Starting phenix.real_space_refine on Mon Jun 16 17:33:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tnj_26011/06_2025/7tnj_26011.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnj_26011/06_2025/7tnj_26011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tnj_26011/06_2025/7tnj_26011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnj_26011/06_2025/7tnj_26011.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnj_26011/06_2025/7tnj_26011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnj_26011/06_2025/7tnj_26011.cif" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 136 5.16 5 Cl 4 4.86 5 C 12212 2.51 5 N 3044 2.21 5 O 3414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18810 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4669 Classifications: {'peptide': 599} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 583} Chain breaks: 4 Chain: "B" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4688 Classifications: {'peptide': 602} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 586} Chain breaks: 4 Chain: "C" Number of atoms: 4669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4669 Classifications: {'peptide': 599} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 583} Chain breaks: 4 Chain: "D" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4688 Classifications: {'peptide': 602} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 586} Chain breaks: 4 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.60, per 1000 atoms: 0.56 Number of scatterers: 18810 At special positions: 0 Unit cell: (128.65, 113.71, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 136 16.00 O 3414 8.00 N 3044 7.00 C 12212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.02 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.02 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.02 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.03 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.61 Conformation dependent library (CDL) restraints added in 2.6 seconds 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4384 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 26 sheets defined 57.2% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 416 through 419 removed outlier: 4.113A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 462 through 470 Processing helix chain 'A' and resid 482 through 488 removed outlier: 3.979A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.538A pdb=" N SER A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.983A pdb=" N TRP A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 630 removed outlier: 3.636A pdb=" N TRP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.900A pdb=" N GLN A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.707A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.600A pdb=" N GLY A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.544A pdb=" N GLU A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.597A pdb=" N GLU A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 756 " --> pdb=" O LYS A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 767 Processing helix chain 'A' and resid 780 through 785 removed outlier: 3.727A pdb=" N LYS A 783 " --> pdb=" O SER A 780 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR A 784 " --> pdb=" O LYS A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 820 removed outlier: 3.916A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1028 removed outlier: 3.767A pdb=" N ALA A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1103 Processing helix chain 'A' and resid 1105 through 1123 Processing helix chain 'A' and resid 1132 through 1159 removed outlier: 3.820A pdb=" N PHE A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A1143 " --> pdb=" O ILE A1139 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A1158 " --> pdb=" O VAL A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1206 removed outlier: 3.514A pdb=" N ILE A1187 " --> pdb=" O ALA A1183 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 489 removed outlier: 4.101A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.607A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 547 removed outlier: 4.439A pdb=" N SER B 547 " --> pdb=" O VAL B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 624 removed outlier: 3.512A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 642 Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.654A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 695 removed outlier: 3.608A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 694 " --> pdb=" O VAL B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 715 removed outlier: 3.562A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 770 removed outlier: 3.558A pdb=" N TRP B 766 " --> pdb=" O LEU B 762 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 779 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 820 removed outlier: 3.783A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1029 removed outlier: 3.787A pdb=" N GLN B1008 " --> pdb=" O ASP B1004 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B1026 " --> pdb=" O LEU B1022 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY B1028 " --> pdb=" O THR B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1092 through 1103 removed outlier: 4.136A pdb=" N PHE B1096 " --> pdb=" O THR B1092 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B1097 " --> pdb=" O ALA B1093 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1126 removed outlier: 3.990A pdb=" N ILE B1108 " --> pdb=" O SER B1104 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS B1120 " --> pdb=" O MET B1116 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B1121 " --> pdb=" O GLY B1117 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B1122 " --> pdb=" O GLY B1118 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B1126 " --> pdb=" O ALA B1122 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1160 removed outlier: 3.688A pdb=" N ILE B1139 " --> pdb=" O LEU B1135 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B1140 " --> pdb=" O SER B1136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B1160 " --> pdb=" O ILE B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1209 removed outlier: 3.758A pdb=" N TYR B1180 " --> pdb=" O GLY B1176 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B1188 " --> pdb=" O LEU B1184 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS B1204 " --> pdb=" O PHE B1200 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 removed outlier: 4.112A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 462 through 470 Processing helix chain 'C' and resid 482 through 488 removed outlier: 3.979A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 545 removed outlier: 3.537A pdb=" N SER C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.983A pdb=" N TRP C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 630 removed outlier: 3.636A pdb=" N TRP C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.900A pdb=" N GLN C 642 " --> pdb=" O ASP C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.706A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.599A pdb=" N GLY C 689 " --> pdb=" O THR C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.544A pdb=" N GLU C 713 " --> pdb=" O ASN C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.597A pdb=" N GLU C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN C 756 " --> pdb=" O LYS C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 767 Processing helix chain 'C' and resid 780 through 785 removed outlier: 3.728A pdb=" N LYS C 783 " --> pdb=" O SER C 780 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR C 784 " --> pdb=" O LYS C 781 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 820 removed outlier: 3.915A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE C 812 " --> pdb=" O LEU C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1028 removed outlier: 3.767A pdb=" N ALA C1026 " --> pdb=" O LEU C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1093 through 1103 Processing helix chain 'C' and resid 1105 through 1123 Processing helix chain 'C' and resid 1132 through 1159 removed outlier: 3.821A pdb=" N PHE C1140 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C1143 " --> pdb=" O ILE C1139 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C1158 " --> pdb=" O VAL C1154 " (cutoff:3.500A) Processing helix chain 'C' and resid 1177 through 1206 removed outlier: 3.515A pdb=" N ILE C1187 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 489 removed outlier: 4.101A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.607A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 547 removed outlier: 4.439A pdb=" N SER D 547 " --> pdb=" O VAL D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 624 removed outlier: 3.512A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 642 Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.653A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG D 660 " --> pdb=" O LYS D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.609A pdb=" N VAL D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG D 694 " --> pdb=" O VAL D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 715 removed outlier: 3.561A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 770 removed outlier: 3.558A pdb=" N TRP D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 779 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 820 removed outlier: 3.782A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 1004 through 1029 removed outlier: 3.787A pdb=" N GLN D1008 " --> pdb=" O ASP D1004 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D1026 " --> pdb=" O LEU D1022 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY D1028 " --> pdb=" O THR D1024 " (cutoff:3.500A) Processing helix chain 'D' and resid 1092 through 1103 removed outlier: 4.136A pdb=" N PHE D1096 " --> pdb=" O THR D1092 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D1097 " --> pdb=" O ALA D1093 " (cutoff:3.500A) Processing helix chain 'D' and resid 1104 through 1126 removed outlier: 3.991A pdb=" N ILE D1108 " --> pdb=" O SER D1104 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS D1120 " --> pdb=" O MET D1116 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE D1121 " --> pdb=" O GLY D1117 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA D1122 " --> pdb=" O GLY D1118 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE D1126 " --> pdb=" O ALA D1122 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1160 removed outlier: 3.688A pdb=" N ILE D1139 " --> pdb=" O LEU D1135 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA D1160 " --> pdb=" O ILE D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1176 through 1209 removed outlier: 3.758A pdb=" N TYR D1180 " --> pdb=" O GLY D1176 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D1188 " --> pdb=" O LEU D1184 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS D1204 " --> pdb=" O PHE D1200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 399 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.697A pdb=" N ALA A 452 " --> pdb=" O ASN A 461 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 454 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 459 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA5, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.750A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.108A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1033 through 1036 removed outlier: 3.806A pdb=" N SER A1035 " --> pdb=" O THR A1058 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 395 through 399 removed outlier: 6.922A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB1, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.626A pdb=" N ILE B 459 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 490 through 498 removed outlier: 6.792A pdb=" N SER B 492 " --> pdb=" O THR B 736 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N THR B 736 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE B 734 " --> pdb=" O PRO B 494 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.789A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1057 through 1060 Processing sheet with id=AB5, first strand: chain 'C' and resid 395 through 399 Processing sheet with id=AB6, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB7, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.697A pdb=" N ALA C 452 " --> pdb=" O ASN C 461 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP C 454 " --> pdb=" O ILE C 459 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 459 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB9, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.750A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.108A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1033 through 1036 removed outlier: 3.807A pdb=" N SER C1035 " --> pdb=" O THR C1058 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 395 through 399 removed outlier: 6.922A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC5, first strand: chain 'D' and resid 452 through 454 removed outlier: 3.627A pdb=" N ILE D 459 " --> pdb=" O ASP D 454 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 490 through 498 removed outlier: 6.793A pdb=" N SER D 492 " --> pdb=" O THR D 736 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N THR D 736 " --> pdb=" O SER D 492 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE D 734 " --> pdb=" O PRO D 494 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.790A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 1057 through 1060 1014 hydrogen bonds defined for protein. 2964 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.67 Time building geometry restraints manager: 5.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5722 1.34 - 1.46: 4829 1.46 - 1.58: 8455 1.58 - 1.70: 8 1.70 - 1.82: 220 Bond restraints: 19234 Sorted by residual: bond pdb=" N3 CYZ C1301 " pdb=" S2 CYZ C1301 " ideal model delta sigma weight residual 1.644 1.601 0.043 2.00e-02 2.50e+03 4.57e+00 bond pdb=" N3 CYZ B1301 " pdb=" S2 CYZ B1301 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" N3 CYZ A1301 " pdb=" S2 CYZ A1301 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" N3 CYZ D1301 " pdb=" S2 CYZ D1301 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.37e+00 bond pdb=" C ASP B 519 " pdb=" N PRO B 520 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.25e-02 6.40e+03 3.53e+00 ... (remaining 19229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 25075 2.11 - 4.23: 745 4.23 - 6.34: 118 6.34 - 8.46: 39 8.46 - 10.57: 9 Bond angle restraints: 25986 Sorted by residual: angle pdb=" N ASN D1132 " pdb=" CA ASN D1132 " pdb=" C ASN D1132 " ideal model delta sigma weight residual 114.56 107.79 6.77 1.27e+00 6.20e-01 2.84e+01 angle pdb=" C ASP A1091 " pdb=" N THR A1092 " pdb=" CA THR A1092 " ideal model delta sigma weight residual 121.54 131.65 -10.11 1.91e+00 2.74e-01 2.80e+01 angle pdb=" N ASN B1132 " pdb=" CA ASN B1132 " pdb=" C ASN B1132 " ideal model delta sigma weight residual 114.56 107.84 6.72 1.27e+00 6.20e-01 2.80e+01 angle pdb=" C LYS C1128 " pdb=" N THR C1129 " pdb=" CA THR C1129 " ideal model delta sigma weight residual 122.74 130.36 -7.62 1.44e+00 4.82e-01 2.80e+01 angle pdb=" C LYS A1128 " pdb=" N THR A1129 " pdb=" CA THR A1129 " ideal model delta sigma weight residual 122.74 130.35 -7.61 1.44e+00 4.82e-01 2.79e+01 ... (remaining 25981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 11038 24.42 - 48.84: 290 48.84 - 73.27: 18 73.27 - 97.69: 11 97.69 - 122.11: 9 Dihedral angle restraints: 11366 sinusoidal: 4488 harmonic: 6878 Sorted by residual: dihedral pdb=" CB CYS B1039 " pdb=" SG CYS B1039 " pdb=" SG CYS B1067 " pdb=" CB CYS B1067 " ideal model delta sinusoidal sigma weight residual 93.00 40.68 52.32 1 1.00e+01 1.00e-02 3.73e+01 dihedral pdb=" CB CYS D1039 " pdb=" SG CYS D1039 " pdb=" SG CYS D1067 " pdb=" CB CYS D1067 " ideal model delta sinusoidal sigma weight residual 93.00 40.74 52.26 1 1.00e+01 1.00e-02 3.72e+01 dihedral pdb=" CA PRO D 632 " pdb=" C PRO D 632 " pdb=" N ILE D 633 " pdb=" CA ILE D 633 " ideal model delta harmonic sigma weight residual 180.00 -152.42 -27.58 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 11363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2367 0.061 - 0.121: 439 0.121 - 0.182: 83 0.182 - 0.243: 13 0.243 - 0.304: 6 Chirality restraints: 2908 Sorted by residual: chirality pdb=" CB ILE D 525 " pdb=" CA ILE D 525 " pdb=" CG1 ILE D 525 " pdb=" CG2 ILE D 525 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB ILE B 525 " pdb=" CA ILE B 525 " pdb=" CG1 ILE B 525 " pdb=" CG2 ILE B 525 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C8 CYZ A1301 " pdb=" C1 CYZ A1301 " pdb=" N1 CYZ A1301 " pdb=" N2 CYZ A1301 " both_signs ideal model delta sigma weight residual False 2.20 2.47 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 2905 not shown) Planarity restraints: 3184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D1088 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.98e+00 pdb=" C TYR D1088 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR D1088 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU D1089 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B1088 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.91e+00 pdb=" C TYR B1088 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR B1088 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU B1089 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 477 " -0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO C 478 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 478 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 478 " -0.037 5.00e-02 4.00e+02 ... (remaining 3181 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4404 2.78 - 3.31: 17338 3.31 - 3.84: 30296 3.84 - 4.37: 36016 4.37 - 4.90: 60875 Nonbonded interactions: 148929 Sorted by model distance: nonbonded pdb=" OG SER C 597 " pdb=" O ALA D 806 " model vdw 2.246 3.040 nonbonded pdb=" OD1 ASP C 760 " pdb="CL CYZ C1301 " model vdw 2.286 3.270 nonbonded pdb=" O THR D 643 " pdb=" OH TYR D 673 " model vdw 2.291 3.040 nonbonded pdb=" O THR B 643 " pdb=" OH TYR B 673 " model vdw 2.292 3.040 nonbonded pdb=" O PHE B 517 " pdb=" OH TYR B 616 " model vdw 2.299 3.040 ... (remaining 148924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 41.100 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 : 0.005 0.070 19246 Z= 0.248 Angle : 0.941 10.572 26010 Z= 0.527 Chirality : 0.052 0.304 2908 Planarity : 0.007 0.067 3184 Dihedral : 11.627 122.110 6946 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.20 % Allowed : 4.69 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -4.89 (0.12), residues: 2362 helix: -3.76 (0.07), residues: 1314 sheet: -1.78 (0.36), residues: 170 loop : -2.34 (0.17), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C1032 HIS 0.005 0.001 HIS A1059 PHE 0.041 0.003 PHE C1082 TYR 0.042 0.002 TYR C1031 ARG 0.015 0.001 ARG D 599 Details of bonding type rmsd hydrogen bonds : bond 0.29210 ( 1014) hydrogen bonds : angle 9.39770 ( 2964) SS BOND : bond 0.00551 ( 12) SS BOND : angle 1.24805 ( 24) covalent geometry : bond 0.00543 (19234) covalent geometry : angle 0.94112 (25986) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 697 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 VAL cc_start: 0.8376 (t) cc_final: 0.7577 (t) REVERT: A 440 TYR cc_start: 0.7341 (p90) cc_final: 0.6726 (p90) REVERT: A 460 TRP cc_start: 0.4917 (m100) cc_final: 0.3952 (m100) REVERT: A 464 VAL cc_start: 0.8497 (t) cc_final: 0.8136 (p) REVERT: A 474 ILE cc_start: 0.8437 (tt) cc_final: 0.8210 (mp) REVERT: A 531 PHE cc_start: 0.8115 (m-10) cc_final: 0.7882 (m-80) REVERT: A 575 ASN cc_start: 0.8475 (m-40) cc_final: 0.8111 (m110) REVERT: A 671 TRP cc_start: 0.6522 (t-100) cc_final: 0.6078 (t60) REVERT: A 751 LEU cc_start: 0.9062 (mm) cc_final: 0.8855 (mp) REVERT: A 814 PHE cc_start: 0.6883 (t80) cc_final: 0.6469 (t80) REVERT: A 1128 LYS cc_start: 0.5014 (ttmm) cc_final: 0.4714 (tptt) REVERT: A 1171 ASN cc_start: 0.5165 (t160) cc_final: 0.4778 (t0) REVERT: B 401 LEU cc_start: 0.7746 (tt) cc_final: 0.7534 (tp) REVERT: B 496 MET cc_start: 0.8217 (ttp) cc_final: 0.7749 (ttp) REVERT: B 671 TRP cc_start: 0.5925 (t-100) cc_final: 0.5697 (t-100) REVERT: B 772 GLU cc_start: 0.7306 (pt0) cc_final: 0.6445 (mm-30) REVERT: B 1075 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7115 (tm) REVERT: C 442 LEU cc_start: 0.8075 (mt) cc_final: 0.7871 (mp) REVERT: C 460 TRP cc_start: 0.4414 (m100) cc_final: 0.3810 (m100) REVERT: C 578 TRP cc_start: 0.8950 (t-100) cc_final: 0.8749 (t-100) REVERT: C 642 GLN cc_start: 0.6559 (pp30) cc_final: 0.6291 (pp30) REVERT: C 671 TRP cc_start: 0.6350 (t-100) cc_final: 0.5903 (t60) REVERT: C 697 LYS cc_start: 0.7156 (mttm) cc_final: 0.6459 (pttp) REVERT: C 788 SER cc_start: 0.8173 (p) cc_final: 0.7894 (p) REVERT: C 800 VAL cc_start: 0.8002 (t) cc_final: 0.7513 (p) REVERT: C 1022 LEU cc_start: 0.6751 (mt) cc_final: 0.6478 (mt) REVERT: C 1105 ILE cc_start: 0.7611 (pt) cc_final: 0.7321 (pt) REVERT: C 1112 ILE cc_start: 0.8661 (mt) cc_final: 0.8443 (mm) REVERT: C 1140 PHE cc_start: 0.7940 (m-80) cc_final: 0.7681 (m-10) REVERT: C 1149 ILE cc_start: 0.8227 (tt) cc_final: 0.8015 (tp) REVERT: C 1173 TYR cc_start: 0.6741 (p90) cc_final: 0.5953 (p90) REVERT: D 427 ASP cc_start: 0.7690 (m-30) cc_final: 0.7342 (t70) REVERT: D 435 HIS cc_start: 0.6822 (m-70) cc_final: 0.6617 (m170) REVERT: D 508 GLN cc_start: 0.6986 (pm20) cc_final: 0.6352 (tt0) REVERT: D 713 GLU cc_start: 0.7233 (tt0) cc_final: 0.6919 (tm-30) REVERT: D 762 LEU cc_start: 0.8866 (mt) cc_final: 0.8396 (mt) REVERT: D 1009 MET cc_start: 0.7326 (ttp) cc_final: 0.7095 (ptm) REVERT: D 1023 MET cc_start: 0.7349 (tpt) cc_final: 0.6698 (ttm) REVERT: D 1075 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6855 (tm) REVERT: D 1139 ILE cc_start: 0.8220 (pt) cc_final: 0.7840 (mt) REVERT: D 1179 PHE cc_start: 0.8286 (t80) cc_final: 0.7960 (t80) outliers start: 4 outliers final: 1 residues processed: 701 average time/residue: 0.3178 time to fit residues: 328.6215 Evaluate side-chains 398 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 395 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 96 optimal weight: 0.3980 chunk 186 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1198 HIS C 714 GLN D 412 HIS D1008 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.139576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111999 restraints weight = 38265.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113793 restraints weight = 28071.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114385 restraints weight = 20970.635| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19246 Z= 0.140 Angle : 0.621 20.021 26010 Z= 0.327 Chirality : 0.042 0.586 2908 Planarity : 0.005 0.047 3184 Dihedral : 9.099 106.006 2698 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.10 % Allowed : 3.49 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.15), residues: 2362 helix: -0.54 (0.12), residues: 1344 sheet: -1.60 (0.35), residues: 170 loop : -1.80 (0.18), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C1032 HIS 0.006 0.001 HIS B1198 PHE 0.034 0.002 PHE B1017 TYR 0.019 0.001 TYR C 533 ARG 0.010 0.001 ARG A 692 Details of bonding type rmsd hydrogen bonds : bond 0.04451 ( 1014) hydrogen bonds : angle 4.33444 ( 2964) SS BOND : bond 0.00382 ( 12) SS BOND : angle 0.87441 ( 24) covalent geometry : bond 0.00304 (19234) covalent geometry : angle 0.62120 (25986) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 553 time to evaluate : 2.237 Fit side-chains revert: symmetry clash REVERT: A 449 LYS cc_start: 0.6612 (mptt) cc_final: 0.6320 (mtmt) REVERT: A 460 TRP cc_start: 0.4930 (m100) cc_final: 0.4036 (m100) REVERT: A 474 ILE cc_start: 0.8350 (tt) cc_final: 0.8002 (mp) REVERT: A 568 THR cc_start: 0.6635 (p) cc_final: 0.6147 (t) REVERT: A 575 ASN cc_start: 0.8017 (m-40) cc_final: 0.7807 (m-40) REVERT: A 697 LYS cc_start: 0.7560 (mttm) cc_final: 0.6674 (pttp) REVERT: A 710 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7095 (mt-10) REVERT: A 814 PHE cc_start: 0.6869 (t80) cc_final: 0.6602 (t80) REVERT: A 1003 PHE cc_start: 0.4890 (m-80) cc_final: 0.4224 (m-80) REVERT: A 1009 MET cc_start: 0.7777 (tmm) cc_final: 0.7256 (tmm) REVERT: A 1023 MET cc_start: 0.7807 (mmm) cc_final: 0.7602 (mmm) REVERT: A 1142 VAL cc_start: 0.8069 (t) cc_final: 0.7840 (m) REVERT: A 1191 MET cc_start: 0.5767 (tpt) cc_final: 0.5434 (tpt) REVERT: A 1195 LEU cc_start: 0.8224 (mt) cc_final: 0.7963 (mt) REVERT: A 1201 ILE cc_start: 0.8187 (mm) cc_final: 0.7904 (mm) REVERT: B 496 MET cc_start: 0.8172 (ttp) cc_final: 0.7879 (ttp) REVERT: B 545 ARG cc_start: 0.6552 (mmt180) cc_final: 0.6303 (mmt180) REVERT: B 752 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7727 (ttpt) REVERT: B 772 GLU cc_start: 0.7130 (pt0) cc_final: 0.6169 (mm-30) REVERT: C 460 TRP cc_start: 0.4310 (m100) cc_final: 0.3725 (m100) REVERT: C 697 LYS cc_start: 0.7152 (mttm) cc_final: 0.6501 (pttp) REVERT: C 710 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6757 (mt-10) REVERT: C 713 GLU cc_start: 0.6997 (tt0) cc_final: 0.6696 (tm-30) REVERT: C 1022 LEU cc_start: 0.6611 (mt) cc_final: 0.6360 (mt) REVERT: C 1128 LYS cc_start: 0.5859 (ttmm) cc_final: 0.5211 (tptp) REVERT: C 1191 MET cc_start: 0.5883 (tpt) cc_final: 0.5646 (tpt) REVERT: C 1194 VAL cc_start: 0.7726 (t) cc_final: 0.7478 (p) REVERT: D 431 GLU cc_start: 0.6899 (tp30) cc_final: 0.6562 (tp30) REVERT: D 435 HIS cc_start: 0.6131 (m-70) cc_final: 0.5659 (m170) REVERT: D 508 GLN cc_start: 0.7071 (pm20) cc_final: 0.6199 (tt0) REVERT: D 523 TYR cc_start: 0.6162 (t80) cc_final: 0.5914 (t80) REVERT: D 527 MET cc_start: 0.7783 (tmm) cc_final: 0.6811 (mmt) REVERT: D 570 GLU cc_start: 0.7297 (pm20) cc_final: 0.6805 (pt0) REVERT: D 645 ILE cc_start: 0.6938 (mm) cc_final: 0.6512 (tt) REVERT: D 709 ASN cc_start: 0.8678 (t0) cc_final: 0.8371 (t0) REVERT: D 713 GLU cc_start: 0.7452 (tt0) cc_final: 0.7056 (tm-30) REVERT: D 752 LYS cc_start: 0.8177 (ttmm) cc_final: 0.7428 (ttpt) REVERT: D 772 GLU cc_start: 0.6756 (pt0) cc_final: 0.6056 (mm-30) REVERT: D 799 LEU cc_start: 0.8356 (tp) cc_final: 0.8073 (tt) REVERT: D 1023 MET cc_start: 0.7354 (tpt) cc_final: 0.6404 (ttt) REVERT: D 1027 VAL cc_start: 0.8053 (t) cc_final: 0.7810 (m) REVERT: D 1031 TYR cc_start: 0.6120 (m-80) cc_final: 0.5862 (m-80) REVERT: D 1139 ILE cc_start: 0.8247 (pt) cc_final: 0.7863 (mt) REVERT: D 1179 PHE cc_start: 0.8029 (t80) cc_final: 0.7789 (t80) REVERT: D 1190 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7556 (mm-30) REVERT: D 1206 GLN cc_start: 0.3768 (mp10) cc_final: 0.2665 (tp40) outliers start: 2 outliers final: 0 residues processed: 554 average time/residue: 0.2989 time to fit residues: 254.6793 Evaluate side-chains 392 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 189 optimal weight: 0.0870 chunk 170 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 174 optimal weight: 0.7980 chunk 4 optimal weight: 0.1980 chunk 215 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 overall best weight: 1.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 619 ASN ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1008 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.135869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.107177 restraints weight = 38926.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.109096 restraints weight = 29831.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110321 restraints weight = 20858.201| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19246 Z= 0.186 Angle : 0.613 6.149 26010 Z= 0.326 Chirality : 0.041 0.197 2908 Planarity : 0.004 0.045 3184 Dihedral : 8.732 101.538 2698 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.20 % Allowed : 3.29 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -0.51 (0.16), residues: 2362 helix: 0.62 (0.14), residues: 1348 sheet: -1.77 (0.35), residues: 172 loop : -1.53 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 767 HIS 0.007 0.001 HIS A1204 PHE 0.028 0.002 PHE B1017 TYR 0.021 0.002 TYR C1031 ARG 0.009 0.001 ARG D 628 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 1014) hydrogen bonds : angle 4.18782 ( 2964) SS BOND : bond 0.00459 ( 12) SS BOND : angle 0.92770 ( 24) covalent geometry : bond 0.00415 (19234) covalent geometry : angle 0.61303 (25986) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 464 time to evaluate : 2.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7154 (p90) cc_final: 0.6913 (p90) REVERT: A 460 TRP cc_start: 0.5008 (m100) cc_final: 0.3989 (m100) REVERT: A 568 THR cc_start: 0.6477 (p) cc_final: 0.6039 (t) REVERT: A 697 LYS cc_start: 0.7437 (mttm) cc_final: 0.6477 (pttp) REVERT: A 785 SER cc_start: 0.7121 (m) cc_final: 0.6869 (p) REVERT: A 814 PHE cc_start: 0.7154 (t80) cc_final: 0.6898 (t80) REVERT: A 1009 MET cc_start: 0.7876 (tmm) cc_final: 0.7357 (tmm) REVERT: A 1032 TRP cc_start: 0.8140 (m-10) cc_final: 0.7872 (m-10) REVERT: B 772 GLU cc_start: 0.6859 (pt0) cc_final: 0.6071 (mm-30) REVERT: B 1188 ILE cc_start: 0.7625 (mm) cc_final: 0.7408 (mm) REVERT: B 1191 MET cc_start: 0.5555 (tpp) cc_final: 0.5312 (tpp) REVERT: C 460 TRP cc_start: 0.4582 (m100) cc_final: 0.3643 (m100) REVERT: C 467 LEU cc_start: 0.8002 (tp) cc_final: 0.7798 (tt) REVERT: C 697 LYS cc_start: 0.7201 (mttm) cc_final: 0.6513 (pttp) REVERT: C 1128 LYS cc_start: 0.5685 (ttmm) cc_final: 0.5115 (tptp) REVERT: C 1156 ILE cc_start: 0.9066 (mt) cc_final: 0.8848 (mt) REVERT: C 1191 MET cc_start: 0.5996 (tpt) cc_final: 0.5626 (tpt) REVERT: D 435 HIS cc_start: 0.6155 (m-70) cc_final: 0.5723 (m170) REVERT: D 508 GLN cc_start: 0.7017 (pm20) cc_final: 0.6163 (tt0) REVERT: D 549 TYR cc_start: 0.4426 (p90) cc_final: 0.4212 (p90) REVERT: D 570 GLU cc_start: 0.7312 (pm20) cc_final: 0.6743 (pt0) REVERT: D 709 ASN cc_start: 0.8739 (t0) cc_final: 0.8490 (t0) REVERT: D 713 GLU cc_start: 0.7487 (tt0) cc_final: 0.7118 (tm-30) REVERT: D 752 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7801 (ttpt) REVERT: D 772 GLU cc_start: 0.6499 (pt0) cc_final: 0.6011 (mm-30) REVERT: D 1009 MET cc_start: 0.7045 (ptm) cc_final: 0.6844 (ptm) REVERT: D 1023 MET cc_start: 0.7293 (tpt) cc_final: 0.6420 (ttm) REVERT: D 1027 VAL cc_start: 0.8184 (t) cc_final: 0.7915 (m) REVERT: D 1139 ILE cc_start: 0.8188 (pt) cc_final: 0.7753 (mt) REVERT: D 1179 PHE cc_start: 0.8093 (t80) cc_final: 0.7883 (t80) outliers start: 4 outliers final: 0 residues processed: 466 average time/residue: 0.2787 time to fit residues: 205.3610 Evaluate side-chains 356 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 138 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 187 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 231 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 234 optimal weight: 8.9990 chunk 169 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN A 642 GLN B 619 ASN B1148 ASN ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.137320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.110614 restraints weight = 38367.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.111290 restraints weight = 28165.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112182 restraints weight = 27664.546| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19246 Z= 0.125 Angle : 0.557 7.302 26010 Z= 0.294 Chirality : 0.040 0.187 2908 Planarity : 0.004 0.042 3184 Dihedral : 8.166 95.825 2698 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.20 % Allowed : 2.69 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.17 (0.17), residues: 2362 helix: 1.26 (0.14), residues: 1338 sheet: -1.41 (0.35), residues: 180 loop : -1.38 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1032 HIS 0.003 0.001 HIS B1198 PHE 0.032 0.002 PHE D 574 TYR 0.019 0.001 TYR C1175 ARG 0.010 0.001 ARG C 692 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 1014) hydrogen bonds : angle 3.95444 ( 2964) SS BOND : bond 0.00414 ( 12) SS BOND : angle 1.10788 ( 24) covalent geometry : bond 0.00279 (19234) covalent geometry : angle 0.55653 (25986) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 453 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7249 (p90) cc_final: 0.7035 (p90) REVERT: A 460 TRP cc_start: 0.4962 (m100) cc_final: 0.3971 (m100) REVERT: A 568 THR cc_start: 0.6308 (p) cc_final: 0.5875 (t) REVERT: A 575 ASN cc_start: 0.8196 (m-40) cc_final: 0.7742 (m-40) REVERT: A 697 LYS cc_start: 0.7351 (mttm) cc_final: 0.6423 (pttp) REVERT: A 772 GLU cc_start: 0.6404 (pm20) cc_final: 0.5336 (mm-30) REVERT: A 785 SER cc_start: 0.7042 (m) cc_final: 0.6698 (p) REVERT: A 814 PHE cc_start: 0.7289 (t80) cc_final: 0.6925 (t80) REVERT: A 1009 MET cc_start: 0.7760 (tmm) cc_final: 0.7476 (tmm) REVERT: B 546 PHE cc_start: 0.7303 (p90) cc_final: 0.6723 (m-10) REVERT: B 772 GLU cc_start: 0.6497 (pt0) cc_final: 0.5874 (mm-30) REVERT: B 1191 MET cc_start: 0.5532 (tpp) cc_final: 0.5242 (tpp) REVERT: C 460 TRP cc_start: 0.4635 (m100) cc_final: 0.3715 (m100) REVERT: C 575 ASN cc_start: 0.8376 (t0) cc_final: 0.8146 (t0) REVERT: C 697 LYS cc_start: 0.7160 (mttm) cc_final: 0.6567 (pttp) REVERT: C 769 ASP cc_start: 0.7555 (m-30) cc_final: 0.7285 (m-30) REVERT: C 772 GLU cc_start: 0.6587 (pm20) cc_final: 0.5166 (mm-30) REVERT: C 1105 ILE cc_start: 0.8070 (pt) cc_final: 0.7730 (tp) REVERT: C 1128 LYS cc_start: 0.5725 (ttmm) cc_final: 0.5116 (tptp) REVERT: D 435 HIS cc_start: 0.6289 (m-70) cc_final: 0.5848 (m170) REVERT: D 508 GLN cc_start: 0.6925 (pm20) cc_final: 0.6062 (tt0) REVERT: D 527 MET cc_start: 0.7852 (tmm) cc_final: 0.7504 (ttp) REVERT: D 570 GLU cc_start: 0.7307 (pm20) cc_final: 0.6716 (pt0) REVERT: D 645 ILE cc_start: 0.6721 (mm) cc_final: 0.6328 (tt) REVERT: D 709 ASN cc_start: 0.8707 (t0) cc_final: 0.8391 (t0) REVERT: D 713 GLU cc_start: 0.7459 (tt0) cc_final: 0.7151 (tm-30) REVERT: D 752 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7754 (ttpt) REVERT: D 772 GLU cc_start: 0.6326 (pt0) cc_final: 0.5926 (mm-30) REVERT: D 1009 MET cc_start: 0.7022 (ptm) cc_final: 0.6757 (ptm) REVERT: D 1023 MET cc_start: 0.7244 (tpt) cc_final: 0.6362 (ttm) REVERT: D 1027 VAL cc_start: 0.8236 (t) cc_final: 0.7927 (m) REVERT: D 1179 PHE cc_start: 0.8040 (t80) cc_final: 0.7780 (t80) outliers start: 4 outliers final: 0 residues processed: 455 average time/residue: 0.2700 time to fit residues: 193.6552 Evaluate side-chains 347 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 167 optimal weight: 8.9990 chunk 81 optimal weight: 0.0980 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 183 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN B 619 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.134367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108505 restraints weight = 39101.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108385 restraints weight = 30805.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108890 restraints weight = 28922.516| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19246 Z= 0.183 Angle : 0.629 11.072 26010 Z= 0.332 Chirality : 0.042 0.223 2908 Planarity : 0.004 0.041 3184 Dihedral : 7.959 93.649 2698 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.15 % Allowed : 2.79 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.23 (0.17), residues: 2362 helix: 1.25 (0.14), residues: 1360 sheet: -1.49 (0.35), residues: 172 loop : -1.30 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1032 HIS 0.005 0.001 HIS C1131 PHE 0.023 0.002 PHE D 623 TYR 0.020 0.002 TYR C1031 ARG 0.006 0.001 ARG A 692 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 1014) hydrogen bonds : angle 4.14884 ( 2964) SS BOND : bond 0.00900 ( 12) SS BOND : angle 1.65262 ( 24) covalent geometry : bond 0.00423 (19234) covalent geometry : angle 0.62691 (25986) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 418 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7246 (p90) cc_final: 0.7018 (p90) REVERT: A 568 THR cc_start: 0.6021 (p) cc_final: 0.5684 (t) REVERT: A 697 LYS cc_start: 0.7455 (mttm) cc_final: 0.6518 (pttp) REVERT: A 772 GLU cc_start: 0.6545 (pm20) cc_final: 0.5539 (mm-30) REVERT: A 785 SER cc_start: 0.7178 (m) cc_final: 0.6881 (p) REVERT: A 814 PHE cc_start: 0.7353 (t80) cc_final: 0.7042 (t80) REVERT: A 1032 TRP cc_start: 0.8052 (m-10) cc_final: 0.7632 (m-10) REVERT: B 487 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7239 (tt0) REVERT: B 772 GLU cc_start: 0.6439 (pt0) cc_final: 0.5790 (mm-30) REVERT: C 460 TRP cc_start: 0.4783 (m100) cc_final: 0.3794 (m100) REVERT: C 697 LYS cc_start: 0.7157 (mttm) cc_final: 0.6566 (pttp) REVERT: C 772 GLU cc_start: 0.6672 (pm20) cc_final: 0.5563 (mm-30) REVERT: C 1098 ARG cc_start: 0.7002 (mtp180) cc_final: 0.6626 (mtp85) REVERT: C 1128 LYS cc_start: 0.5699 (ttmm) cc_final: 0.5112 (tptp) REVERT: D 414 MET cc_start: 0.7817 (mpp) cc_final: 0.7189 (tmm) REVERT: D 508 GLN cc_start: 0.6950 (pm20) cc_final: 0.6102 (tt0) REVERT: D 570 GLU cc_start: 0.7416 (pm20) cc_final: 0.6809 (pt0) REVERT: D 591 ILE cc_start: 0.8201 (pt) cc_final: 0.7888 (pt) REVERT: D 713 GLU cc_start: 0.7551 (tt0) cc_final: 0.7038 (tm-30) REVERT: D 772 GLU cc_start: 0.6328 (pt0) cc_final: 0.6072 (mm-30) REVERT: D 1009 MET cc_start: 0.7058 (ptm) cc_final: 0.6744 (ptm) REVERT: D 1023 MET cc_start: 0.7183 (tpt) cc_final: 0.6257 (ttm) REVERT: D 1027 VAL cc_start: 0.8321 (t) cc_final: 0.8042 (m) REVERT: D 1066 CYS cc_start: 0.3514 (m) cc_final: 0.3176 (m) REVERT: D 1116 MET cc_start: 0.6741 (mpp) cc_final: 0.6347 (mtt) REVERT: D 1175 TYR cc_start: 0.6003 (m-80) cc_final: 0.5510 (m-10) REVERT: D 1179 PHE cc_start: 0.8069 (t80) cc_final: 0.7755 (t80) REVERT: D 1188 ILE cc_start: 0.7947 (mm) cc_final: 0.7726 (mm) outliers start: 3 outliers final: 0 residues processed: 420 average time/residue: 0.2627 time to fit residues: 175.1731 Evaluate side-chains 343 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 234 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 191 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN C 642 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.134888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.107123 restraints weight = 39391.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.108985 restraints weight = 31320.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.109729 restraints weight = 22775.305| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19246 Z= 0.129 Angle : 0.578 8.247 26010 Z= 0.302 Chirality : 0.040 0.204 2908 Planarity : 0.004 0.041 3184 Dihedral : 7.411 89.930 2698 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.15 % Allowed : 1.90 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.17), residues: 2362 helix: 1.53 (0.14), residues: 1352 sheet: -1.34 (0.35), residues: 182 loop : -1.37 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1032 HIS 0.018 0.001 HIS A 435 PHE 0.030 0.001 PHE D 574 TYR 0.018 0.001 TYR C1031 ARG 0.006 0.000 ARG B 628 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 1014) hydrogen bonds : angle 3.96670 ( 2964) SS BOND : bond 0.00513 ( 12) SS BOND : angle 1.87302 ( 24) covalent geometry : bond 0.00293 (19234) covalent geometry : angle 0.57524 (25986) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 441 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7157 (p90) cc_final: 0.6946 (p90) REVERT: A 460 TRP cc_start: 0.5031 (m100) cc_final: 0.3783 (m100) REVERT: A 568 THR cc_start: 0.6004 (p) cc_final: 0.5676 (t) REVERT: A 599 ARG cc_start: 0.8086 (mtt-85) cc_final: 0.7474 (mtt90) REVERT: A 639 LEU cc_start: 0.7938 (tp) cc_final: 0.7713 (tp) REVERT: A 697 LYS cc_start: 0.7437 (mttm) cc_final: 0.6484 (pttp) REVERT: A 772 GLU cc_start: 0.6305 (pm20) cc_final: 0.5446 (mm-30) REVERT: A 814 PHE cc_start: 0.7312 (t80) cc_final: 0.7062 (t80) REVERT: A 1032 TRP cc_start: 0.8018 (m-10) cc_final: 0.7638 (m-10) REVERT: B 487 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7175 (tt0) REVERT: B 772 GLU cc_start: 0.6383 (pt0) cc_final: 0.5641 (mm-30) REVERT: B 1111 VAL cc_start: 0.6640 (t) cc_final: 0.6307 (p) REVERT: B 1179 PHE cc_start: 0.8347 (t80) cc_final: 0.8014 (t80) REVERT: C 460 TRP cc_start: 0.4648 (m100) cc_final: 0.3668 (m100) REVERT: C 697 LYS cc_start: 0.7087 (mttm) cc_final: 0.6587 (pttp) REVERT: C 710 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6923 (mt-10) REVERT: C 772 GLU cc_start: 0.6532 (pm20) cc_final: 0.5433 (mm-30) REVERT: C 1017 PHE cc_start: 0.7218 (t80) cc_final: 0.6875 (m-10) REVERT: C 1098 ARG cc_start: 0.6962 (mtp180) cc_final: 0.6359 (ptm160) REVERT: C 1128 LYS cc_start: 0.5623 (ttmm) cc_final: 0.5053 (tptp) REVERT: D 414 MET cc_start: 0.7847 (mpp) cc_final: 0.7182 (tmm) REVERT: D 500 ILE cc_start: 0.8547 (mm) cc_final: 0.8159 (mm) REVERT: D 508 GLN cc_start: 0.6981 (pm20) cc_final: 0.6134 (tt0) REVERT: D 527 MET cc_start: 0.7844 (tmm) cc_final: 0.7557 (ttp) REVERT: D 570 GLU cc_start: 0.7386 (pm20) cc_final: 0.6783 (pt0) REVERT: D 591 ILE cc_start: 0.8192 (pt) cc_final: 0.7934 (pt) REVERT: D 709 ASN cc_start: 0.8717 (t0) cc_final: 0.8403 (t0) REVERT: D 713 GLU cc_start: 0.7565 (tt0) cc_final: 0.6980 (tm-30) REVERT: D 772 GLU cc_start: 0.6474 (pt0) cc_final: 0.5997 (mm-30) REVERT: D 1009 MET cc_start: 0.7038 (ptm) cc_final: 0.6713 (ptm) REVERT: D 1023 MET cc_start: 0.7071 (tpt) cc_final: 0.6133 (ttm) REVERT: D 1027 VAL cc_start: 0.8284 (t) cc_final: 0.8042 (m) REVERT: D 1063 TRP cc_start: 0.4551 (m100) cc_final: 0.4104 (m100) REVERT: D 1175 TYR cc_start: 0.5781 (m-80) cc_final: 0.5245 (m-10) REVERT: D 1179 PHE cc_start: 0.8042 (t80) cc_final: 0.7621 (t80) REVERT: D 1188 ILE cc_start: 0.7960 (mm) cc_final: 0.7747 (mm) REVERT: D 1191 MET cc_start: 0.7067 (mtp) cc_final: 0.5532 (tpp) outliers start: 3 outliers final: 0 residues processed: 442 average time/residue: 0.2703 time to fit residues: 187.7385 Evaluate side-chains 353 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 205 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 236 optimal weight: 0.9980 chunk 233 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN C 642 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.135132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.107529 restraints weight = 38901.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.109542 restraints weight = 30617.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110170 restraints weight = 22515.659| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19246 Z= 0.124 Angle : 0.572 7.649 26010 Z= 0.300 Chirality : 0.040 0.190 2908 Planarity : 0.004 0.040 3184 Dihedral : 7.044 87.255 2698 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.10 % Allowed : 1.80 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.17), residues: 2362 helix: 1.70 (0.14), residues: 1364 sheet: -1.30 (0.35), residues: 182 loop : -1.33 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1177 HIS 0.005 0.001 HIS C1131 PHE 0.029 0.001 PHE D 574 TYR 0.024 0.001 TYR C1031 ARG 0.012 0.000 ARG C 692 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 1014) hydrogen bonds : angle 3.89016 ( 2964) SS BOND : bond 0.00549 ( 12) SS BOND : angle 1.79111 ( 24) covalent geometry : bond 0.00282 (19234) covalent geometry : angle 0.57012 (25986) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 426 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7153 (p90) cc_final: 0.6825 (p90) REVERT: A 460 TRP cc_start: 0.5052 (m100) cc_final: 0.3933 (m100) REVERT: A 568 THR cc_start: 0.5985 (p) cc_final: 0.5723 (t) REVERT: A 599 ARG cc_start: 0.8061 (mtt-85) cc_final: 0.7481 (mtt90) REVERT: A 697 LYS cc_start: 0.7309 (mttm) cc_final: 0.6449 (pttp) REVERT: A 772 GLU cc_start: 0.6328 (pm20) cc_final: 0.5457 (mm-30) REVERT: A 788 SER cc_start: 0.8185 (p) cc_final: 0.7940 (p) REVERT: A 814 PHE cc_start: 0.7381 (t80) cc_final: 0.7081 (t80) REVERT: A 1032 TRP cc_start: 0.7996 (m-10) cc_final: 0.7652 (m-10) REVERT: B 542 LEU cc_start: 0.8496 (tt) cc_final: 0.7921 (tp) REVERT: B 549 TYR cc_start: 0.4138 (p90) cc_final: 0.3913 (p90) REVERT: B 709 ASN cc_start: 0.8634 (t0) cc_final: 0.8424 (t0) REVERT: B 772 GLU cc_start: 0.6324 (pt0) cc_final: 0.5628 (mm-30) REVERT: B 1111 VAL cc_start: 0.6673 (t) cc_final: 0.6363 (p) REVERT: B 1179 PHE cc_start: 0.8321 (t80) cc_final: 0.8119 (t80) REVERT: C 460 TRP cc_start: 0.4668 (m100) cc_final: 0.3662 (m100) REVERT: C 531 PHE cc_start: 0.7933 (m-10) cc_final: 0.7373 (m-10) REVERT: C 697 LYS cc_start: 0.7023 (mttm) cc_final: 0.6600 (pttp) REVERT: C 772 GLU cc_start: 0.6454 (pm20) cc_final: 0.5391 (mm-30) REVERT: C 1017 PHE cc_start: 0.7345 (t80) cc_final: 0.6933 (m-10) REVERT: C 1057 MET cc_start: 0.6149 (ttt) cc_final: 0.5654 (ttm) REVERT: C 1098 ARG cc_start: 0.6969 (mtp180) cc_final: 0.6459 (ptm160) REVERT: C 1105 ILE cc_start: 0.8086 (pt) cc_final: 0.7818 (tp) REVERT: C 1128 LYS cc_start: 0.5677 (ttmm) cc_final: 0.5007 (tptp) REVERT: D 414 MET cc_start: 0.7825 (mpp) cc_final: 0.7182 (tmm) REVERT: D 500 ILE cc_start: 0.8574 (mm) cc_final: 0.8227 (mm) REVERT: D 508 GLN cc_start: 0.7027 (pm20) cc_final: 0.6322 (tt0) REVERT: D 527 MET cc_start: 0.7796 (tmm) cc_final: 0.7517 (ttp) REVERT: D 570 GLU cc_start: 0.7403 (pm20) cc_final: 0.6811 (pt0) REVERT: D 591 ILE cc_start: 0.8189 (pt) cc_final: 0.7933 (pt) REVERT: D 709 ASN cc_start: 0.8699 (t0) cc_final: 0.8351 (t0) REVERT: D 713 GLU cc_start: 0.7547 (tt0) cc_final: 0.6943 (tm-30) REVERT: D 772 GLU cc_start: 0.6204 (pt0) cc_final: 0.5991 (mm-30) REVERT: D 1009 MET cc_start: 0.7072 (ptm) cc_final: 0.6710 (ptm) REVERT: D 1023 MET cc_start: 0.7056 (tpt) cc_final: 0.6188 (ttm) REVERT: D 1027 VAL cc_start: 0.8292 (t) cc_final: 0.7987 (m) REVERT: D 1063 TRP cc_start: 0.4860 (m100) cc_final: 0.4401 (m100) REVERT: D 1175 TYR cc_start: 0.5674 (m-80) cc_final: 0.5220 (m-10) REVERT: D 1179 PHE cc_start: 0.8028 (t80) cc_final: 0.7500 (t80) REVERT: D 1188 ILE cc_start: 0.7886 (mm) cc_final: 0.7667 (mm) REVERT: D 1191 MET cc_start: 0.6993 (mtp) cc_final: 0.5532 (tpp) outliers start: 2 outliers final: 0 residues processed: 427 average time/residue: 0.2650 time to fit residues: 179.6817 Evaluate side-chains 352 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 66 optimal weight: 5.9990 chunk 219 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 229 optimal weight: 0.0670 chunk 102 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN B 619 ASN B1132 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.132909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.106135 restraints weight = 39575.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106755 restraints weight = 30884.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.107362 restraints weight = 26749.248| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 19246 Z= 0.184 Angle : 0.635 7.564 26010 Z= 0.334 Chirality : 0.043 0.215 2908 Planarity : 0.004 0.042 3184 Dihedral : 7.113 90.929 2698 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.15 % Allowed : 1.25 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.17), residues: 2362 helix: 1.54 (0.14), residues: 1346 sheet: -1.13 (0.37), residues: 170 loop : -1.42 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D1177 HIS 0.005 0.001 HIS C1131 PHE 0.025 0.002 PHE D 574 TYR 0.030 0.002 TYR C 700 ARG 0.006 0.001 ARG D 485 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 1014) hydrogen bonds : angle 4.15661 ( 2964) SS BOND : bond 0.00503 ( 12) SS BOND : angle 1.81018 ( 24) covalent geometry : bond 0.00429 (19234) covalent geometry : angle 0.63332 (25986) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 403 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7171 (p90) cc_final: 0.6828 (p90) REVERT: A 460 TRP cc_start: 0.5217 (m100) cc_final: 0.4040 (m100) REVERT: A 568 THR cc_start: 0.5762 (p) cc_final: 0.5544 (t) REVERT: A 697 LYS cc_start: 0.7256 (mttm) cc_final: 0.6462 (pttp) REVERT: A 713 GLU cc_start: 0.7139 (tt0) cc_final: 0.6926 (tt0) REVERT: A 772 GLU cc_start: 0.6377 (pm20) cc_final: 0.5706 (mm-30) REVERT: A 814 PHE cc_start: 0.7394 (t80) cc_final: 0.7105 (t80) REVERT: A 1096 PHE cc_start: 0.7293 (m-10) cc_final: 0.7069 (m-10) REVERT: B 542 LEU cc_start: 0.8510 (tt) cc_final: 0.8015 (tp) REVERT: B 770 LYS cc_start: 0.7774 (mmtp) cc_final: 0.7179 (ttmt) REVERT: B 772 GLU cc_start: 0.6359 (pt0) cc_final: 0.5693 (mm-30) REVERT: B 1023 MET cc_start: 0.7057 (mmm) cc_final: 0.6198 (mtt) REVERT: B 1179 PHE cc_start: 0.8310 (t80) cc_final: 0.7921 (t80) REVERT: C 460 TRP cc_start: 0.4823 (m100) cc_final: 0.3671 (m100) REVERT: C 697 LYS cc_start: 0.6946 (mttm) cc_final: 0.6587 (pttp) REVERT: C 710 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7012 (mt-10) REVERT: C 772 GLU cc_start: 0.6268 (pm20) cc_final: 0.5320 (mm-30) REVERT: C 814 PHE cc_start: 0.7545 (t80) cc_final: 0.7329 (t80) REVERT: C 1057 MET cc_start: 0.6260 (ttt) cc_final: 0.5820 (ttm) REVERT: C 1098 ARG cc_start: 0.7073 (mtp180) cc_final: 0.6217 (mmt90) REVERT: C 1128 LYS cc_start: 0.5693 (ttmm) cc_final: 0.5018 (tptp) REVERT: D 414 MET cc_start: 0.7829 (mpp) cc_final: 0.7176 (tmm) REVERT: D 445 VAL cc_start: 0.7886 (p) cc_final: 0.7525 (m) REVERT: D 500 ILE cc_start: 0.8625 (mm) cc_final: 0.8255 (mm) REVERT: D 508 GLN cc_start: 0.6828 (pm20) cc_final: 0.6181 (tt0) REVERT: D 570 GLU cc_start: 0.7496 (pm20) cc_final: 0.6931 (pt0) REVERT: D 591 ILE cc_start: 0.8220 (pt) cc_final: 0.7870 (pt) REVERT: D 713 GLU cc_start: 0.7568 (tt0) cc_final: 0.7190 (tm-30) REVERT: D 772 GLU cc_start: 0.6371 (pt0) cc_final: 0.6066 (mm-30) REVERT: D 1009 MET cc_start: 0.7065 (ptm) cc_final: 0.6720 (ptm) REVERT: D 1023 MET cc_start: 0.7152 (tpt) cc_final: 0.6227 (ttm) REVERT: D 1027 VAL cc_start: 0.8399 (t) cc_final: 0.8083 (m) REVERT: D 1175 TYR cc_start: 0.5702 (m-80) cc_final: 0.5161 (m-10) REVERT: D 1179 PHE cc_start: 0.8060 (t80) cc_final: 0.7665 (t80) REVERT: D 1191 MET cc_start: 0.7048 (mtp) cc_final: 0.5578 (tpp) outliers start: 3 outliers final: 1 residues processed: 405 average time/residue: 0.2663 time to fit residues: 171.1011 Evaluate side-chains 334 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 333 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 209 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 166 optimal weight: 0.0170 chunk 154 optimal weight: 0.7980 chunk 235 optimal weight: 4.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN B 619 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.135315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.107698 restraints weight = 39451.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.108284 restraints weight = 31825.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.108721 restraints weight = 25599.097| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19246 Z= 0.121 Angle : 0.584 12.041 26010 Z= 0.304 Chirality : 0.041 0.234 2908 Planarity : 0.004 0.041 3184 Dihedral : 6.650 85.025 2698 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.10 % Allowed : 0.60 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.17), residues: 2362 helix: 1.70 (0.14), residues: 1352 sheet: -1.17 (0.37), residues: 170 loop : -1.43 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D1177 HIS 0.005 0.001 HIS C1131 PHE 0.030 0.001 PHE C1082 TYR 0.025 0.001 TYR C1031 ARG 0.004 0.000 ARG C 692 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 1014) hydrogen bonds : angle 3.94241 ( 2964) SS BOND : bond 0.00529 ( 12) SS BOND : angle 1.90995 ( 24) covalent geometry : bond 0.00274 (19234) covalent geometry : angle 0.58090 (25986) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 425 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7191 (p90) cc_final: 0.6831 (p90) REVERT: A 460 TRP cc_start: 0.5275 (m100) cc_final: 0.4060 (m100) REVERT: A 568 THR cc_start: 0.5941 (p) cc_final: 0.5728 (t) REVERT: A 673 TYR cc_start: 0.6772 (t80) cc_final: 0.6533 (t80) REVERT: A 697 LYS cc_start: 0.7271 (mttm) cc_final: 0.6483 (pttp) REVERT: A 713 GLU cc_start: 0.7247 (tt0) cc_final: 0.6927 (tt0) REVERT: A 772 GLU cc_start: 0.6283 (pm20) cc_final: 0.5496 (mm-30) REVERT: A 788 SER cc_start: 0.8341 (p) cc_final: 0.8037 (p) REVERT: A 814 PHE cc_start: 0.7420 (t80) cc_final: 0.7137 (t80) REVERT: B 500 ILE cc_start: 0.8714 (mm) cc_final: 0.8491 (mm) REVERT: B 709 ASN cc_start: 0.8602 (t0) cc_final: 0.8374 (t0) REVERT: B 770 LYS cc_start: 0.7624 (mmtp) cc_final: 0.6945 (ttmt) REVERT: B 772 GLU cc_start: 0.6359 (pt0) cc_final: 0.5687 (mm-30) REVERT: B 1175 TYR cc_start: 0.5275 (m-80) cc_final: 0.4834 (m-10) REVERT: B 1179 PHE cc_start: 0.8279 (t80) cc_final: 0.7995 (t80) REVERT: C 460 TRP cc_start: 0.4930 (m100) cc_final: 0.3774 (m100) REVERT: C 673 TYR cc_start: 0.6574 (t80) cc_final: 0.6305 (t80) REVERT: C 697 LYS cc_start: 0.6880 (mttm) cc_final: 0.6540 (pttp) REVERT: C 772 GLU cc_start: 0.6029 (pm20) cc_final: 0.5316 (mm-30) REVERT: C 1003 PHE cc_start: 0.4289 (p90) cc_final: 0.3783 (m-80) REVERT: C 1098 ARG cc_start: 0.7060 (mtp180) cc_final: 0.6545 (ptm160) REVERT: C 1105 ILE cc_start: 0.8231 (pt) cc_final: 0.7875 (tp) REVERT: C 1128 LYS cc_start: 0.5665 (ttmm) cc_final: 0.4962 (tptp) REVERT: D 414 MET cc_start: 0.7808 (mpp) cc_final: 0.7023 (tmm) REVERT: D 500 ILE cc_start: 0.8563 (mm) cc_final: 0.8294 (mm) REVERT: D 508 GLN cc_start: 0.6953 (pm20) cc_final: 0.6309 (tt0) REVERT: D 527 MET cc_start: 0.7915 (tmm) cc_final: 0.7674 (ttp) REVERT: D 570 GLU cc_start: 0.7448 (pm20) cc_final: 0.6914 (pt0) REVERT: D 591 ILE cc_start: 0.8142 (pt) cc_final: 0.7901 (pt) REVERT: D 709 ASN cc_start: 0.8755 (t0) cc_final: 0.8385 (t0) REVERT: D 713 GLU cc_start: 0.7586 (tt0) cc_final: 0.6966 (tm-30) REVERT: D 1009 MET cc_start: 0.7032 (ptm) cc_final: 0.6689 (ptm) REVERT: D 1023 MET cc_start: 0.7101 (tpt) cc_final: 0.6019 (ttm) REVERT: D 1027 VAL cc_start: 0.8362 (t) cc_final: 0.8042 (m) REVERT: D 1063 TRP cc_start: 0.4525 (m100) cc_final: 0.4064 (m100) REVERT: D 1179 PHE cc_start: 0.8043 (t80) cc_final: 0.7600 (t80) REVERT: D 1191 MET cc_start: 0.6974 (mtp) cc_final: 0.5442 (tpp) outliers start: 2 outliers final: 0 residues processed: 427 average time/residue: 0.2716 time to fit residues: 184.5158 Evaluate side-chains 346 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 8 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 169 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 127 optimal weight: 0.0670 chunk 140 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN B 714 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.132526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.105053 restraints weight = 39662.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.105869 restraints weight = 30022.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.106275 restraints weight = 25468.905| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 19246 Z= 0.187 Angle : 0.657 8.981 26010 Z= 0.344 Chirality : 0.043 0.244 2908 Planarity : 0.004 0.043 3184 Dihedral : 6.915 88.463 2698 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.10 % Allowed : 0.40 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2362 helix: 1.53 (0.14), residues: 1348 sheet: -1.18 (0.38), residues: 168 loop : -1.43 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1177 HIS 0.011 0.001 HIS A1204 PHE 0.032 0.002 PHE C1082 TYR 0.028 0.002 TYR C1031 ARG 0.006 0.001 ARG B 694 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 1014) hydrogen bonds : angle 4.17899 ( 2964) SS BOND : bond 0.00672 ( 12) SS BOND : angle 2.33893 ( 24) covalent geometry : bond 0.00438 (19234) covalent geometry : angle 0.65349 (25986) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 385 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7227 (p90) cc_final: 0.6864 (p90) REVERT: A 460 TRP cc_start: 0.5345 (m100) cc_final: 0.4080 (m100) REVERT: A 599 ARG cc_start: 0.8116 (mtt-85) cc_final: 0.7401 (mtt90) REVERT: A 673 TYR cc_start: 0.6754 (t80) cc_final: 0.6497 (t80) REVERT: A 697 LYS cc_start: 0.7203 (mttm) cc_final: 0.6437 (pttp) REVERT: A 713 GLU cc_start: 0.7191 (tt0) cc_final: 0.6986 (tt0) REVERT: A 814 PHE cc_start: 0.7410 (t80) cc_final: 0.7188 (t80) REVERT: A 1009 MET cc_start: 0.7478 (tmm) cc_final: 0.7119 (tmm) REVERT: A 1076 CYS cc_start: 0.3759 (p) cc_final: 0.2563 (m) REVERT: B 709 ASN cc_start: 0.8638 (t0) cc_final: 0.8400 (t0) REVERT: B 772 GLU cc_start: 0.6344 (pt0) cc_final: 0.5669 (mm-30) REVERT: B 1008 GLN cc_start: 0.7173 (mt0) cc_final: 0.6888 (mt0) REVERT: B 1023 MET cc_start: 0.7055 (mmm) cc_final: 0.6252 (mtt) REVERT: B 1175 TYR cc_start: 0.5379 (m-80) cc_final: 0.4902 (m-10) REVERT: C 673 TYR cc_start: 0.6632 (t80) cc_final: 0.6332 (t80) REVERT: C 697 LYS cc_start: 0.6837 (mttm) cc_final: 0.6510 (pttp) REVERT: C 772 GLU cc_start: 0.6004 (pm20) cc_final: 0.5479 (mm-30) REVERT: C 1003 PHE cc_start: 0.4345 (p90) cc_final: 0.3888 (m-80) REVERT: C 1057 MET cc_start: 0.6284 (ttt) cc_final: 0.5893 (ttm) REVERT: C 1098 ARG cc_start: 0.7041 (mtp180) cc_final: 0.6235 (mmt90) REVERT: C 1128 LYS cc_start: 0.5747 (ttmm) cc_final: 0.5067 (tptp) REVERT: D 500 ILE cc_start: 0.8623 (mm) cc_final: 0.8385 (mm) REVERT: D 713 GLU cc_start: 0.7626 (tt0) cc_final: 0.7136 (tm-30) REVERT: D 1009 MET cc_start: 0.7048 (ptm) cc_final: 0.6724 (ptm) REVERT: D 1023 MET cc_start: 0.7144 (tpt) cc_final: 0.6214 (ttm) REVERT: D 1027 VAL cc_start: 0.8406 (t) cc_final: 0.8093 (m) REVERT: D 1179 PHE cc_start: 0.8081 (t80) cc_final: 0.7743 (t80) REVERT: D 1191 MET cc_start: 0.6857 (mtp) cc_final: 0.5512 (tpp) outliers start: 2 outliers final: 0 residues processed: 387 average time/residue: 0.2763 time to fit residues: 171.2982 Evaluate side-chains 323 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 53 optimal weight: 0.4980 chunk 135 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105926 restraints weight = 39666.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107249 restraints weight = 31019.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.108339 restraints weight = 22818.318| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 19246 Z= 0.135 Angle : 0.616 8.068 26010 Z= 0.321 Chirality : 0.041 0.214 2908 Planarity : 0.004 0.042 3184 Dihedral : 6.608 83.998 2698 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.05 % Allowed : 0.35 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.52 (0.17), residues: 2362 helix: 1.69 (0.14), residues: 1338 sheet: -1.36 (0.37), residues: 162 loop : -1.50 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 767 HIS 0.004 0.001 HIS C1131 PHE 0.031 0.002 PHE C1082 TYR 0.025 0.001 TYR C1031 ARG 0.006 0.000 ARG B 694 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 1014) hydrogen bonds : angle 4.02598 ( 2964) SS BOND : bond 0.00582 ( 12) SS BOND : angle 2.19401 ( 24) covalent geometry : bond 0.00311 (19234) covalent geometry : angle 0.61258 (25986) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6418.52 seconds wall clock time: 112 minutes 3.12 seconds (6723.12 seconds total)