D 741 " (cutoff:3.500A) Proline residue: D 745 - end of helix removed outlier: 3.685A pdb=" N SER D 754 " --> pdb=" O LEU D 751 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU D 755 " --> pdb=" O LYS D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 766 Processing helix chain 'D' and resid 775 through 780 Processing helix chain 'D' and resid 793 through 818 Processing helix chain 'D' and resid 1005 through 1028 Processing helix chain 'D' and resid 1092 through 1103 Processing helix chain 'D' and resid 1105 through 1125 removed outlier: 3.542A pdb=" N LEU D1114 " --> pdb=" O SER D1110 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU D1125 " --> pdb=" O ILE D1121 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1160 removed outlier: 3.515A pdb=" N ILE D1150 " --> pdb=" O LEU D1146 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA D1160 " --> pdb=" O ILE D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1177 through 1208 removed outlier: 3.550A pdb=" N VAL D1197 " --> pdb=" O GLY D1193 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS D1204 " --> pdb=" O PHE D1200 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= B, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= C, first strand: chain 'A' and resid 720 through 723 removed outlier: 3.582A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1033 through 1036 Processing sheet with id= E, first strand: chain 'A' and resid 1064 through 1066 removed outlier: 3.698A pdb=" N LYS A1077 " --> pdb=" O THR A1065 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 494 through 498 removed outlier: 6.911A pdb=" N TYR A 732 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N SER A 497 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS A 730 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= H, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= I, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.652A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 701 through 705 removed outlier: 3.776A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 1033 through 1037 removed outlier: 3.706A pdb=" N LEU B1033 " --> pdb=" O SER B1060 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B1056 " --> pdb=" O GLY B1037 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 1064 through 1066 Processing sheet with id= M, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= N, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= O, first strand: chain 'C' and resid 720 through 723 removed outlier: 3.582A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 1033 through 1036 Processing sheet with id= Q, first strand: chain 'C' and resid 1064 through 1066 removed outlier: 3.698A pdb=" N LYS C1077 " --> pdb=" O THR C1065 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 494 through 498 removed outlier: 6.910A pdb=" N TYR C 732 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER C 497 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS C 730 " --> pdb=" O SER C 497 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= T, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= U, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.652A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 701 through 705 removed outlier: 3.777A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 1033 through 1037 removed outlier: 3.706A pdb=" N LEU D1033 " --> pdb=" O SER D1060 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL D1056 " --> pdb=" O GLY D1037 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 1064 through 1066 906 hydrogen bonds defined for protein. 2664 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: 5.74 Time building geometry restraints manager: 7.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5667 1.34 - 1.46: 3896 1.46 - 1.57: 10075 1.57 - 1.69: 8 1.69 - 1.81: 220 Bond restraints: 19866 Sorted by residual: bond pdb=" CB ILE A 525 " pdb=" CG2 ILE A 525 " ideal model delta sigma weight residual 1.521 1.389 0.132 3.30e-02 9.18e+02 1.60e+01 bond pdb=" CB ILE C 525 " pdb=" CG2 ILE C 525 " ideal model delta sigma weight residual 1.521 1.390 0.131 3.30e-02 9.18e+02 1.58e+01 bond pdb=" N GLU A1046 " pdb=" CA GLU A1046 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.17e-02 7.31e+03 8.13e+00 bond pdb=" N GLU C1046 " pdb=" CA GLU C1046 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.17e-02 7.31e+03 7.98e+00 bond pdb=" CG1 ILE C 525 " pdb=" CD1 ILE C 525 " ideal model delta sigma weight residual 1.513 1.409 0.104 3.90e-02 6.57e+02 7.16e+00 ... (remaining 19861 not shown) Histogram of bond angle deviations from ideal: 93.27 - 101.47: 100 101.47 - 109.67: 2576 109.67 - 117.86: 12183 117.86 - 126.06: 11679 126.06 - 134.26: 304 Bond angle restraints: 26842 Sorted by residual: angle pdb=" C GLU D1054 " pdb=" N GLU D1055 " pdb=" CA GLU D1055 " ideal model delta sigma weight residual 121.54 133.46 -11.92 1.91e+00 2.74e-01 3.90e+01 angle pdb=" C GLU B1054 " pdb=" N GLU B1055 " pdb=" CA GLU B1055 " ideal model delta sigma weight residual 121.54 133.46 -11.92 1.91e+00 2.74e-01 3.90e+01 angle pdb=" C SER B1045 " pdb=" N GLU B1046 " pdb=" CA GLU B1046 " ideal model delta sigma weight residual 121.19 130.84 -9.65 1.59e+00 3.96e-01 3.68e+01 angle pdb=" C SER D1045 " pdb=" N GLU D1046 " pdb=" CA GLU D1046 " ideal model delta sigma weight residual 121.19 130.82 -9.63 1.59e+00 3.96e-01 3.67e+01 angle pdb=" C SER C1045 " pdb=" N GLU C1046 " pdb=" CA GLU C1046 " ideal model delta sigma weight residual 121.19 130.03 -8.84 1.59e+00 3.96e-01 3.09e+01 ... (remaining 26837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.11: 11406 24.11 - 48.23: 346 48.23 - 72.34: 28 72.34 - 96.45: 6 96.45 - 120.57: 10 Dihedral angle restraints: 11796 sinusoidal: 4666 harmonic: 7130 Sorted by residual: dihedral pdb=" CA GLU A 627 " pdb=" C GLU A 627 " pdb=" N ARG A 628 " pdb=" CA ARG A 628 " ideal model delta harmonic sigma weight residual 180.00 138.84 41.16 0 5.00e+00 4.00e-02 6.77e+01 dihedral pdb=" CA GLU C 627 " pdb=" C GLU C 627 " pdb=" N ARG C 628 " pdb=" CA ARG C 628 " ideal model delta harmonic sigma weight residual 180.00 138.85 41.15 0 5.00e+00 4.00e-02 6.77e+01 dihedral pdb=" CA GLU B1054 " pdb=" C GLU B1054 " pdb=" N GLU B1055 " pdb=" CA GLU B1055 " ideal model delta harmonic sigma weight residual 180.00 142.19 37.81 0 5.00e+00 4.00e-02 5.72e+01 ... (remaining 11793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2471 0.071 - 0.143: 440 0.143 - 0.214: 71 0.214 - 0.285: 14 0.285 - 0.356: 2 Chirality restraints: 2998 Sorted by residual: chirality pdb=" CG LEU A1114 " pdb=" CB LEU A1114 " pdb=" CD1 LEU A1114 " pdb=" CD2 LEU A1114 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CG LEU C1114 " pdb=" CB LEU C1114 " pdb=" CD1 LEU C1114 " pdb=" CD2 LEU C1114 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CB THR C1065 " pdb=" CA THR C1065 " pdb=" OG1 THR C1065 " pdb=" CG2 THR C1065 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2995 not shown) Planarity restraints: 3312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 627 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C GLU C 627 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU C 627 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG C 628 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 627 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C GLU A 627 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU A 627 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG A 628 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 519 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO C 520 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " 0.032 5.00e-02 4.00e+02 ... (remaining 3309 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4721 2.78 - 3.31: 18086 3.31 - 3.84: 31682 3.84 - 4.37: 37337 4.37 - 4.90: 64353 Nonbonded interactions: 156179 Sorted by model distance: nonbonded pdb=" OD1 ASP C1047 " pdb=" OG SER C1050 " model vdw 2.246 2.440 nonbonded pdb=" OD1 ASP A1047 " pdb=" OG SER A1050 " model vdw 2.247 2.440 nonbonded pdb=" OG1 THR C 655 " pdb=" OE2 GLU C 705 " model vdw 2.281 2.440 nonbonded pdb=" OG1 THR A 655 " pdb=" OE2 GLU A 705 " model vdw 2.282 2.440 nonbonded pdb=" OG SER A 597 " pdb=" O ALA B 806 " model vdw 2.315 2.440 ... (remaining 156174 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 'A' and (resid 394 through 548 or (resid 549 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 819 or resid 1002 through 1209 \ or resid 1302)) selection = (chain 'B' and (resid 394 through 549 or resid 564 through 1209 or resid 1301)) selection = (chain 'C' and (resid 394 through 548 or (resid 549 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 819 or resid 1002 through 1209 \ or resid 1302)) selection = (chain 'D' and (resid 394 through 549 or resid 564 through 1209 or resid 1301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.610 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 53.270 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.130 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.009 0.132 19866 Z= 0.593 Angle : 1.029 11.924 26842 Z= 0.555 Chirality : 0.059 0.356 2998 Planarity : 0.007 0.057 3312 Dihedral : 11.859 120.568 7212 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.63 % Favored : 95.12 % Rotamer: Outliers : 0.38 % Allowed : 5.75 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -4.39 (0.12), residues: 2460 helix: -3.43 (0.07), residues: 1320 sheet: -1.45 (0.35), residues: 168 loop : -2.12 (0.16), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP A 671 HIS 0.007 0.003 HIS A1131 PHE 0.038 0.003 PHE C 623 TYR 0.028 0.003 TYR D 702 ARG 0.012 0.001 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 554 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7602 (mpt) cc_final: 0.7376 (mtp) REVERT: A 668 ASP cc_start: 0.7611 (t70) cc_final: 0.7335 (t0) REVERT: A 695 LYS cc_start: 0.8648 (mptt) cc_final: 0.8349 (pttp) REVERT: A 817 LYS cc_start: 0.7706 (mmtp) cc_final: 0.7440 (mtmt) REVERT: A 1095 TYR cc_start: 0.7152 (t80) cc_final: 0.6949 (t80) REVERT: A 1126 PHE cc_start: 0.7627 (t80) cc_final: 0.7358 (m-80) REVERT: B 399 THR cc_start: 0.9289 (t) cc_final: 0.8967 (m) REVERT: B 410 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7875 (mmmm) REVERT: B 412 HIS cc_start: 0.6831 (p90) cc_final: 0.6592 (p90) REVERT: B 642 GLN cc_start: 0.8006 (pp30) cc_final: 0.7698 (pp30) REVERT: B 656 LYS cc_start: 0.8729 (tttt) cc_final: 0.8277 (ttmt) REVERT: B 684 ARG cc_start: 0.7990 (pmm150) cc_final: 0.7541 (mtm-85) REVERT: B 713 GLU cc_start: 0.7577 (tt0) cc_final: 0.7302 (tt0) REVERT: B 1035 SER cc_start: 0.8127 (p) cc_final: 0.7787 (t) REVERT: B 1119 LEU cc_start: 0.7361 (tt) cc_final: 0.6972 (tp) REVERT: B 1200 PHE cc_start: 0.8409 (t80) cc_final: 0.8134 (t80) REVERT: B 1202 ASP cc_start: 0.7815 (t70) cc_final: 0.7576 (t0) REVERT: C 414 MET cc_start: 0.7602 (mpt) cc_final: 0.7342 (mtp) REVERT: C 668 ASP cc_start: 0.7648 (t70) cc_final: 0.7362 (t0) REVERT: C 695 LYS cc_start: 0.8606 (mptt) cc_final: 0.8371 (pttp) REVERT: C 788 SER cc_start: 0.8751 (m) cc_final: 0.8469 (t) REVERT: C 813 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6730 (tp30) REVERT: C 1095 TYR cc_start: 0.7250 (t80) cc_final: 0.7044 (t80) REVERT: C 1114 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8659 (mm) REVERT: C 1173 TYR cc_start: 0.7832 (p90) cc_final: 0.7567 (p90) REVERT: D 410 LYS cc_start: 0.8036 (mtmm) cc_final: 0.7771 (mmmm) REVERT: D 467 LEU cc_start: 0.8577 (mt) cc_final: 0.8367 (mt) REVERT: D 642 GLN cc_start: 0.7949 (pp30) cc_final: 0.7584 (pp30) REVERT: D 656 LYS cc_start: 0.8528 (tttt) cc_final: 0.8185 (ttmt) REVERT: D 684 ARG cc_start: 0.7915 (pmm150) cc_final: 0.7549 (mtm-85) REVERT: D 713 GLU cc_start: 0.7503 (tt0) cc_final: 0.7270 (tt0) REVERT: D 813 GLU cc_start: 0.7558 (pp20) cc_final: 0.7263 (tm-30) REVERT: D 1035 SER cc_start: 0.8152 (p) cc_final: 0.7792 (t) REVERT: D 1108 ILE cc_start: 0.8873 (mt) cc_final: 0.8616 (pt) REVERT: D 1115 PHE cc_start: 0.7943 (t80) cc_final: 0.7708 (t80) REVERT: D 1202 ASP cc_start: 0.7265 (t70) cc_final: 0.6778 (t0) outliers start: 8 outliers final: 0 residues processed: 560 average time/residue: 0.3408 time to fit residues: 282.2130 Evaluate side-chains 306 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 305 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1114 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 194 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 144 optimal weight: 0.7980 chunk 225 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 714 GLN A 756 GLN A1206 GLN B 791 ASN B1071 ASN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS C 756 GLN C1131 HIS C1206 GLN D 791 ASN D1071 ASN ** D1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1204 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19866 Z= 0.166 Angle : 0.558 9.437 26842 Z= 0.292 Chirality : 0.040 0.215 2998 Planarity : 0.004 0.041 3312 Dihedral : 8.646 106.521 2790 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.49 % Allowed : 11.70 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.15), residues: 2460 helix: -0.27 (0.12), residues: 1322 sheet: -1.12 (0.37), residues: 162 loop : -1.81 (0.17), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 766 HIS 0.020 0.002 HIS A1059 PHE 0.022 0.001 PHE D1200 TYR 0.021 0.001 TYR C 523 ARG 0.005 0.000 ARG A 715 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 396 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7692 (mpt) cc_final: 0.7360 (mtp) REVERT: A 642 GLN cc_start: 0.8347 (pp30) cc_final: 0.7982 (pp30) REVERT: A 668 ASP cc_start: 0.7660 (t70) cc_final: 0.7459 (t0) REVERT: A 695 LYS cc_start: 0.8513 (mptt) cc_final: 0.8262 (pttp) REVERT: A 729 SER cc_start: 0.8748 (t) cc_final: 0.8536 (m) REVERT: A 1025 ILE cc_start: 0.8409 (mm) cc_final: 0.8173 (mm) REVERT: A 1126 PHE cc_start: 0.7574 (t80) cc_final: 0.7281 (m-80) REVERT: B 410 LYS cc_start: 0.8015 (mtmm) cc_final: 0.7788 (mmmm) REVERT: B 563 GLN cc_start: 0.5198 (mt0) cc_final: 0.4611 (tm-30) REVERT: B 594 ARG cc_start: 0.7592 (ttp80) cc_final: 0.7388 (ttp-110) REVERT: B 642 GLN cc_start: 0.7993 (pp30) cc_final: 0.7499 (pp30) REVERT: B 645 ILE cc_start: 0.7323 (mp) cc_final: 0.7097 (mt) REVERT: B 656 LYS cc_start: 0.8583 (tttt) cc_final: 0.8182 (ttmt) REVERT: B 684 ARG cc_start: 0.8069 (pmm150) cc_final: 0.7804 (mtm-85) REVERT: B 713 GLU cc_start: 0.7563 (tt0) cc_final: 0.7302 (tt0) REVERT: B 1032 TRP cc_start: 0.8535 (m100) cc_final: 0.8119 (m-10) REVERT: B 1035 SER cc_start: 0.8044 (p) cc_final: 0.7706 (t) REVERT: C 414 MET cc_start: 0.7722 (mpt) cc_final: 0.7423 (mtp) REVERT: C 642 GLN cc_start: 0.8159 (pp30) cc_final: 0.7841 (pp30) REVERT: C 668 ASP cc_start: 0.7646 (t70) cc_final: 0.7433 (t0) REVERT: C 812 ILE cc_start: 0.8059 (pp) cc_final: 0.7674 (mt) REVERT: C 813 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6545 (tp30) REVERT: C 1095 TYR cc_start: 0.7248 (t80) cc_final: 0.6657 (t80) REVERT: D 410 LYS cc_start: 0.8031 (mtmm) cc_final: 0.7814 (mmmm) REVERT: D 656 LYS cc_start: 0.8375 (tttt) cc_final: 0.8090 (ttmt) REVERT: D 684 ARG cc_start: 0.7897 (pmm150) cc_final: 0.7575 (mtm-85) REVERT: D 713 GLU cc_start: 0.7464 (tt0) cc_final: 0.7228 (tt0) REVERT: D 1035 SER cc_start: 0.7896 (p) cc_final: 0.7555 (t) REVERT: D 1057 MET cc_start: 0.5561 (mmm) cc_final: 0.5303 (ttp) REVERT: D 1202 ASP cc_start: 0.7174 (t70) cc_final: 0.6817 (t0) outliers start: 52 outliers final: 23 residues processed: 431 average time/residue: 0.2928 time to fit residues: 196.0293 Evaluate side-chains 332 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 309 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1191 MET Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1187 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 225 optimal weight: 0.9980 chunk 243 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1131 HIS B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS ** C1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 19866 Z= 0.375 Angle : 0.637 8.858 26842 Z= 0.334 Chirality : 0.044 0.223 2998 Planarity : 0.004 0.060 3312 Dihedral : 8.568 99.916 2790 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.89 % Allowed : 13.37 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.45 (0.16), residues: 2460 helix: 0.88 (0.14), residues: 1296 sheet: -1.17 (0.37), residues: 166 loop : -1.74 (0.18), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D1063 HIS 0.014 0.002 HIS A1059 PHE 0.017 0.002 PHE A1115 TYR 0.025 0.002 TYR C 523 ARG 0.006 0.001 ARG D1036 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 303 time to evaluate : 2.475 Fit side-chains REVERT: A 414 MET cc_start: 0.7707 (mpt) cc_final: 0.7344 (mtp) REVERT: A 642 GLN cc_start: 0.8212 (pp30) cc_final: 0.7892 (pp30) REVERT: A 668 ASP cc_start: 0.7704 (t70) cc_final: 0.7475 (t0) REVERT: A 695 LYS cc_start: 0.8583 (mptt) cc_final: 0.8307 (pttp) REVERT: A 817 LYS cc_start: 0.7478 (mmtp) cc_final: 0.7257 (mttt) REVERT: A 1025 ILE cc_start: 0.8478 (mm) cc_final: 0.8265 (mm) REVERT: A 1121 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7705 (tt) REVERT: A 1126 PHE cc_start: 0.7554 (t80) cc_final: 0.7279 (m-80) REVERT: B 642 GLN cc_start: 0.8058 (pp30) cc_final: 0.7510 (pp30) REVERT: B 647 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.7283 (m-10) REVERT: B 656 LYS cc_start: 0.8599 (tttt) cc_final: 0.8198 (tmtt) REVERT: B 684 ARG cc_start: 0.8054 (pmm150) cc_final: 0.7760 (mtm-85) REVERT: B 713 GLU cc_start: 0.7687 (tt0) cc_final: 0.7381 (tt0) REVERT: B 1032 TRP cc_start: 0.8527 (m100) cc_final: 0.8110 (m-10) REVERT: B 1035 SER cc_start: 0.7966 (p) cc_final: 0.7604 (t) REVERT: B 1125 GLU cc_start: 0.7792 (tp30) cc_final: 0.7328 (tm-30) REVERT: C 414 MET cc_start: 0.7830 (mpt) cc_final: 0.7476 (mtp) REVERT: C 642 GLN cc_start: 0.8016 (pp30) cc_final: 0.7772 (pp30) REVERT: C 668 ASP cc_start: 0.7692 (t70) cc_final: 0.7460 (t0) REVERT: C 813 GLU cc_start: 0.6846 (mm-30) cc_final: 0.6562 (tp30) REVERT: C 1095 TYR cc_start: 0.7388 (t80) cc_final: 0.6770 (t80) REVERT: C 1198 HIS cc_start: 0.8251 (m-70) cc_final: 0.8029 (m-70) REVERT: D 647 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.7247 (m-10) REVERT: D 656 LYS cc_start: 0.8430 (tttt) cc_final: 0.8065 (ttmt) REVERT: D 684 ARG cc_start: 0.7973 (pmm150) cc_final: 0.7653 (mtm-85) REVERT: D 713 GLU cc_start: 0.7598 (tt0) cc_final: 0.7295 (tt0) REVERT: D 1035 SER cc_start: 0.7829 (p) cc_final: 0.7497 (t) REVERT: D 1069 GLU cc_start: 0.6606 (tp30) cc_final: 0.6224 (tm-30) REVERT: D 1202 ASP cc_start: 0.7317 (t70) cc_final: 0.6943 (t0) outliers start: 102 outliers final: 56 residues processed: 377 average time/residue: 0.2656 time to fit residues: 160.8620 Evaluate side-chains 325 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 266 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1188 ILE Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1111 VAL Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1187 ILE Chi-restraints excluded: chain D residue 1192 VAL Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 226 optimal weight: 0.9990 chunk 239 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19866 Z= 0.295 Angle : 0.576 8.475 26842 Z= 0.300 Chirality : 0.042 0.206 2998 Planarity : 0.004 0.037 3312 Dihedral : 8.189 95.473 2790 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.41 % Allowed : 15.10 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.04 (0.17), residues: 2460 helix: 1.42 (0.14), residues: 1292 sheet: -1.12 (0.39), residues: 166 loop : -1.67 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 766 HIS 0.017 0.002 HIS B1204 PHE 0.014 0.002 PHE D1072 TYR 0.022 0.001 TYR C 523 ARG 0.004 0.000 ARG D1036 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 292 time to evaluate : 2.147 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.7730 (mpt) cc_final: 0.7371 (mtp) REVERT: A 450 TYR cc_start: 0.8331 (m-80) cc_final: 0.7850 (m-80) REVERT: A 642 GLN cc_start: 0.8165 (pp30) cc_final: 0.7890 (pp30) REVERT: A 668 ASP cc_start: 0.7695 (t70) cc_final: 0.7462 (t0) REVERT: A 695 LYS cc_start: 0.8535 (mptt) cc_final: 0.8297 (pttp) REVERT: A 817 LYS cc_start: 0.7389 (mmtp) cc_final: 0.7189 (mttt) REVERT: A 1121 ILE cc_start: 0.8024 (tp) cc_final: 0.7813 (tt) REVERT: A 1126 PHE cc_start: 0.7466 (t80) cc_final: 0.7191 (m-80) REVERT: A 1204 HIS cc_start: 0.7430 (t70) cc_final: 0.7018 (t-90) REVERT: B 563 GLN cc_start: 0.5499 (mt0) cc_final: 0.4617 (tm-30) REVERT: B 656 LYS cc_start: 0.8566 (tttt) cc_final: 0.8153 (tmtt) REVERT: B 684 ARG cc_start: 0.8048 (pmm150) cc_final: 0.7746 (mtm-85) REVERT: B 713 GLU cc_start: 0.7696 (tt0) cc_final: 0.7334 (tt0) REVERT: B 719 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8315 (p0) REVERT: B 1032 TRP cc_start: 0.8512 (m100) cc_final: 0.8121 (m-10) REVERT: B 1035 SER cc_start: 0.7818 (p) cc_final: 0.7471 (t) REVERT: B 1125 GLU cc_start: 0.7724 (tp30) cc_final: 0.7321 (tm-30) REVERT: C 414 MET cc_start: 0.7871 (mpt) cc_final: 0.7516 (mtp) REVERT: C 642 GLN cc_start: 0.7956 (pp30) cc_final: 0.7744 (pp30) REVERT: C 668 ASP cc_start: 0.7714 (t70) cc_final: 0.7486 (t0) REVERT: C 813 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6676 (tp30) REVERT: C 1095 TYR cc_start: 0.7427 (t80) cc_final: 0.6871 (t80) REVERT: D 486 GLU cc_start: 0.7458 (tp30) cc_final: 0.7073 (tp30) REVERT: D 563 GLN cc_start: 0.5275 (mt0) cc_final: 0.4600 (tm-30) REVERT: D 684 ARG cc_start: 0.7972 (pmm150) cc_final: 0.7619 (mtm-85) REVERT: D 713 GLU cc_start: 0.7585 (tt0) cc_final: 0.7269 (tt0) REVERT: D 813 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7497 (pt0) REVERT: D 1032 TRP cc_start: 0.8486 (m100) cc_final: 0.8103 (m-10) REVERT: D 1035 SER cc_start: 0.7744 (p) cc_final: 0.7446 (t) REVERT: D 1069 GLU cc_start: 0.6506 (tp30) cc_final: 0.6161 (tm-30) REVERT: D 1202 ASP cc_start: 0.7290 (t70) cc_final: 0.6950 (t0) outliers start: 92 outliers final: 64 residues processed: 355 average time/residue: 0.2687 time to fit residues: 153.0428 Evaluate side-chains 342 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 277 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1103 SER Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1077 LYS Chi-restraints excluded: chain D residue 1111 VAL Chi-restraints excluded: chain D residue 1120 CYS Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1187 ILE Chi-restraints excluded: chain D residue 1192 VAL Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 178 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 204 optimal weight: 7.9990 chunk 165 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1131 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1008 GLN D1198 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19866 Z= 0.208 Angle : 0.533 9.261 26842 Z= 0.275 Chirality : 0.040 0.189 2998 Planarity : 0.003 0.035 3312 Dihedral : 7.654 90.308 2790 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.69 % Allowed : 16.40 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.37 (0.17), residues: 2460 helix: 1.75 (0.15), residues: 1310 sheet: -1.33 (0.38), residues: 176 loop : -1.62 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 766 HIS 0.011 0.001 HIS A1059 PHE 0.013 0.001 PHE C 495 TYR 0.021 0.001 TYR C 523 ARG 0.004 0.000 ARG B1005 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 303 time to evaluate : 2.491 Fit side-chains REVERT: A 407 MET cc_start: 0.8323 (mtm) cc_final: 0.7978 (mtm) REVERT: A 414 MET cc_start: 0.7736 (mpt) cc_final: 0.7365 (mtp) REVERT: A 450 TYR cc_start: 0.8185 (m-80) cc_final: 0.7530 (m-80) REVERT: A 642 GLN cc_start: 0.8047 (pp30) cc_final: 0.7805 (pp30) REVERT: A 668 ASP cc_start: 0.7690 (t70) cc_final: 0.7482 (t0) REVERT: A 695 LYS cc_start: 0.8533 (mptt) cc_final: 0.8298 (pttp) REVERT: A 1126 PHE cc_start: 0.7468 (t80) cc_final: 0.7179 (m-80) REVERT: B 563 GLN cc_start: 0.5477 (mt0) cc_final: 0.4561 (tm-30) REVERT: B 629 MET cc_start: 0.7204 (mmm) cc_final: 0.6672 (tpp) REVERT: B 656 LYS cc_start: 0.8582 (tttt) cc_final: 0.8155 (tmtt) REVERT: B 684 ARG cc_start: 0.8008 (pmm150) cc_final: 0.7726 (mtm-85) REVERT: B 713 GLU cc_start: 0.7705 (tt0) cc_final: 0.7311 (tt0) REVERT: B 719 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8300 (p0) REVERT: B 1032 TRP cc_start: 0.8535 (m100) cc_final: 0.8125 (m-10) REVERT: B 1035 SER cc_start: 0.7820 (p) cc_final: 0.7499 (t) REVERT: B 1125 GLU cc_start: 0.7772 (tp30) cc_final: 0.7527 (tm-30) REVERT: C 414 MET cc_start: 0.7884 (mpt) cc_final: 0.7504 (mtp) REVERT: C 668 ASP cc_start: 0.7705 (t70) cc_final: 0.7499 (t0) REVERT: C 1095 TYR cc_start: 0.7373 (t80) cc_final: 0.6868 (t80) REVERT: D 486 GLU cc_start: 0.7382 (tp30) cc_final: 0.6966 (tp30) REVERT: D 656 LYS cc_start: 0.8420 (tttt) cc_final: 0.8078 (tmtt) REVERT: D 684 ARG cc_start: 0.7906 (pmm150) cc_final: 0.7566 (mtm-85) REVERT: D 713 GLU cc_start: 0.7606 (tt0) cc_final: 0.7236 (tt0) REVERT: D 813 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7514 (pt0) REVERT: D 1032 TRP cc_start: 0.8476 (m100) cc_final: 0.8078 (m-10) REVERT: D 1035 SER cc_start: 0.7776 (p) cc_final: 0.7480 (t) REVERT: D 1069 GLU cc_start: 0.6400 (tp30) cc_final: 0.6048 (tm-30) REVERT: D 1202 ASP cc_start: 0.7390 (t70) cc_final: 0.7055 (t0) outliers start: 77 outliers final: 52 residues processed: 351 average time/residue: 0.2920 time to fit residues: 163.6101 Evaluate side-chains 337 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 284 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1077 LYS Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1131 HIS Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1120 CYS Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 239 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A1131 HIS B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19866 Z= 0.196 Angle : 0.530 9.449 26842 Z= 0.271 Chirality : 0.040 0.184 2998 Planarity : 0.003 0.033 3312 Dihedral : 7.107 83.862 2790 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.64 % Allowed : 17.40 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.58 (0.17), residues: 2460 helix: 1.93 (0.15), residues: 1314 sheet: -1.14 (0.39), residues: 166 loop : -1.56 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 766 HIS 0.012 0.002 HIS A1131 PHE 0.013 0.001 PHE C 495 TYR 0.021 0.001 TYR C 523 ARG 0.004 0.000 ARG C 628 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 302 time to evaluate : 2.269 Fit side-chains REVERT: A 407 MET cc_start: 0.8309 (mtm) cc_final: 0.7856 (mtm) REVERT: A 414 MET cc_start: 0.7773 (mpt) cc_final: 0.7332 (mtp) REVERT: A 450 TYR cc_start: 0.8153 (m-80) cc_final: 0.7565 (m-80) REVERT: A 642 GLN cc_start: 0.8011 (pp30) cc_final: 0.7768 (pp30) REVERT: A 668 ASP cc_start: 0.7713 (t70) cc_final: 0.7474 (t0) REVERT: A 695 LYS cc_start: 0.8528 (mptt) cc_final: 0.8257 (pttp) REVERT: A 1126 PHE cc_start: 0.7382 (t80) cc_final: 0.7089 (m-80) REVERT: B 486 GLU cc_start: 0.7557 (tp30) cc_final: 0.7302 (tp30) REVERT: B 563 GLN cc_start: 0.5435 (mt0) cc_final: 0.4597 (tm-30) REVERT: B 656 LYS cc_start: 0.8571 (tttt) cc_final: 0.8151 (tmtt) REVERT: B 684 ARG cc_start: 0.8002 (pmm150) cc_final: 0.7725 (mtm-85) REVERT: B 713 GLU cc_start: 0.7688 (tt0) cc_final: 0.7386 (tt0) REVERT: B 719 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8300 (p0) REVERT: B 1032 TRP cc_start: 0.8535 (m100) cc_final: 0.8105 (m-10) REVERT: B 1035 SER cc_start: 0.7828 (p) cc_final: 0.7512 (t) REVERT: B 1125 GLU cc_start: 0.7738 (tp30) cc_final: 0.7470 (pt0) REVERT: C 414 MET cc_start: 0.7889 (mpt) cc_final: 0.7501 (mtp) REVERT: C 668 ASP cc_start: 0.7723 (t70) cc_final: 0.7500 (t0) REVERT: C 1023 MET cc_start: 0.8849 (tpt) cc_final: 0.8508 (tpt) REVERT: C 1095 TYR cc_start: 0.7382 (t80) cc_final: 0.6881 (t80) REVERT: D 486 GLU cc_start: 0.7333 (tp30) cc_final: 0.6909 (tp30) REVERT: D 656 LYS cc_start: 0.8423 (tttt) cc_final: 0.8088 (tmtt) REVERT: D 684 ARG cc_start: 0.7955 (pmm150) cc_final: 0.7589 (mtm-85) REVERT: D 713 GLU cc_start: 0.7642 (tt0) cc_final: 0.7355 (tt0) REVERT: D 813 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7503 (pt0) REVERT: D 1032 TRP cc_start: 0.8451 (m100) cc_final: 0.8057 (m-10) REVERT: D 1035 SER cc_start: 0.7835 (p) cc_final: 0.7535 (t) REVERT: D 1202 ASP cc_start: 0.7450 (t70) cc_final: 0.7113 (t0) outliers start: 76 outliers final: 57 residues processed: 347 average time/residue: 0.2658 time to fit residues: 149.1428 Evaluate side-chains 343 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 285 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1131 HIS Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1103 SER Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1058 THR Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 201 optimal weight: 0.0070 chunk 133 optimal weight: 3.9990 chunk 239 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1131 HIS ** A1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS ** C1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19866 Z= 0.392 Angle : 0.631 9.311 26842 Z= 0.327 Chirality : 0.045 0.241 2998 Planarity : 0.004 0.049 3312 Dihedral : 7.449 87.129 2790 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.51 % Allowed : 17.02 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.18 (0.17), residues: 2460 helix: 1.58 (0.14), residues: 1308 sheet: -1.31 (0.39), residues: 168 loop : -1.70 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 578 HIS 0.010 0.002 HIS A1059 PHE 0.018 0.002 PHE D1140 TYR 0.025 0.002 TYR C 523 ARG 0.007 0.001 ARG B1203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 277 time to evaluate : 2.328 Fit side-chains REVERT: A 414 MET cc_start: 0.7835 (mpt) cc_final: 0.7378 (mtp) REVERT: A 450 TYR cc_start: 0.8236 (m-80) cc_final: 0.7721 (m-80) REVERT: A 668 ASP cc_start: 0.7763 (t70) cc_final: 0.7528 (t0) REVERT: A 695 LYS cc_start: 0.8523 (mptt) cc_final: 0.8308 (pttp) REVERT: A 817 LYS cc_start: 0.7322 (mmtp) cc_final: 0.7120 (mttt) REVERT: A 1126 PHE cc_start: 0.7299 (t80) cc_final: 0.7032 (m-80) REVERT: B 656 LYS cc_start: 0.8613 (tttt) cc_final: 0.8140 (tmtt) REVERT: B 661 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7089 (ptt90) REVERT: B 684 ARG cc_start: 0.8085 (pmm150) cc_final: 0.7771 (mtm-85) REVERT: B 713 GLU cc_start: 0.7711 (tt0) cc_final: 0.7312 (tt0) REVERT: B 719 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8393 (p0) REVERT: B 1032 TRP cc_start: 0.8545 (m100) cc_final: 0.8107 (m-10) REVERT: B 1035 SER cc_start: 0.7727 (p) cc_final: 0.7414 (t) REVERT: B 1125 GLU cc_start: 0.7743 (tp30) cc_final: 0.7486 (pt0) REVERT: C 414 MET cc_start: 0.7837 (mpt) cc_final: 0.7468 (mtp) REVERT: C 668 ASP cc_start: 0.7775 (t70) cc_final: 0.7547 (t0) REVERT: C 1095 TYR cc_start: 0.7467 (t80) cc_final: 0.6907 (t80) REVERT: D 486 GLU cc_start: 0.7570 (tp30) cc_final: 0.7192 (tp30) REVERT: D 629 MET cc_start: 0.7241 (mmm) cc_final: 0.6172 (tpp) REVERT: D 656 LYS cc_start: 0.8486 (tttt) cc_final: 0.8122 (tmtt) REVERT: D 684 ARG cc_start: 0.8022 (pmm150) cc_final: 0.7625 (mtm-85) REVERT: D 713 GLU cc_start: 0.7699 (tt0) cc_final: 0.7322 (tt0) REVERT: D 813 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7547 (pt0) REVERT: D 1032 TRP cc_start: 0.8511 (m100) cc_final: 0.8093 (m-10) REVERT: D 1035 SER cc_start: 0.7673 (p) cc_final: 0.7367 (t) REVERT: D 1055 GLU cc_start: 0.5086 (OUTLIER) cc_final: 0.4853 (mm-30) REVERT: D 1202 ASP cc_start: 0.7376 (t70) cc_final: 0.7013 (t0) outliers start: 94 outliers final: 74 residues processed: 342 average time/residue: 0.2744 time to fit residues: 149.7158 Evaluate side-chains 344 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 267 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1131 HIS Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1091 ASP Chi-restraints excluded: chain C residue 1103 SER Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1055 GLU Chi-restraints excluded: chain D residue 1058 THR Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1187 ILE Chi-restraints excluded: chain D residue 1192 VAL Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 0.3980 chunk 72 optimal weight: 0.9990 chunk 46 optimal weight: 0.0470 chunk 151 optimal weight: 7.9990 chunk 162 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 217 optimal weight: 0.9980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1198 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19866 Z= 0.155 Angle : 0.534 11.414 26842 Z= 0.271 Chirality : 0.040 0.194 2998 Planarity : 0.003 0.034 3312 Dihedral : 6.468 74.951 2790 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.40 % Allowed : 19.18 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.66 (0.17), residues: 2460 helix: 2.04 (0.15), residues: 1310 sheet: -1.26 (0.39), residues: 168 loop : -1.56 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 766 HIS 0.012 0.001 HIS A1131 PHE 0.012 0.001 PHE C 495 TYR 0.019 0.001 TYR C 523 ARG 0.004 0.000 ARG B1203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 299 time to evaluate : 2.100 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.7793 (mpt) cc_final: 0.7343 (mtp) REVERT: A 450 TYR cc_start: 0.7998 (m-80) cc_final: 0.7621 (m-80) REVERT: A 668 ASP cc_start: 0.7692 (t70) cc_final: 0.7472 (t0) REVERT: A 695 LYS cc_start: 0.8475 (mptt) cc_final: 0.8247 (pttp) REVERT: A 817 LYS cc_start: 0.7274 (mmtp) cc_final: 0.7058 (mttt) REVERT: A 1126 PHE cc_start: 0.7273 (t80) cc_final: 0.7050 (m-80) REVERT: B 486 GLU cc_start: 0.7511 (tp30) cc_final: 0.7275 (tp30) REVERT: B 563 GLN cc_start: 0.5575 (mt0) cc_final: 0.4772 (tm-30) REVERT: B 656 LYS cc_start: 0.8566 (tttt) cc_final: 0.8137 (tmtt) REVERT: B 661 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6902 (ptt90) REVERT: B 684 ARG cc_start: 0.7956 (pmm150) cc_final: 0.7651 (mtm-85) REVERT: B 713 GLU cc_start: 0.7639 (tt0) cc_final: 0.7337 (tt0) REVERT: B 1032 TRP cc_start: 0.8548 (m100) cc_final: 0.8123 (m-10) REVERT: B 1035 SER cc_start: 0.7828 (p) cc_final: 0.7507 (t) REVERT: B 1125 GLU cc_start: 0.7753 (tp30) cc_final: 0.7539 (pt0) REVERT: B 1199 MET cc_start: 0.8556 (mmt) cc_final: 0.8093 (mmp) REVERT: C 414 MET cc_start: 0.7890 (mpt) cc_final: 0.7489 (mtp) REVERT: C 668 ASP cc_start: 0.7723 (t70) cc_final: 0.7501 (t0) REVERT: C 1023 MET cc_start: 0.8744 (tpt) cc_final: 0.8460 (tpt) REVERT: C 1095 TYR cc_start: 0.7459 (t80) cc_final: 0.6956 (t80) REVERT: D 486 GLU cc_start: 0.7335 (tp30) cc_final: 0.6933 (tp30) REVERT: D 563 GLN cc_start: 0.5613 (mt0) cc_final: 0.4709 (tm-30) REVERT: D 629 MET cc_start: 0.7041 (mmm) cc_final: 0.6125 (tpp) REVERT: D 656 LYS cc_start: 0.8429 (tttt) cc_final: 0.8061 (tmtt) REVERT: D 684 ARG cc_start: 0.8008 (pmm150) cc_final: 0.7608 (mtm-85) REVERT: D 713 GLU cc_start: 0.7605 (tt0) cc_final: 0.7309 (tt0) REVERT: D 813 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7489 (pt0) REVERT: D 1032 TRP cc_start: 0.8493 (m100) cc_final: 0.8089 (m-10) REVERT: D 1035 SER cc_start: 0.7736 (p) cc_final: 0.7286 (t) REVERT: D 1202 ASP cc_start: 0.7452 (t70) cc_final: 0.7117 (t0) outliers start: 50 outliers final: 43 residues processed: 330 average time/residue: 0.2915 time to fit residues: 151.7219 Evaluate side-chains 331 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 287 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1091 ASP Chi-restraints excluded: chain C residue 1103 SER Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 174 optimal weight: 3.9990 chunk 68 optimal weight: 0.0040 chunk 201 optimal weight: 0.0370 chunk 210 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.6672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1198 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19866 Z= 0.156 Angle : 0.526 10.875 26842 Z= 0.268 Chirality : 0.040 0.225 2998 Planarity : 0.003 0.033 3312 Dihedral : 5.391 53.200 2790 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.49 % Allowed : 19.13 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.78 (0.17), residues: 2460 helix: 2.16 (0.15), residues: 1310 sheet: -1.47 (0.36), residues: 190 loop : -1.46 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 766 HIS 0.018 0.001 HIS A1059 PHE 0.013 0.001 PHE C 495 TYR 0.019 0.001 TYR C 523 ARG 0.007 0.000 ARG A 715 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 298 time to evaluate : 2.240 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.7792 (mpt) cc_final: 0.7345 (mtp) REVERT: A 450 TYR cc_start: 0.7984 (m-80) cc_final: 0.7604 (m-80) REVERT: A 668 ASP cc_start: 0.7691 (t70) cc_final: 0.7463 (t0) REVERT: A 695 LYS cc_start: 0.8441 (mptt) cc_final: 0.8196 (pttp) REVERT: A 1126 PHE cc_start: 0.7280 (t80) cc_final: 0.7032 (m-80) REVERT: B 486 GLU cc_start: 0.7374 (tp30) cc_final: 0.7111 (tp30) REVERT: B 563 GLN cc_start: 0.5528 (mt0) cc_final: 0.4694 (tm-30) REVERT: B 656 LYS cc_start: 0.8563 (tttt) cc_final: 0.8215 (tmtt) REVERT: B 661 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6830 (ptt90) REVERT: B 684 ARG cc_start: 0.7939 (pmm150) cc_final: 0.7635 (mtm-85) REVERT: B 713 GLU cc_start: 0.7643 (tt0) cc_final: 0.7316 (tt0) REVERT: B 1032 TRP cc_start: 0.8502 (m100) cc_final: 0.8067 (m-10) REVERT: B 1035 SER cc_start: 0.7877 (p) cc_final: 0.7300 (t) REVERT: B 1125 GLU cc_start: 0.7765 (tp30) cc_final: 0.7461 (tm-30) REVERT: C 414 MET cc_start: 0.7842 (mpt) cc_final: 0.7428 (mtp) REVERT: C 668 ASP cc_start: 0.7745 (t70) cc_final: 0.7540 (t0) REVERT: C 1023 MET cc_start: 0.8736 (tpt) cc_final: 0.8535 (tpt) REVERT: C 1095 TYR cc_start: 0.7450 (t80) cc_final: 0.6962 (t80) REVERT: D 486 GLU cc_start: 0.7253 (tp30) cc_final: 0.6848 (tp30) REVERT: D 563 GLN cc_start: 0.5589 (mt0) cc_final: 0.4677 (tm-30) REVERT: D 656 LYS cc_start: 0.8406 (tttt) cc_final: 0.8061 (tmtt) REVERT: D 684 ARG cc_start: 0.7967 (pmm150) cc_final: 0.7564 (mtm-85) REVERT: D 713 GLU cc_start: 0.7590 (tt0) cc_final: 0.7283 (tt0) REVERT: D 1032 TRP cc_start: 0.8443 (m100) cc_final: 0.8008 (m-10) REVERT: D 1035 SER cc_start: 0.7811 (p) cc_final: 0.7590 (t) REVERT: D 1202 ASP cc_start: 0.7425 (t70) cc_final: 0.7083 (t0) outliers start: 52 outliers final: 47 residues processed: 331 average time/residue: 0.2815 time to fit residues: 147.4091 Evaluate side-chains 331 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 283 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1091 ASP Chi-restraints excluded: chain C residue 1103 SER Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.0170 chunk 143 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 163 optimal weight: 0.6980 chunk 247 optimal weight: 0.4980 chunk 227 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 overall best weight: 1.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1131 HIS ** A1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19866 Z= 0.235 Angle : 0.554 10.836 26842 Z= 0.285 Chirality : 0.041 0.202 2998 Planarity : 0.003 0.033 3312 Dihedral : 5.099 47.309 2790 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.40 % Allowed : 19.61 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.71 (0.17), residues: 2460 helix: 2.07 (0.15), residues: 1312 sheet: -1.49 (0.37), residues: 190 loop : -1.46 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 766 HIS 0.016 0.001 HIS A1059 PHE 0.013 0.001 PHE A 495 TYR 0.021 0.001 TYR C 523 ARG 0.007 0.000 ARG D1036 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 297 time to evaluate : 2.339 Fit side-chains REVERT: A 414 MET cc_start: 0.7838 (mpt) cc_final: 0.7377 (mtp) REVERT: A 450 TYR cc_start: 0.8018 (m-80) cc_final: 0.7570 (m-80) REVERT: A 668 ASP cc_start: 0.7728 (t70) cc_final: 0.7500 (t0) REVERT: A 817 LYS cc_start: 0.7301 (mmtp) cc_final: 0.7091 (mttt) REVERT: A 1126 PHE cc_start: 0.7307 (t80) cc_final: 0.7039 (m-80) REVERT: B 486 GLU cc_start: 0.7511 (tp30) cc_final: 0.7276 (tp30) REVERT: B 563 GLN cc_start: 0.5581 (mt0) cc_final: 0.4753 (tm-30) REVERT: B 656 LYS cc_start: 0.8589 (tttt) cc_final: 0.8146 (tmtt) REVERT: B 661 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6908 (ptt90) REVERT: B 684 ARG cc_start: 0.7953 (pmm150) cc_final: 0.7629 (mtm-85) REVERT: B 713 GLU cc_start: 0.7670 (tt0) cc_final: 0.7352 (tt0) REVERT: B 1032 TRP cc_start: 0.8512 (m100) cc_final: 0.8055 (m-10) REVERT: B 1035 SER cc_start: 0.7848 (p) cc_final: 0.7552 (t) REVERT: C 414 MET cc_start: 0.7842 (mpt) cc_final: 0.7432 (mtp) REVERT: C 1023 MET cc_start: 0.8878 (tpt) cc_final: 0.8578 (tpt) REVERT: C 1095 TYR cc_start: 0.7443 (t80) cc_final: 0.6925 (t80) REVERT: D 486 GLU cc_start: 0.7376 (tp30) cc_final: 0.6989 (tp30) REVERT: D 563 GLN cc_start: 0.5623 (mt0) cc_final: 0.4698 (tm-30) REVERT: D 656 LYS cc_start: 0.8435 (tttt) cc_final: 0.8041 (tmtt) REVERT: D 684 ARG cc_start: 0.8024 (pmm150) cc_final: 0.7619 (mtm-85) REVERT: D 713 GLU cc_start: 0.7634 (tt0) cc_final: 0.7328 (tt0) REVERT: D 813 GLU cc_start: 0.7750 (tp30) cc_final: 0.7534 (pt0) REVERT: D 1032 TRP cc_start: 0.8471 (m100) cc_final: 0.8030 (m-10) REVERT: D 1202 ASP cc_start: 0.7456 (t70) cc_final: 0.7107 (t0) outliers start: 50 outliers final: 43 residues processed: 329 average time/residue: 0.2801 time to fit residues: 146.4896 Evaluate side-chains 330 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 286 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 696 SER Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1091 ASP Chi-restraints excluded: chain C residue 1103 SER Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 202 optimal weight: 0.0470 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1131 HIS ** A1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.137894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108299 restraints weight = 30587.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.110119 restraints weight = 20863.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110518 restraints weight = 15151.781| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19866 Z= 0.205 Angle : 0.544 10.792 26842 Z= 0.281 Chirality : 0.041 0.194 2998 Planarity : 0.003 0.031 3312 Dihedral : 4.951 43.071 2790 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.11 % Allowed : 20.04 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.71 (0.17), residues: 2460 helix: 2.11 (0.15), residues: 1308 sheet: -1.62 (0.36), residues: 180 loop : -1.48 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 766 HIS 0.014 0.001 HIS A1059 PHE 0.020 0.001 PHE B1126 TYR 0.020 0.001 TYR C 523 ARG 0.006 0.000 ARG D1036 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4104.80 seconds wall clock time: 75 minutes 28.35 seconds (4528.35 seconds total)