Starting phenix.real_space_refine on Mon Feb 19 14:15:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxo_25502/02_2024/7sxo_25502_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxo_25502/02_2024/7sxo_25502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxo_25502/02_2024/7sxo_25502.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxo_25502/02_2024/7sxo_25502.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxo_25502/02_2024/7sxo_25502_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxo_25502/02_2024/7sxo_25502_updated.pdb" } resolution = 3.3 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= 0.001 sd= 0.051 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 4 5.21 5 S 108 5.16 5 C 15849 2.51 5 N 4216 2.21 5 O 4701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 922": "OE1" <-> "OE2" Residue "C GLU 612": "OE1" <-> "OE2" Residue "C PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 816": "OE1" <-> "OE2" Residue "C GLU 1057": "OE1" <-> "OE2" Residue "C PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1124": "OE1" <-> "OE2" Residue "D GLU 781": "OE1" <-> "OE2" Residue "D GLU 1089": "OE1" <-> "OE2" Residue "E PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 767": "OE1" <-> "OE2" Residue "E GLU 816": "OE1" <-> "OE2" Residue "E GLU 972": "OE1" <-> "OE2" Residue "E GLU 1057": "OE1" <-> "OE2" Residue "E GLU 1122": "OE1" <-> "OE2" Residue "F GLU 585": "OE1" <-> "OE2" Residue "F GLU 598": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24894 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4256 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 27, 'TRANS': 516} Chain breaks: 3 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3793 Classifications: {'peptide': 487} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 25, 'TRANS': 461} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "C" Number of atoms: 3786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3786 Classifications: {'peptide': 487} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 25, 'TRANS': 461} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 4262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4262 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 27, 'TRANS': 519} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 4278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4278 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 518} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4292 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 521} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.63, per 1000 atoms: 0.51 Number of scatterers: 24894 At special positions: 0 Unit cell: (131.1, 136.85, 141.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 16 15.00 Mg 4 11.99 O 4701 8.00 N 4216 7.00 C 15849 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 629 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B 629 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS D 629 " - pdb=" SG CYS D 747 " distance=2.04 Simple disulfide: pdb=" SG CYS F 629 " - pdb=" SG CYS F 747 " distance=2.03 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.46 Conformation dependent library (CDL) restraints added in 5.0 seconds 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5890 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 126 helices and 25 sheets defined 40.9% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.34 Creating SS restraints... Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 541 through 556 Processing helix chain 'A' and resid 562 through 576 Processing helix chain 'A' and resid 589 through 599 removed outlier: 4.073A pdb=" N ASP A 599 " --> pdb=" O ILE A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 618 Processing helix chain 'A' and resid 640 through 648 removed outlier: 3.601A pdb=" N LYS A 643 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 668 removed outlier: 3.898A pdb=" N LYS A 668 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 689 Processing helix chain 'A' and resid 713 through 721 Processing helix chain 'A' and resid 726 through 728 No H-bonds generated for 'chain 'A' and resid 726 through 728' Processing helix chain 'A' and resid 757 through 762 Processing helix chain 'A' and resid 773 through 791 removed outlier: 5.327A pdb=" N VAL A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) Proline residue: A 786 - end of helix Processing helix chain 'A' and resid 803 through 812 Processing helix chain 'A' and resid 820 through 839 Processing helix chain 'A' and resid 906 through 910 removed outlier: 4.014A pdb=" N VAL A 910 " --> pdb=" O LYS A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 988 Processing helix chain 'A' and resid 994 through 996 No H-bonds generated for 'chain 'A' and resid 994 through 996' Processing helix chain 'A' and resid 1017 through 1029 removed outlier: 3.595A pdb=" N ALA A1021 " --> pdb=" O GLY A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1064 Processing helix chain 'A' and resid 1074 through 1082 removed outlier: 4.689A pdb=" N ASN A1078 " --> pdb=" O ASP A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1088 No H-bonds generated for 'chain 'A' and resid 1085 through 1088' Processing helix chain 'A' and resid 1099 through 1106 Processing helix chain 'A' and resid 1120 through 1128 removed outlier: 3.850A pdb=" N ILE A1125 " --> pdb=" O ALA A1121 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A1126 " --> pdb=" O GLU A1122 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 599 removed outlier: 3.747A pdb=" N GLU B 598 " --> pdb=" O LYS B 594 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP B 599 " --> pdb=" O ILE B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 619 Processing helix chain 'B' and resid 640 through 649 Processing helix chain 'B' and resid 681 through 689 Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'B' and resid 723 through 728 removed outlier: 4.064A pdb=" N ASN B 727 " --> pdb=" O PRO B 723 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N SER B 728 " --> pdb=" O GLU B 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 723 through 728' Processing helix chain 'B' and resid 757 through 760 No H-bonds generated for 'chain 'B' and resid 757 through 760' Processing helix chain 'B' and resid 773 through 792 removed outlier: 4.823A pdb=" N VAL B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) Proline residue: B 786 - end of helix Processing helix chain 'B' and resid 803 through 813 Processing helix chain 'B' and resid 820 through 840 Processing helix chain 'B' and resid 967 through 988 Processing helix chain 'B' and resid 994 through 997 No H-bonds generated for 'chain 'B' and resid 994 through 997' Processing helix chain 'B' and resid 1014 through 1029 removed outlier: 4.882A pdb=" N VAL B1018 " --> pdb=" O SER B1015 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET B1020 " --> pdb=" O GLY B1017 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR B1022 " --> pdb=" O THR B1019 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B1024 " --> pdb=" O ALA B1021 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU B1025 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1064 Processing helix chain 'B' and resid 1074 through 1082 removed outlier: 4.566A pdb=" N ASN B1078 " --> pdb=" O ASP B1075 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B1082 " --> pdb=" O ASP B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1088 No H-bonds generated for 'chain 'B' and resid 1085 through 1088' Processing helix chain 'B' and resid 1099 through 1106 Processing helix chain 'C' and resid 589 through 599 Processing helix chain 'C' and resid 604 through 618 Processing helix chain 'C' and resid 641 through 648 Processing helix chain 'C' and resid 665 through 668 No H-bonds generated for 'chain 'C' and resid 665 through 668' Processing helix chain 'C' and resid 681 through 689 Processing helix chain 'C' and resid 713 through 721 Processing helix chain 'C' and resid 757 through 761 Processing helix chain 'C' and resid 773 through 791 removed outlier: 5.099A pdb=" N VAL C 785 " --> pdb=" O GLU C 781 " (cutoff:3.500A) Proline residue: C 786 - end of helix Processing helix chain 'C' and resid 803 through 812 Processing helix chain 'C' and resid 820 through 840 Processing helix chain 'C' and resid 952 through 954 No H-bonds generated for 'chain 'C' and resid 952 through 954' Processing helix chain 'C' and resid 967 through 988 removed outlier: 3.641A pdb=" N ALA C 986 " --> pdb=" O LYS C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 996 No H-bonds generated for 'chain 'C' and resid 994 through 996' Processing helix chain 'C' and resid 1014 through 1029 removed outlier: 4.874A pdb=" N VAL C1018 " --> pdb=" O SER C1015 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET C1020 " --> pdb=" O GLY C1017 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C1021 " --> pdb=" O VAL C1018 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C1022 " --> pdb=" O THR C1019 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE C1024 " --> pdb=" O ALA C1021 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C1025 " --> pdb=" O THR C1022 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C1029 " --> pdb=" O SER C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1056 through 1064 Processing helix chain 'C' and resid 1074 through 1082 removed outlier: 4.333A pdb=" N ASN C1078 " --> pdb=" O ASP C1075 " (cutoff:3.500A) Processing helix chain 'C' and resid 1085 through 1088 No H-bonds generated for 'chain 'C' and resid 1085 through 1088' Processing helix chain 'C' and resid 1099 through 1106 Processing helix chain 'C' and resid 1120 through 1122 No H-bonds generated for 'chain 'C' and resid 1120 through 1122' Processing helix chain 'D' and resid 531 through 536 Processing helix chain 'D' and resid 541 through 555 Processing helix chain 'D' and resid 562 through 575 Processing helix chain 'D' and resid 589 through 597 Processing helix chain 'D' and resid 605 through 619 Processing helix chain 'D' and resid 640 through 648 Processing helix chain 'D' and resid 665 through 668 No H-bonds generated for 'chain 'D' and resid 665 through 668' Processing helix chain 'D' and resid 681 through 689 Processing helix chain 'D' and resid 713 through 721 Processing helix chain 'D' and resid 725 through 728 Processing helix chain 'D' and resid 757 through 762 removed outlier: 3.866A pdb=" N ARG D 762 " --> pdb=" O PRO D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 791 removed outlier: 4.798A pdb=" N VAL D 785 " --> pdb=" O GLU D 781 " (cutoff:3.500A) Proline residue: D 786 - end of helix Processing helix chain 'D' and resid 803 through 813 Processing helix chain 'D' and resid 820 through 838 Processing helix chain 'D' and resid 906 through 908 No H-bonds generated for 'chain 'D' and resid 906 through 908' Processing helix chain 'D' and resid 967 through 988 Processing helix chain 'D' and resid 994 through 996 No H-bonds generated for 'chain 'D' and resid 994 through 996' Processing helix chain 'D' and resid 1014 through 1029 removed outlier: 4.874A pdb=" N VAL D1018 " --> pdb=" O SER D1015 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET D1020 " --> pdb=" O GLY D1017 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR D1022 " --> pdb=" O THR D1019 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE D1024 " --> pdb=" O ALA D1021 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU D1025 " --> pdb=" O THR D1022 " (cutoff:3.500A) Processing helix chain 'D' and resid 1056 through 1064 Processing helix chain 'D' and resid 1074 through 1081 removed outlier: 4.320A pdb=" N ASN D1078 " --> pdb=" O ASP D1075 " (cutoff:3.500A) Processing helix chain 'D' and resid 1085 through 1088 No H-bonds generated for 'chain 'D' and resid 1085 through 1088' Processing helix chain 'D' and resid 1099 through 1106 Processing helix chain 'D' and resid 1120 through 1124 Processing helix chain 'E' and resid 531 through 537 Processing helix chain 'E' and resid 541 through 556 removed outlier: 3.720A pdb=" N THR E 556 " --> pdb=" O THR E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 576 Processing helix chain 'E' and resid 589 through 597 Processing helix chain 'E' and resid 604 through 620 removed outlier: 3.595A pdb=" N LEU E 620 " --> pdb=" O VAL E 616 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 648 removed outlier: 3.898A pdb=" N SER E 644 " --> pdb=" O SER E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 665 through 668 No H-bonds generated for 'chain 'E' and resid 665 through 668' Processing helix chain 'E' and resid 681 through 689 Processing helix chain 'E' and resid 713 through 720 Processing helix chain 'E' and resid 726 through 728 No H-bonds generated for 'chain 'E' and resid 726 through 728' Processing helix chain 'E' and resid 757 through 761 Processing helix chain 'E' and resid 773 through 792 removed outlier: 5.221A pdb=" N VAL E 785 " --> pdb=" O GLU E 781 " (cutoff:3.500A) Proline residue: E 786 - end of helix Processing helix chain 'E' and resid 803 through 812 Processing helix chain 'E' and resid 820 through 840 Processing helix chain 'E' and resid 903 through 910 removed outlier: 4.834A pdb=" N LYS E 907 " --> pdb=" O LYS E 904 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP E 908 " --> pdb=" O ASN E 905 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL E 910 " --> pdb=" O LYS E 907 " (cutoff:3.500A) Processing helix chain 'E' and resid 952 through 954 No H-bonds generated for 'chain 'E' and resid 952 through 954' Processing helix chain 'E' and resid 967 through 988 removed outlier: 3.561A pdb=" N ALA E 986 " --> pdb=" O LYS E 982 " (cutoff:3.500A) Processing helix chain 'E' and resid 994 through 996 No H-bonds generated for 'chain 'E' and resid 994 through 996' Processing helix chain 'E' and resid 1014 through 1029 removed outlier: 4.851A pdb=" N VAL E1018 " --> pdb=" O SER E1015 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET E1020 " --> pdb=" O GLY E1017 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA E1021 " --> pdb=" O VAL E1018 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR E1022 " --> pdb=" O THR E1019 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE E1024 " --> pdb=" O ALA E1021 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA E1028 " --> pdb=" O LEU E1025 " (cutoff:3.500A) Processing helix chain 'E' and resid 1056 through 1064 Processing helix chain 'E' and resid 1074 through 1081 removed outlier: 4.592A pdb=" N ASN E1078 " --> pdb=" O ASP E1075 " (cutoff:3.500A) Processing helix chain 'E' and resid 1085 through 1088 No H-bonds generated for 'chain 'E' and resid 1085 through 1088' Processing helix chain 'E' and resid 1099 through 1106 Processing helix chain 'E' and resid 1121 through 1126 removed outlier: 3.651A pdb=" N ILE E1125 " --> pdb=" O ALA E1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 537 Processing helix chain 'F' and resid 541 through 556 removed outlier: 3.752A pdb=" N THR F 556 " --> pdb=" O THR F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 576 Processing helix chain 'F' and resid 589 through 597 Processing helix chain 'F' and resid 604 through 619 removed outlier: 3.533A pdb=" N LEU F 619 " --> pdb=" O ALA F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 648 Processing helix chain 'F' and resid 664 through 666 No H-bonds generated for 'chain 'F' and resid 664 through 666' Processing helix chain 'F' and resid 681 through 689 Processing helix chain 'F' and resid 713 through 720 Processing helix chain 'F' and resid 757 through 762 removed outlier: 3.854A pdb=" N ARG F 762 " --> pdb=" O PRO F 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 773 through 792 removed outlier: 5.370A pdb=" N VAL F 785 " --> pdb=" O GLU F 781 " (cutoff:3.500A) Proline residue: F 786 - end of helix removed outlier: 3.755A pdb=" N ALA F 792 " --> pdb=" O ALA F 788 " (cutoff:3.500A) Processing helix chain 'F' and resid 803 through 812 Processing helix chain 'F' and resid 820 through 840 Processing helix chain 'F' and resid 903 through 905 No H-bonds generated for 'chain 'F' and resid 903 through 905' Processing helix chain 'F' and resid 968 through 988 removed outlier: 3.501A pdb=" N SER F 979 " --> pdb=" O ARG F 975 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA F 986 " --> pdb=" O LYS F 982 " (cutoff:3.500A) Processing helix chain 'F' and resid 1018 through 1028 removed outlier: 3.644A pdb=" N LEU F1025 " --> pdb=" O ALA F1021 " (cutoff:3.500A) Processing helix chain 'F' and resid 1055 through 1064 removed outlier: 3.500A pdb=" N ALA F1061 " --> pdb=" O GLU F1057 " (cutoff:3.500A) Processing helix chain 'F' and resid 1074 through 1082 removed outlier: 4.367A pdb=" N ASN F1078 " --> pdb=" O ASP F1075 " (cutoff:3.500A) Processing helix chain 'F' and resid 1085 through 1088 No H-bonds generated for 'chain 'F' and resid 1085 through 1088' Processing helix chain 'F' and resid 1099 through 1106 Processing sheet with id= A, first strand: chain 'A' and resid 764 through 768 removed outlier: 6.587A pdb=" N PHE A 745 " --> pdb=" O ILE A 628 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N PHE A 630 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N CYS A 747 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N GLY A 632 " --> pdb=" O CYS A 747 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA A 749 " --> pdb=" O GLY A 632 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 799 through 801 removed outlier: 7.101A pdb=" N VAL A 899 " --> pdb=" O ASP A 800 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 928 through 935 Processing sheet with id= D, first strand: chain 'A' and resid 1037 through 1039 removed outlier: 5.955A pdb=" N THR A1069 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU A1092 " --> pdb=" O ILE A1070 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N PHE A1072 " --> pdb=" O GLU A1092 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU A1094 " --> pdb=" O PHE A1072 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 628 through 631 Processing sheet with id= F, first strand: chain 'B' and resid 653 through 656 removed outlier: 6.098A pdb=" N LEU B 695 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE B 656 " --> pdb=" O LEU B 695 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU B 697 " --> pdb=" O PHE B 656 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 799 through 801 removed outlier: 7.084A pdb=" N VAL B 899 " --> pdb=" O ASP B 800 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 928 through 935 removed outlier: 6.185A pdb=" N THR B 959 " --> pdb=" O ILE B1000 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU B1002 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLU B 961 " --> pdb=" O LEU B1002 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 1069 through 1073 removed outlier: 5.866A pdb=" N GLU B1092 " --> pdb=" O ILE B1070 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N PHE B1072 " --> pdb=" O GLU B1092 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU B1094 " --> pdb=" O PHE B1072 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 629 through 631 Processing sheet with id= K, first strand: chain 'C' and resid 654 through 656 Processing sheet with id= L, first strand: chain 'C' and resid 799 through 801 removed outlier: 6.750A pdb=" N VAL C 899 " --> pdb=" O ASP C 800 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 928 through 934 Processing sheet with id= N, first strand: chain 'C' and resid 1037 through 1039 removed outlier: 6.347A pdb=" N THR C1069 " --> pdb=" O ALA C1038 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU C1092 " --> pdb=" O ILE C1070 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N PHE C1072 " --> pdb=" O GLU C1092 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU C1094 " --> pdb=" O PHE C1072 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 764 through 767 Processing sheet with id= P, first strand: chain 'D' and resid 799 through 801 removed outlier: 6.791A pdb=" N VAL D 899 " --> pdb=" O ASP D 800 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 928 through 935 Processing sheet with id= R, first strand: chain 'D' and resid 1037 through 1039 removed outlier: 6.194A pdb=" N THR D1069 " --> pdb=" O ALA D1038 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLU D1092 " --> pdb=" O ILE D1070 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N PHE D1072 " --> pdb=" O GLU D1092 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU D1094 " --> pdb=" O PHE D1072 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 764 through 768 removed outlier: 6.268A pdb=" N PHE E 745 " --> pdb=" O ILE E 628 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N PHE E 630 " --> pdb=" O PHE E 745 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS E 747 " --> pdb=" O PHE E 630 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N GLY E 632 " --> pdb=" O CYS E 747 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA E 749 " --> pdb=" O GLY E 632 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE E 696 " --> pdb=" O LEU E 744 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 928 through 930 removed outlier: 6.519A pdb=" N THR E 959 " --> pdb=" O ILE E1000 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU E1002 " --> pdb=" O THR E 959 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU E 961 " --> pdb=" O LEU E1002 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 1037 through 1039 removed outlier: 5.827A pdb=" N THR E1069 " --> pdb=" O ALA E1038 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLU E1092 " --> pdb=" O ILE E1070 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N PHE E1072 " --> pdb=" O GLU E1092 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU E1094 " --> pdb=" O PHE E1072 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'F' and resid 628 through 632 removed outlier: 6.004A pdb=" N GLU F 764 " --> pdb=" O CYS F 629 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL F 631 " --> pdb=" O GLU F 764 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE F 766 " --> pdb=" O VAL F 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 653 through 656 removed outlier: 6.019A pdb=" N LEU F 695 " --> pdb=" O PHE F 654 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N PHE F 656 " --> pdb=" O LEU F 695 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU F 697 " --> pdb=" O PHE F 656 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU F 744 " --> pdb=" O ILE F 696 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE F 698 " --> pdb=" O LEU F 744 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL F 746 " --> pdb=" O ILE F 698 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'F' and resid 928 through 934 Processing sheet with id= Y, first strand: chain 'F' and resid 1037 through 1039 removed outlier: 6.336A pdb=" N THR F1069 " --> pdb=" O ALA F1038 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLU F1092 " --> pdb=" O ILE F1070 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE F1072 " --> pdb=" O GLU F1092 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU F1094 " --> pdb=" O PHE F1072 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y 849 hydrogen bonds defined for protein. 2313 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.69 Time building geometry restraints manager: 12.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4633 1.33 - 1.45: 6219 1.45 - 1.58: 14325 1.58 - 1.71: 22 1.71 - 1.84: 178 Bond restraints: 25377 Sorted by residual: bond pdb=" C LEU F 920 " pdb=" N TYR F 921 " ideal model delta sigma weight residual 1.331 1.243 0.088 1.33e-02 5.65e+03 4.40e+01 bond pdb=" C LYS C1120 " pdb=" O LYS C1120 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.26e-02 6.30e+03 8.33e+00 bond pdb=" C PRO F 912 " pdb=" N PRO F 913 " ideal model delta sigma weight residual 1.331 1.363 -0.032 1.27e-02 6.20e+03 6.38e+00 bond pdb=" CA LYS C1120 " pdb=" CB LYS C1120 " ideal model delta sigma weight residual 1.530 1.511 0.019 1.69e-02 3.50e+03 1.25e+00 bond pdb=" CB ASN D 693 " pdb=" CG ASN D 693 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.02e+00 ... (remaining 25372 not shown) Histogram of bond angle deviations from ideal: 84.20 - 96.89: 1 96.89 - 109.57: 2403 109.57 - 122.26: 27900 122.26 - 134.94: 4015 134.94 - 147.63: 12 Bond angle restraints: 34331 Sorted by residual: angle pdb=" N LEU F 920 " pdb=" CA LEU F 920 " pdb=" C LEU F 920 " ideal model delta sigma weight residual 110.91 147.63 -36.72 1.17e+00 7.31e-01 9.85e+02 angle pdb=" C LEU F 920 " pdb=" CA LEU F 920 " pdb=" CB LEU F 920 " ideal model delta sigma weight residual 112.27 84.20 28.07 1.75e+00 3.27e-01 2.57e+02 angle pdb=" N PRO E 958 " pdb=" CA PRO E 958 " pdb=" CB PRO E 958 " ideal model delta sigma weight residual 103.25 111.52 -8.27 1.05e+00 9.07e-01 6.21e+01 angle pdb=" O LEU F 920 " pdb=" C LEU F 920 " pdb=" N TYR F 921 " ideal model delta sigma weight residual 123.33 116.85 6.48 1.22e+00 6.72e-01 2.82e+01 angle pdb=" CA LEU F 920 " pdb=" C LEU F 920 " pdb=" N TYR F 921 " ideal model delta sigma weight residual 114.17 121.44 -7.27 1.45e+00 4.76e-01 2.51e+01 ... (remaining 34326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.88: 14628 24.88 - 49.77: 819 49.77 - 74.65: 77 74.65 - 99.53: 33 99.53 - 124.42: 2 Dihedral angle restraints: 15559 sinusoidal: 6415 harmonic: 9144 Sorted by residual: dihedral pdb=" CB CYS B 629 " pdb=" SG CYS B 629 " pdb=" SG CYS B 747 " pdb=" CB CYS B 747 " ideal model delta sinusoidal sigma weight residual -86.00 -32.71 -53.29 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" O1B ADP B1200 " pdb=" O3A ADP B1200 " pdb=" PB ADP B1200 " pdb=" PA ADP B1200 " ideal model delta sinusoidal sigma weight residual -60.00 64.41 -124.42 1 2.00e+01 2.50e-03 3.76e+01 dihedral pdb=" CB CYS A 629 " pdb=" SG CYS A 629 " pdb=" SG CYS A 747 " pdb=" CB CYS A 747 " ideal model delta sinusoidal sigma weight residual -86.00 -36.24 -49.76 1 1.00e+01 1.00e-02 3.40e+01 ... (remaining 15556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 3887 0.189 - 0.378: 3 0.378 - 0.568: 0 0.568 - 0.757: 0 0.757 - 0.946: 1 Chirality restraints: 3891 Sorted by residual: chirality pdb=" CA LEU F 920 " pdb=" N LEU F 920 " pdb=" C LEU F 920 " pdb=" CB LEU F 920 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.24e+01 chirality pdb=" CA ASN F 954 " pdb=" N ASN F 954 " pdb=" C ASN F 954 " pdb=" CB ASN F 954 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA ASN D 693 " pdb=" N ASN D 693 " pdb=" C ASN D 693 " pdb=" CB ASN D 693 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3888 not shown) Planarity restraints: 4343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 757 " -0.055 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO D 758 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO D 758 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 758 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 678 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO E 679 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 679 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 679 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 912 " -0.041 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO F 913 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO F 913 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 913 " -0.035 5.00e-02 4.00e+02 ... (remaining 4340 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 352 2.65 - 3.22: 23097 3.22 - 3.78: 37904 3.78 - 4.34: 52474 4.34 - 4.90: 86057 Nonbonded interactions: 199884 Sorted by model distance: nonbonded pdb=" O LEU F 920 " pdb=" CB LEU F 920 " model vdw 2.092 2.752 nonbonded pdb=" OD1 ASN D 750 " pdb="MG MG D1201 " model vdw 2.114 2.170 nonbonded pdb=" NH1 ARG C 651 " pdb=" O GLN C 692 " model vdw 2.139 2.520 nonbonded pdb=" OG SER B 946 " pdb=" OH TYR B 978 " model vdw 2.193 2.440 nonbonded pdb=" OG1 THR D1046 " pdb=" OH TYR E 921 " model vdw 2.206 2.440 ... (remaining 199879 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 585 and (name N or name CA or name C or name O or name CB \ )) or resid 586 or (resid 587 and (name N or name CA or name C or name O or nam \ e CB )) or resid 588 through 628 or (resid 629 and (name N or name CA or name C \ or name O or name CB )) or resid 630 through 637 or (resid 638 and (name N or na \ me CA or name C or name O or name CB )) or resid 639 through 702 or (resid 703 a \ nd (name N or name CA or name C or name O or name CB )) or resid 704 or resid 71 \ 2 through 761 or (resid 762 and (name N or name CA or name C or name O or name C \ B )) or resid 763 through 841 or resid 896 through 903 or (resid 904 and (name N \ or name CA or name C or name O or name CB )) or resid 905 or (resid 906 through \ 908 and (name N or name CA or name C or name O or name CB )) or resid 909 throu \ gh 917 or (resid 918 through 919 and (name N or name CA or name C or name O or n \ ame CB )) or resid 920 through 953 or (resid 957 through 958 and (name N or name \ CA or name C or name O or name CB )) or resid 959 through 1123 or (resid 1124 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1125 or (resid \ 1126 and (name N or name CA or name C or name O or name CB )) or resid 1127)) selection = (chain 'B' and ((resid 585 and (name N or name CA or name C or name O or name CB \ )) or resid 586 or (resid 587 and (name N or name CA or name C or name O or nam \ e CB )) or resid 588 through 621 or (resid 622 and (name N or name CA or name C \ or name O or name CB )) or resid 623 or (resid 624 and (name N or name CA or nam \ e C or name O or name CB )) or resid 625 through 628 or (resid 629 and (name N o \ r name CA or name C or name O or name CB )) or resid 630 through 704 or resid 71 \ 2 through 761 or (resid 762 and (name N or name CA or name C or name O or name C \ B )) or resid 763 through 905 or (resid 906 through 908 and (name N or name CA o \ r name C or name O or name CB )) or resid 909 through 917 or (resid 918 through \ 919 and (name N or name CA or name C or name O or name CB )) or resid 920 throug \ h 953 or (resid 957 through 958 and (name N or name CA or name C or name O or na \ me CB )) or resid 959 through 1030 or resid 1032 through 1123 or (resid 1124 and \ (name N or name CA or name C or name O or name CB )) or resid 1125 or (resid 11 \ 26 and (name N or name CA or name C or name O or name CB )) or resid 1127)) selection = (chain 'C' and (resid 585 through 621 or (resid 622 and (name N or name CA or na \ me C or name O or name CB )) or resid 623 or (resid 624 and (name N or name CA o \ r name C or name O or name CB )) or resid 625 through 637 or (resid 638 and (nam \ e N or name CA or name C or name O or name CB )) or resid 639 through 702 or (re \ sid 703 and (name N or name CA or name C or name O or name CB )) or resid 704 or \ resid 712 through 761 or (resid 762 and (name N or name CA or name C or name O \ or name CB )) or resid 763 through 841 or resid 896 through 906 or (resid 907 th \ rough 908 and (name N or name CA or name C or name O or name CB )) or resid 909 \ through 917 or (resid 918 through 919 and (name N or name CA or name C or name O \ or name CB )) or resid 920 through 953 or (resid 957 through 958 and (name N or \ name CA or name C or name O or name CB )) or resid 959 through 1030 or resid 10 \ 32 through 1123 or (resid 1124 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1125 or (resid 1126 and (name N or name CA or name C or name O \ or name CB )) or resid 1127)) selection = (chain 'D' and ((resid 585 and (name N or name CA or name C or name O or name CB \ )) or resid 586 or (resid 587 and (name N or name CA or name C or name O or nam \ e CB )) or resid 588 through 621 or (resid 622 and (name N or name CA or name C \ or name O or name CB )) or resid 623 or (resid 624 and (name N or name CA or nam \ e C or name O or name CB )) or resid 625 through 628 or (resid 629 and (name N o \ r name CA or name C or name O or name CB )) or resid 630 through 637 or (resid 6 \ 38 and (name N or name CA or name C or name O or name CB )) or resid 639 through \ 702 or (resid 703 and (name N or name CA or name C or name O or name CB )) or r \ esid 704 or resid 712 through 841 or resid 896 through 903 or (resid 904 and (na \ me N or name CA or name C or name O or name CB )) or resid 905 or (resid 906 thr \ ough 908 and (name N or name CA or name C or name O or name CB )) or resid 909 t \ hrough 917 or (resid 918 through 919 and (name N or name CA or name C or name O \ or name CB )) or resid 920 through 953 or (resid 957 through 958 and (name N or \ name CA or name C or name O or name CB )) or resid 959 through 1030 or resid 103 \ 2 through 1127)) selection = (chain 'E' and ((resid 585 and (name N or name CA or name C or name O or name CB \ )) or resid 586 or (resid 587 and (name N or name CA or name C or name O or nam \ e CB )) or resid 588 through 621 or (resid 622 and (name N or name CA or name C \ or name O or name CB )) or resid 623 or (resid 624 and (name N or name CA or nam \ e C or name O or name CB )) or resid 625 through 637 or (resid 638 and (name N o \ r name CA or name C or name O or name CB )) or resid 639 through 702 or (resid 7 \ 03 and (name N or name CA or name C or name O or name CB )) or resid 704 or resi \ d 712 through 761 or (resid 762 and (name N or name CA or name C or name O or na \ me CB )) or resid 763 through 841 or resid 896 through 903 or (resid 904 and (na \ me N or name CA or name C or name O or name CB )) or resid 905 or (resid 906 thr \ ough 908 and (name N or name CA or name C or name O or name CB )) or resid 909 t \ hrough 917 or (resid 918 through 919 and (name N or name CA or name C or name O \ or name CB )) or resid 920 through 953 or (resid 957 through 958 and (name N or \ name CA or name C or name O or name CB )) or resid 959 through 1030 or resid 103 \ 2 through 1123 or (resid 1124 and (name N or name CA or name C or name O or name \ CB )) or resid 1125 or (resid 1126 and (name N or name CA or name C or name O o \ r name CB )) or resid 1127)) selection = (chain 'F' and ((resid 585 and (name N or name CA or name C or name O or name CB \ )) or resid 586 or (resid 587 and (name N or name CA or name C or name O or nam \ e CB )) or resid 588 through 621 or (resid 622 and (name N or name CA or name C \ or name O or name CB )) or resid 623 or (resid 624 and (name N or name CA or nam \ e C or name O or name CB )) or resid 625 through 628 or (resid 629 and (name N o \ r name CA or name C or name O or name CB )) or resid 630 through 637 or (resid 6 \ 38 and (name N or name CA or name C or name O or name CB )) or resid 639 through \ 702 or (resid 703 and (name N or name CA or name C or name O or name CB )) or r \ esid 704 or resid 712 through 761 or (resid 762 and (name N or name CA or name C \ or name O or name CB )) or resid 763 through 903 or (resid 904 and (name N or n \ ame CA or name C or name O or name CB )) or resid 905 or (resid 906 through 908 \ and (name N or name CA or name C or name O or name CB )) or resid 909 through 95 \ 3 or (resid 957 through 958 and (name N or name CA or name C or name O or name C \ B )) or resid 959 through 1030 or resid 1032 through 1125 or (resid 1126 and (na \ me N or name CA or name C or name O or name CB )) or resid 1127)) } 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 individual isotropic 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.080 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 68.400 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.002 0.088 25377 Z= 0.164 Angle : 0.649 36.718 34331 Z= 0.376 Chirality : 0.045 0.946 3891 Planarity : 0.005 0.084 4343 Dihedral : 14.857 124.418 9657 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.02 % Favored : 94.85 % Rotamer: Outliers : 0.07 % Allowed : 0.19 % Favored : 99.74 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 3128 helix: 0.53 (0.15), residues: 1363 sheet: -0.45 (0.24), residues: 474 loop : -1.52 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 934 HIS 0.005 0.001 HIS A 957 PHE 0.015 0.001 PHE C1024 TYR 0.014 0.001 TYR D 812 ARG 0.008 0.000 ARG D 533 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 326 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 960 PHE cc_start: 0.5482 (m-10) cc_final: 0.4767 (m-10) REVERT: C 628 ILE cc_start: 0.7778 (mp) cc_final: 0.7568 (mp) REVERT: C 661 MET cc_start: 0.2022 (tmm) cc_final: 0.1113 (ttp) REVERT: C 810 MET cc_start: 0.6460 (ppp) cc_final: 0.5703 (ptm) REVERT: D 920 LEU cc_start: 0.4602 (mp) cc_final: 0.3209 (tt) REVERT: E 546 ILE cc_start: 0.8397 (mm) cc_final: 0.8060 (mm) REVERT: F 531 LYS cc_start: 0.5901 (mptt) cc_final: 0.5503 (mmtm) REVERT: F 904 LYS cc_start: 0.8516 (ptmm) cc_final: 0.8294 (ttpp) outliers start: 2 outliers final: 0 residues processed: 328 average time/residue: 0.4049 time to fit residues: 202.3936 Evaluate side-chains 271 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.5980 chunk 236 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 182 optimal weight: 6.9990 chunk 283 optimal weight: 0.0040 overall best weight: 1.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 ASN ** B 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 ASN ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 693 ASN F 569 ASN ** F 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25377 Z= 0.241 Angle : 0.578 10.106 34331 Z= 0.285 Chirality : 0.042 0.179 3891 Planarity : 0.005 0.062 4343 Dihedral : 7.972 115.282 3538 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.56 % Favored : 94.31 % Rotamer: Outliers : 0.48 % Allowed : 6.94 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.75 (0.15), residues: 3128 helix: 0.52 (0.14), residues: 1375 sheet: -0.48 (0.24), residues: 483 loop : -1.60 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 934 HIS 0.009 0.001 HIS A 798 PHE 0.031 0.002 PHE C 960 TYR 0.023 0.001 TYR C 978 ARG 0.003 0.000 ARG E1056 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 283 time to evaluate : 3.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 PHE cc_start: 0.5312 (m-10) cc_final: 0.4601 (m-10) REVERT: C 626 LYS cc_start: 0.7500 (tmtt) cc_final: 0.7186 (tmtt) REVERT: C 628 ILE cc_start: 0.7832 (mp) cc_final: 0.7553 (mp) REVERT: D 920 LEU cc_start: 0.5139 (mp) cc_final: 0.3436 (tt) REVERT: D 978 TYR cc_start: 0.5662 (m-80) cc_final: 0.5262 (m-80) REVERT: F 904 LYS cc_start: 0.8561 (ptmm) cc_final: 0.8328 (tmmt) outliers start: 13 outliers final: 8 residues processed: 290 average time/residue: 0.3981 time to fit residues: 177.3909 Evaluate side-chains 269 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 261 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 1078 ASN Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain F residue 569 ASN Chi-restraints excluded: chain F residue 608 ASP Chi-restraints excluded: chain F residue 702 ASP Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 235 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 283 optimal weight: 0.0870 chunk 306 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 281 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 HIS C 821 ASN ** D 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25377 Z= 0.177 Angle : 0.541 9.573 34331 Z= 0.266 Chirality : 0.041 0.160 3891 Planarity : 0.004 0.060 4343 Dihedral : 7.729 113.907 3538 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.24 % Favored : 94.66 % Rotamer: Outliers : 0.93 % Allowed : 9.35 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.65 (0.15), residues: 3128 helix: 0.62 (0.14), residues: 1371 sheet: -0.48 (0.24), residues: 483 loop : -1.55 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 934 HIS 0.006 0.001 HIS A 798 PHE 0.028 0.001 PHE C 960 TYR 0.019 0.001 TYR C 978 ARG 0.004 0.000 ARG E1056 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 270 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 PHE cc_start: 0.5572 (m-10) cc_final: 0.4993 (m-10) REVERT: C 628 ILE cc_start: 0.7656 (mp) cc_final: 0.7361 (mp) REVERT: D 603 MET cc_start: 0.8151 (ptp) cc_final: 0.7909 (mtm) REVERT: D 920 LEU cc_start: 0.5168 (mp) cc_final: 0.3497 (tt) REVERT: D 978 TYR cc_start: 0.5748 (m-80) cc_final: 0.5368 (m-80) REVERT: F 904 LYS cc_start: 0.8568 (ptmm) cc_final: 0.8341 (tmmt) outliers start: 25 outliers final: 9 residues processed: 285 average time/residue: 0.4077 time to fit residues: 177.9964 Evaluate side-chains 264 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 255 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain D residue 922 GLU Chi-restraints excluded: chain E residue 935 THR Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 0.6980 chunk 213 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 284 optimal weight: 0.9980 chunk 301 optimal weight: 0.0270 chunk 148 optimal weight: 0.0040 chunk 269 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 overall best weight: 0.4850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 836 GLN B1078 ASN C 821 ASN D 693 ASN ** F 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.092 25377 Z= 0.149 Angle : 0.532 19.194 34331 Z= 0.260 Chirality : 0.040 0.164 3891 Planarity : 0.004 0.060 4343 Dihedral : 7.451 111.723 3538 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.12 % Favored : 94.79 % Rotamer: Outliers : 0.97 % Allowed : 10.99 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3128 helix: 0.78 (0.15), residues: 1364 sheet: -0.34 (0.24), residues: 471 loop : -1.52 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 934 HIS 0.003 0.000 HIS A 582 PHE 0.024 0.001 PHE C 960 TYR 0.019 0.001 TYR C 978 ARG 0.004 0.000 ARG E1056 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 269 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 PHE cc_start: 0.5527 (m-10) cc_final: 0.5006 (m-10) REVERT: B 649 LEU cc_start: 0.5895 (tp) cc_final: 0.5621 (mt) REVERT: C 628 ILE cc_start: 0.7555 (mp) cc_final: 0.7255 (mp) REVERT: D 725 GLN cc_start: 0.7603 (mt0) cc_final: 0.7370 (mm-40) REVERT: D 920 LEU cc_start: 0.5004 (mp) cc_final: 0.3408 (tt) REVERT: D 978 TYR cc_start: 0.5757 (m-80) cc_final: 0.5208 (m-80) REVERT: F 904 LYS cc_start: 0.8554 (ptmm) cc_final: 0.8340 (tmmt) outliers start: 26 outliers final: 9 residues processed: 285 average time/residue: 0.3983 time to fit residues: 175.2588 Evaluate side-chains 264 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 255 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 747 CYS Chi-restraints excluded: chain D residue 922 GLU Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 1036 THR Chi-restraints excluded: chain F residue 702 ASP Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 6.9990 chunk 171 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 224 optimal weight: 0.0040 chunk 124 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 10.0000 chunk 270 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 903 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 684 GLN ** F 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 25377 Z= 0.303 Angle : 0.613 16.955 34331 Z= 0.302 Chirality : 0.043 0.178 3891 Planarity : 0.005 0.060 4343 Dihedral : 7.572 111.632 3538 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.75 % Favored : 94.15 % Rotamer: Outliers : 1.15 % Allowed : 12.14 % Favored : 86.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.70 (0.15), residues: 3128 helix: 0.57 (0.14), residues: 1369 sheet: -0.42 (0.24), residues: 459 loop : -1.58 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 934 HIS 0.004 0.001 HIS C1001 PHE 0.038 0.002 PHE C 960 TYR 0.026 0.001 TYR C 978 ARG 0.007 0.000 ARG E 651 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 262 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 PHE cc_start: 0.5724 (m-10) cc_final: 0.5002 (m-10) REVERT: A 983 MET cc_start: 0.8540 (tpt) cc_final: 0.8276 (tpt) REVERT: D 978 TYR cc_start: 0.6127 (m-80) cc_final: 0.5559 (m-80) REVERT: F 904 LYS cc_start: 0.8564 (ptmm) cc_final: 0.8340 (ttpp) REVERT: F 1043 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8008 (pt) outliers start: 31 outliers final: 14 residues processed: 282 average time/residue: 0.3840 time to fit residues: 167.8249 Evaluate side-chains 266 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 251 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain B residue 1078 ASN Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 907 LYS Chi-restraints excluded: chain E residue 935 THR Chi-restraints excluded: chain E residue 1036 THR Chi-restraints excluded: chain E residue 1109 ASP Chi-restraints excluded: chain F residue 599 ASP Chi-restraints excluded: chain F residue 702 ASP Chi-restraints excluded: chain F residue 736 ILE Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 963 THR Chi-restraints excluded: chain F residue 1043 LEU Chi-restraints excluded: chain F residue 1110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 0.7980 chunk 271 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 177 optimal weight: 0.0970 chunk 74 optimal weight: 10.0000 chunk 301 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 25 optimal weight: 0.0770 chunk 99 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 693 ASN ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 25377 Z= 0.146 Angle : 0.539 14.940 34331 Z= 0.265 Chirality : 0.041 0.162 3891 Planarity : 0.004 0.061 4343 Dihedral : 7.279 109.476 3538 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.76 % Favored : 95.14 % Rotamer: Outliers : 0.67 % Allowed : 13.18 % Favored : 86.15 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 3128 helix: 0.79 (0.15), residues: 1360 sheet: -0.30 (0.24), residues: 468 loop : -1.46 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 934 HIS 0.004 0.001 HIS F 798 PHE 0.016 0.001 PHE D 653 TYR 0.014 0.001 TYR C 978 ARG 0.004 0.000 ARG A 681 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 255 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 798 HIS cc_start: 0.3724 (m90) cc_final: 0.3304 (m-70) REVERT: A 960 PHE cc_start: 0.5434 (m-10) cc_final: 0.4932 (m-10) REVERT: A 983 MET cc_start: 0.8466 (tpt) cc_final: 0.8233 (tpt) REVERT: C 661 MET cc_start: 0.2316 (tmm) cc_final: 0.1878 (ttp) REVERT: C 810 MET cc_start: 0.6319 (ppp) cc_final: 0.5707 (ttt) REVERT: C 978 TYR cc_start: 0.6105 (m-80) cc_final: 0.5708 (m-80) REVERT: D 978 TYR cc_start: 0.5926 (m-80) cc_final: 0.5409 (m-80) REVERT: E 703 LYS cc_start: 0.7976 (mmtt) cc_final: 0.7395 (mttt) REVERT: F 904 LYS cc_start: 0.8555 (ptmm) cc_final: 0.8352 (tmmt) outliers start: 18 outliers final: 9 residues processed: 266 average time/residue: 0.3947 time to fit residues: 162.0048 Evaluate side-chains 254 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 245 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 957 HIS Chi-restraints excluded: chain E residue 1036 THR Chi-restraints excluded: chain F residue 702 ASP Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 0.0270 chunk 34 optimal weight: 0.2980 chunk 171 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 chunk 300 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 183 optimal weight: 0.2980 chunk 138 optimal weight: 0.8980 overall best weight: 0.5040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 582 HIS ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 25377 Z= 0.146 Angle : 0.534 13.755 34331 Z= 0.260 Chirality : 0.040 0.145 3891 Planarity : 0.004 0.059 4343 Dihedral : 7.114 108.074 3538 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 0.85 % Allowed : 13.36 % Favored : 85.78 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 3128 helix: 0.89 (0.15), residues: 1357 sheet: -0.35 (0.24), residues: 472 loop : -1.42 (0.18), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 934 HIS 0.004 0.000 HIS F 798 PHE 0.017 0.001 PHE D 653 TYR 0.016 0.001 TYR C 978 ARG 0.005 0.000 ARG A 681 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 263 time to evaluate : 3.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 PHE cc_start: 0.5428 (m-10) cc_final: 0.4703 (m-10) REVERT: A 983 MET cc_start: 0.8540 (tpt) cc_final: 0.8339 (tpt) REVERT: C 661 MET cc_start: 0.2381 (tmm) cc_final: 0.1745 (ttp) REVERT: D 978 TYR cc_start: 0.5969 (m-80) cc_final: 0.5362 (m-80) outliers start: 23 outliers final: 12 residues processed: 279 average time/residue: 0.4080 time to fit residues: 175.1993 Evaluate side-chains 262 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 250 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 907 LYS Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 957 HIS Chi-restraints excluded: chain E residue 1036 THR Chi-restraints excluded: chain F residue 702 ASP Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 179 optimal weight: 0.8980 chunk 90 optimal weight: 0.0670 chunk 59 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 236 optimal weight: 3.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 582 HIS ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 25377 Z= 0.157 Angle : 0.548 14.046 34331 Z= 0.267 Chirality : 0.040 0.140 3891 Planarity : 0.004 0.058 4343 Dihedral : 7.068 107.057 3538 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.15 % Favored : 94.76 % Rotamer: Outliers : 0.78 % Allowed : 13.33 % Favored : 85.89 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.36 (0.16), residues: 3128 helix: 0.90 (0.15), residues: 1357 sheet: -0.34 (0.24), residues: 470 loop : -1.41 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 934 HIS 0.004 0.001 HIS F 798 PHE 0.027 0.001 PHE D 653 TYR 0.013 0.001 TYR F 813 ARG 0.005 0.000 ARG E 655 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 252 time to evaluate : 3.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 798 HIS cc_start: 0.3787 (m90) cc_final: 0.2906 (m-70) REVERT: A 960 PHE cc_start: 0.5443 (m-10) cc_final: 0.4702 (m-10) REVERT: A 983 MET cc_start: 0.8544 (tpt) cc_final: 0.8340 (tpt) REVERT: C 661 MET cc_start: 0.2379 (tmm) cc_final: 0.1719 (ttp) REVERT: C 810 MET cc_start: 0.6361 (ppp) cc_final: 0.5658 (ttt) REVERT: D 816 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6435 (pp20) REVERT: D 950 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7114 (pt0) REVERT: D 978 TYR cc_start: 0.5970 (m-80) cc_final: 0.5351 (m-80) outliers start: 21 outliers final: 13 residues processed: 268 average time/residue: 0.3909 time to fit residues: 162.5268 Evaluate side-chains 260 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 246 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain D residue 816 GLU Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 907 LYS Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 957 HIS Chi-restraints excluded: chain E residue 1036 THR Chi-restraints excluded: chain F residue 702 ASP Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 1110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 5.9990 chunk 288 optimal weight: 3.9990 chunk 262 optimal weight: 9.9990 chunk 280 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 253 optimal weight: 3.9990 chunk 265 optimal weight: 3.9990 chunk 279 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25377 Z= 0.200 Angle : 0.570 13.778 34331 Z= 0.279 Chirality : 0.041 0.173 3891 Planarity : 0.004 0.057 4343 Dihedral : 7.125 106.528 3538 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.40 % Favored : 94.50 % Rotamer: Outliers : 0.71 % Allowed : 13.73 % Favored : 85.56 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.44 (0.15), residues: 3128 helix: 0.81 (0.15), residues: 1366 sheet: -0.29 (0.24), residues: 451 loop : -1.47 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 934 HIS 0.004 0.001 HIS F 798 PHE 0.025 0.001 PHE D 653 TYR 0.018 0.001 TYR C 978 ARG 0.012 0.000 ARG A 672 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 255 time to evaluate : 3.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 798 HIS cc_start: 0.4095 (m90) cc_final: 0.3318 (m-70) REVERT: A 960 PHE cc_start: 0.5459 (m-10) cc_final: 0.4841 (m-10) REVERT: C 661 MET cc_start: 0.2306 (tmm) cc_final: 0.2060 (ttp) REVERT: C 810 MET cc_start: 0.6378 (ppp) cc_final: 0.5664 (ttt) REVERT: C 960 PHE cc_start: 0.4982 (OUTLIER) cc_final: 0.3673 (m-80) REVERT: D 653 PHE cc_start: 0.7775 (t80) cc_final: 0.7500 (t80) REVERT: D 816 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6515 (pp20) REVERT: D 950 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7168 (pt0) REVERT: D 978 TYR cc_start: 0.6036 (m-80) cc_final: 0.5414 (m-80) REVERT: F 1043 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.7905 (pt) outliers start: 19 outliers final: 13 residues processed: 269 average time/residue: 0.3991 time to fit residues: 166.1721 Evaluate side-chains 267 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 251 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain D residue 816 GLU Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 957 HIS Chi-restraints excluded: chain E residue 1036 THR Chi-restraints excluded: chain F residue 702 ASP Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 963 THR Chi-restraints excluded: chain F residue 1043 LEU Chi-restraints excluded: chain F residue 1110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.8980 chunk 296 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 chunk 310 optimal weight: 0.0370 chunk 286 optimal weight: 0.9980 chunk 247 optimal weight: 0.0050 chunk 25 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 overall best weight: 0.5872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN B 726 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 25377 Z= 0.151 Angle : 0.549 12.708 34331 Z= 0.268 Chirality : 0.040 0.184 3891 Planarity : 0.004 0.058 4343 Dihedral : 7.018 105.107 3538 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % Rotamer: Outliers : 0.52 % Allowed : 13.81 % Favored : 85.67 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.33 (0.16), residues: 3128 helix: 0.91 (0.15), residues: 1361 sheet: -0.25 (0.24), residues: 460 loop : -1.41 (0.18), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 934 HIS 0.004 0.001 HIS F 798 PHE 0.032 0.001 PHE C 960 TYR 0.025 0.001 TYR C 978 ARG 0.010 0.000 ARG A 672 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 255 time to evaluate : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 798 HIS cc_start: 0.3791 (m90) cc_final: 0.3090 (m-70) REVERT: A 960 PHE cc_start: 0.5345 (m-10) cc_final: 0.4668 (m-10) REVERT: A 983 MET cc_start: 0.8544 (tpt) cc_final: 0.8341 (tpt) REVERT: C 661 MET cc_start: 0.2247 (tmm) cc_final: 0.1979 (ttp) REVERT: C 810 MET cc_start: 0.6362 (ppp) cc_final: 0.5682 (ttt) REVERT: C 960 PHE cc_start: 0.4433 (OUTLIER) cc_final: 0.3962 (t80) REVERT: D 653 PHE cc_start: 0.7735 (t80) cc_final: 0.7445 (t80) REVERT: D 950 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7185 (pt0) REVERT: D 978 TYR cc_start: 0.5926 (m-80) cc_final: 0.5309 (m-80) REVERT: E 703 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7512 (mttt) REVERT: F 1043 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.7835 (pt) outliers start: 14 outliers final: 11 residues processed: 264 average time/residue: 0.4336 time to fit residues: 177.7620 Evaluate side-chains 262 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 249 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 907 LYS Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 957 HIS Chi-restraints excluded: chain F residue 702 ASP Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 1043 LEU Chi-restraints excluded: chain F residue 1110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 0.0770 chunk 263 optimal weight: 0.0060 chunk 75 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 254 optimal weight: 5.9990 chunk 31 optimal weight: 0.0870 chunk 45 optimal weight: 0.8980 overall best weight: 0.6134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.165738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128053 restraints weight = 34544.308| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.97 r_work: 0.3171 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 25377 Z= 0.153 Angle : 0.546 12.614 34331 Z= 0.266 Chirality : 0.040 0.166 3891 Planarity : 0.004 0.057 4343 Dihedral : 6.951 103.979 3538 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.95 % Rotamer: Outliers : 0.71 % Allowed : 13.85 % Favored : 85.45 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.32 (0.15), residues: 3128 helix: 0.91 (0.15), residues: 1360 sheet: -0.22 (0.24), residues: 460 loop : -1.41 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 934 HIS 0.004 0.001 HIS F 798 PHE 0.042 0.001 PHE C 960 TYR 0.026 0.001 TYR C 978 ARG 0.008 0.000 ARG A 672 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4962.88 seconds wall clock time: 92 minutes 37.44 seconds (5557.44 seconds total)