Starting phenix.real_space_refine on Sat Jul 4 06:09:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tnj_26011/07_2026/7tnj_26011.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnj_26011/07_2026/7tnj_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_26011/07_2026/7tnj_26011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnj_26011/07_2026/7tnj_26011.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnj_26011/07_2026/7tnj_26011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnj_26011/07_2026/7tnj_26011.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tnj_26011/07_2026/7tnj_26011.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tnj_26011/07_2026/7tnj_26011.cif" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 4.00, per 1000 atoms: 0.21 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: 1.59 Conformation dependent library (CDL) restraints added in 887.7 milliseconds 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: 0.54 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: 3.27 Time building geometry restraints manager: 2.09 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 - 18.45: 10791 18.45 - 36.91: 408 36.91 - 55.36: 55 55.36 - 73.82: 12 73.82 - 92.27: 4 Dihedral angle restraints: 11270 sinusoidal: 4392 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 11267 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 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: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.540 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 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 : 10.528 92.274 6850 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.015 0.001 ARG D 599 TYR 0.042 0.002 TYR C1031 PHE 0.041 0.003 PHE C1082 TRP 0.024 0.003 TRP C1032 HIS 0.005 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.25 (19234) covalent geometry : angle 0.94112 / 0.53 (25986) SS BOND : bond 0.00551 / 0.37 ( 12) SS BOND : angle 1.24805 / 0.77 ( 24) hydrogen bonds : bond 0.29210 / 19.01 ( 1014) hydrogen bonds : angle 9.39770 / 6.54 ( 2964) *********************** 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 : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 VAL cc_start: 0.8376 (t) cc_final: 0.7573 (t) REVERT: A 440 TYR cc_start: 0.7341 (p90) cc_final: 0.6705 (p90) REVERT: A 460 TRP cc_start: 0.4917 (m100) cc_final: 0.3952 (m100) REVERT: A 464 VAL cc_start: 0.8498 (t) cc_final: 0.8138 (p) REVERT: A 474 ILE cc_start: 0.8436 (tt) cc_final: 0.8210 (mp) REVERT: A 531 PHE cc_start: 0.8115 (m-10) cc_final: 0.7883 (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: 0.6073 (t60) REVERT: A 751 LEU cc_start: 0.9062 (mm) cc_final: 0.8857 (mp) REVERT: A 814 PHE cc_start: 0.6883 (t80) cc_final: 0.6471 (t80) REVERT: A 1128 LYS cc_start: 0.5014 (ttmm) cc_final: 0.4718 (tptt) REVERT: A 1171 ASN cc_start: 0.5165 (t160) cc_final: 0.4776 (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: 0.7747 (ttp) REVERT: B 671 TRP cc_start: 0.5925 (t-100) cc_final: 0.5698 (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: 0.7117 (tm) REVERT: C 435 HIS cc_start: 0.6937 (m170) cc_final: 0.6736 (m170) REVERT: C 442 LEU cc_start: 0.8075 (mt) cc_final: 0.7874 (mp) REVERT: C 460 TRP cc_start: 0.4414 (m100) cc_final: 0.3814 (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: 0.6290 (pp30) REVERT: C 644 GLU cc_start: 0.5335 (tt0) cc_final: 0.5130 (tt0) REVERT: C 671 TRP cc_start: 0.6350 (t-100) cc_final: 0.5893 (t60) REVERT: C 697 LYS cc_start: 0.7156 (mttm) cc_final: 0.6454 (pttp) REVERT: C 788 SER cc_start: 0.8173 (p) cc_final: 0.7890 (p) REVERT: C 800 VAL cc_start: 0.8002 (t) cc_final: 0.7515 (p) REVERT: C 1022 LEU cc_start: 0.6751 (mt) cc_final: 0.6484 (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: 0.8444 (mm) REVERT: C 1140 PHE cc_start: 0.7940 (m-80) cc_final: 0.7564 (m-80) REVERT: C 1149 ILE cc_start: 0.8227 (tt) cc_final: 0.8016 (tp) REVERT: C 1173 TYR cc_start: 0.6741 (p90) cc_final: 0.5956 (p90) REVERT: C 1199 MET cc_start: 0.6187 (ttt) cc_final: 0.5846 (ttm) REVERT: D 508 GLN cc_start: 0.6986 (pm20) cc_final: 0.6355 (tt0) REVERT: D 713 GLU cc_start: 0.7233 (tt0) cc_final: 0.6921 (tm-30) REVERT: D 753 LEU cc_start: 0.8846 (mt) cc_final: 0.8622 (mp) REVERT: D 1009 MET cc_start: 0.7326 (ttp) cc_final: 0.7094 (ptm) REVERT: D 1023 MET cc_start: 0.7349 (tpt) cc_final: 0.6699 (ttm) REVERT: D 1075 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6856 (tm) REVERT: D 1139 ILE cc_start: 0.8220 (pt) cc_final: 0.7838 (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: 0.1477 time to fit residues: 155.0201 Evaluate side-chains 399 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 396 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 235 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 HIS ** 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 412 HIS C 714 GLN D 412 HIS D1008 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.138449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.110759 restraints weight = 38008.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.112585 restraints weight = 29085.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.113314 restraints weight = 20823.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113577 restraints weight = 18278.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.113947 restraints weight = 16919.904| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19246 Z= 0.152 Angle : 0.641 19.896 26010 Z= 0.339 Chirality : 0.043 0.645 2908 Planarity : 0.005 0.048 3184 Dihedral : 5.953 81.995 2602 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.15 % Allowed : 3.19 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.15), residues: 2362 helix: -0.60 (0.12), residues: 1344 sheet: -1.61 (0.35), residues: 170 loop : -1.80 (0.18), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1101 TYR 0.018 0.002 TYR C1031 PHE 0.031 0.002 PHE B1017 TRP 0.017 0.002 TRP C1032 HIS 0.007 0.001 HIS B1198 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (19234) covalent geometry : angle 0.64019 / 0.34 (25986) SS BOND : bond 0.00525 / 0.35 ( 12) SS BOND : angle 0.99633 / 0.62 ( 24) hydrogen bonds : bond 0.04799 / 3.18 ( 1014) hydrogen bonds : angle 4.44437 / 3.08 ( 2964) *********************** 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 536 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 533 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 460 TRP cc_start: 0.4883 (m100) cc_final: 0.4002 (m100) REVERT: A 474 ILE cc_start: 0.8347 (tt) cc_final: 0.8010 (mp) REVERT: A 568 THR cc_start: 0.6653 (p) cc_final: 0.6139 (t) REVERT: A 575 ASN cc_start: 0.8046 (m-40) cc_final: 0.7730 (m-40) REVERT: A 697 LYS cc_start: 0.7552 (mttm) cc_final: 0.6606 (pttp) REVERT: A 710 GLU cc_start: 0.7236 (mt-10) cc_final: 0.7002 (mt-10) REVERT: A 808 LEU cc_start: 0.7160 (mt) cc_final: 0.6877 (mp) REVERT: A 814 PHE cc_start: 0.6892 (t80) cc_final: 0.6527 (t80) REVERT: A 1009 MET cc_start: 0.7776 (tmm) cc_final: 0.7273 (tmm) REVERT: A 1142 VAL cc_start: 0.8075 (t) cc_final: 0.7859 (m) REVERT: A 1195 LEU cc_start: 0.8291 (mt) cc_final: 0.8026 (mt) REVERT: A 1201 ILE cc_start: 0.8140 (mm) cc_final: 0.7874 (mm) REVERT: B 496 MET cc_start: 0.8159 (ttp) cc_final: 0.7864 (ttp) REVERT: B 545 ARG cc_start: 0.6658 (mmt180) cc_final: 0.6363 (mmt180) REVERT: B 752 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7669 (ttpt) REVERT: B 754 SER cc_start: 0.7689 (t) cc_final: 0.7487 (p) REVERT: B 772 GLU cc_start: 0.7100 (pt0) cc_final: 0.6190 (mm-30) REVERT: C 460 TRP cc_start: 0.4258 (m100) cc_final: 0.3645 (m100) REVERT: C 644 GLU cc_start: 0.5378 (tt0) cc_final: 0.5148 (tt0) REVERT: C 697 LYS cc_start: 0.7154 (mttm) cc_final: 0.6595 (pttp) REVERT: C 710 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6626 (mt-10) REVERT: C 1022 LEU cc_start: 0.6783 (mt) cc_final: 0.6526 (mt) REVERT: C 1062 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6729 (mt) REVERT: C 1128 LYS cc_start: 0.5868 (ttmm) cc_final: 0.5223 (tptp) REVERT: C 1191 MET cc_start: 0.5852 (tpt) cc_final: 0.5478 (tpt) REVERT: C 1194 VAL cc_start: 0.7739 (t) cc_final: 0.7499 (p) REVERT: D 508 GLN cc_start: 0.7086 (pm20) cc_final: 0.6248 (tt0) REVERT: D 570 GLU cc_start: 0.7276 (pm20) cc_final: 0.6809 (pt0) REVERT: D 645 ILE cc_start: 0.6943 (mm) cc_final: 0.6505 (tt) REVERT: D 709 ASN cc_start: 0.8692 (t0) cc_final: 0.8371 (t0) REVERT: D 713 GLU cc_start: 0.7412 (tt0) cc_final: 0.7054 (tm-30) REVERT: D 772 GLU cc_start: 0.6748 (pt0) cc_final: 0.6057 (mm-30) REVERT: D 1023 MET cc_start: 0.7345 (tpt) cc_final: 0.6371 (ttt) REVERT: D 1027 VAL cc_start: 0.8122 (t) cc_final: 0.7843 (m) REVERT: D 1031 TYR cc_start: 0.6206 (m-80) cc_final: 0.5937 (m-80) REVERT: D 1139 ILE cc_start: 0.8250 (pt) cc_final: 0.7901 (mt) REVERT: D 1179 PHE cc_start: 0.8061 (t80) cc_final: 0.7616 (t80) REVERT: D 1190 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7488 (mm-30) REVERT: D 1206 GLN cc_start: 0.3788 (mp10) cc_final: 0.2636 (tp40) outliers start: 3 outliers final: 0 residues processed: 535 average time/residue: 0.1293 time to fit residues: 107.7677 Evaluate side-chains 387 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 386 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 8 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 216 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1132 ASN ** B1159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3840 r_free = 0.3840 target = 0.138280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.110772 restraints weight = 38729.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111453 restraints weight = 28835.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112405 restraints weight = 23778.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112897 restraints weight = 20110.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113166 restraints weight = 18971.943| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3890 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= 0.131 Angle : 0.565 6.334 26010 Z= 0.299 Chirality : 0.040 0.193 2908 Planarity : 0.004 0.045 3184 Dihedral : 5.566 79.899 2602 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.10 % Allowed : 2.69 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.16), residues: 2362 helix: 0.70 (0.14), residues: 1338 sheet: -1.51 (0.36), residues: 170 loop : -1.59 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 628 TYR 0.020 0.001 TYR C1031 PHE 0.028 0.001 PHE B1017 TRP 0.017 0.001 TRP A 767 HIS 0.006 0.001 HIS A1204 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (19234) covalent geometry : angle 0.56461 / 0.30 (25986) SS BOND : bond 0.00344 / 0.23 ( 12) SS BOND : angle 0.96906 / 0.67 ( 24) hydrogen bonds : bond 0.03964 / 2.62 ( 1014) hydrogen bonds : angle 4.07695 / 2.81 ( 2964) *********************** 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 491 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 489 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7159 (p90) cc_final: 0.6947 (p90) REVERT: A 460 TRP cc_start: 0.5012 (m100) cc_final: 0.4028 (m100) REVERT: A 568 THR cc_start: 0.6460 (p) cc_final: 0.6007 (t) REVERT: A 575 ASN cc_start: 0.7863 (m-40) cc_final: 0.7571 (m-40) REVERT: A 697 LYS cc_start: 0.7507 (mttm) cc_final: 0.6546 (pttp) REVERT: A 788 SER cc_start: 0.8361 (p) cc_final: 0.8153 (p) REVERT: A 808 LEU cc_start: 0.7212 (mt) cc_final: 0.6915 (mp) REVERT: A 814 PHE cc_start: 0.7172 (t80) cc_final: 0.6866 (t80) REVERT: A 1003 PHE cc_start: 0.4972 (m-80) cc_final: 0.4351 (m-80) REVERT: A 1009 MET cc_start: 0.7837 (tmm) cc_final: 0.7334 (tmm) REVERT: A 1195 LEU cc_start: 0.8208 (mt) cc_final: 0.7982 (mt) REVERT: B 752 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7704 (ttpt) REVERT: B 772 GLU cc_start: 0.7008 (pt0) cc_final: 0.6153 (mm-30) REVERT: C 460 TRP cc_start: 0.4462 (m100) cc_final: 0.3817 (m100) REVERT: C 467 LEU cc_start: 0.7951 (tp) cc_final: 0.7659 (tt) REVERT: C 697 LYS cc_start: 0.7211 (mttm) cc_final: 0.6582 (pttp) REVERT: C 713 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6762 (tm-30) REVERT: C 1022 LEU cc_start: 0.6699 (mt) cc_final: 0.6426 (mt) REVERT: C 1128 LYS cc_start: 0.5740 (ttmm) cc_final: 0.5127 (tptp) REVERT: C 1191 MET cc_start: 0.5939 (tpt) cc_final: 0.5613 (tpt) REVERT: C 1194 VAL cc_start: 0.7915 (t) cc_final: 0.7684 (p) REVERT: D 508 GLN cc_start: 0.7044 (pm20) cc_final: 0.6145 (tt0) REVERT: D 570 GLU cc_start: 0.7297 (pm20) cc_final: 0.6824 (pt0) REVERT: D 581 LEU cc_start: 0.9121 (tp) cc_final: 0.8898 (tt) REVERT: D 645 ILE cc_start: 0.6919 (mm) cc_final: 0.6406 (tt) REVERT: D 709 ASN cc_start: 0.8596 (t0) cc_final: 0.8375 (t0) REVERT: D 713 GLU cc_start: 0.7429 (tt0) cc_final: 0.7013 (tm-30) REVERT: D 772 GLU cc_start: 0.6550 (pt0) cc_final: 0.5913 (mm-30) REVERT: D 1023 MET cc_start: 0.7292 (tpt) cc_final: 0.6465 (mtp) REVERT: D 1027 VAL cc_start: 0.8151 (t) cc_final: 0.7890 (m) REVERT: D 1031 TYR cc_start: 0.6054 (m-80) cc_final: 0.5848 (m-80) REVERT: D 1033 LEU cc_start: 0.6775 (tp) cc_final: 0.6569 (tp) REVERT: D 1139 ILE cc_start: 0.8211 (pt) cc_final: 0.7888 (mt) REVERT: D 1179 PHE cc_start: 0.8055 (t80) cc_final: 0.7819 (t80) REVERT: D 1190 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7501 (mm-30) outliers start: 2 outliers final: 0 residues processed: 490 average time/residue: 0.1156 time to fit residues: 90.8330 Evaluate side-chains 373 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 22 optimal weight: 0.9990 chunk 229 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 158 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 642 GLN B 619 ASN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1148 ASN ** 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 = 0.3800 r_free = 0.3800 target = 0.135521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109191 restraints weight = 38891.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.108115 restraints weight = 31329.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109535 restraints weight = 27743.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.109925 restraints weight = 21665.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110181 restraints weight = 20888.097| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4419 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= 0.173 Angle : 0.597 9.341 26010 Z= 0.316 Chirality : 0.041 0.238 2908 Planarity : 0.004 0.043 3184 Dihedral : 5.554 77.769 2602 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.20 % Allowed : 3.89 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.17), residues: 2362 helix: 1.14 (0.14), residues: 1360 sheet: -1.70 (0.35), residues: 172 loop : -1.39 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 692 TYR 0.020 0.002 TYR C 700 PHE 0.032 0.002 PHE D 574 TRP 0.017 0.001 TRP A 767 HIS 0.004 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (19234) covalent geometry : angle 0.59594 / 0.32 (25986) SS BOND : bond 0.00758 / 0.32 ( 12) SS BOND : angle 1.47795 / 0.77 ( 24) hydrogen bonds : bond 0.03904 / 2.59 ( 1014) hydrogen bonds : angle 4.07725 / 2.82 ( 2964) *********************** 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 455 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 451 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7232 (p90) cc_final: 0.7002 (p90) REVERT: A 460 TRP cc_start: 0.5002 (m100) cc_final: 0.3973 (m100) REVERT: A 568 THR cc_start: 0.6309 (p) cc_final: 0.5929 (t) REVERT: A 575 ASN cc_start: 0.8034 (m-40) cc_final: 0.7731 (m-40) REVERT: A 697 LYS cc_start: 0.7382 (mttm) cc_final: 0.6414 (pttp) REVERT: A 772 GLU cc_start: 0.6492 (pm20) cc_final: 0.5435 (mm-30) REVERT: A 814 PHE cc_start: 0.7245 (t80) cc_final: 0.6938 (t80) REVERT: A 1009 MET cc_start: 0.7782 (tmm) cc_final: 0.7506 (tmm) REVERT: A 1032 TRP cc_start: 0.8123 (m-10) cc_final: 0.7872 (m-10) REVERT: B 546 PHE cc_start: 0.7414 (p90) cc_final: 0.6742 (m-10) REVERT: B 670 MET cc_start: 0.6940 (mtt) cc_final: 0.6686 (mtm) REVERT: B 772 GLU cc_start: 0.6669 (pt0) cc_final: 0.5894 (mm-30) REVERT: B 1188 ILE cc_start: 0.7626 (mm) cc_final: 0.7418 (mm) REVERT: B 1191 MET cc_start: 0.5604 (tpp) cc_final: 0.5336 (tpp) REVERT: C 460 TRP cc_start: 0.4696 (m100) cc_final: 0.3710 (m100) REVERT: C 575 ASN cc_start: 0.8454 (t0) cc_final: 0.8206 (t0) REVERT: C 697 LYS cc_start: 0.7207 (mttm) cc_final: 0.6568 (pttp) REVERT: C 1098 ARG cc_start: 0.6556 (mtp-110) cc_final: 0.6189 (mtp85) REVERT: C 1128 LYS cc_start: 0.5759 (ttmm) cc_final: 0.5144 (tptp) REVERT: C 1191 MET cc_start: 0.6224 (tpt) cc_final: 0.5759 (tpt) REVERT: D 508 GLN cc_start: 0.6941 (pm20) cc_final: 0.6135 (tt0) REVERT: D 527 MET cc_start: 0.7929 (tmm) cc_final: 0.7569 (ttp) REVERT: D 570 GLU cc_start: 0.7343 (pm20) cc_final: 0.6762 (pt0) REVERT: D 645 ILE cc_start: 0.6745 (mm) cc_final: 0.6337 (tt) REVERT: D 709 ASN cc_start: 0.8744 (t0) cc_final: 0.8429 (t0) REVERT: D 713 GLU cc_start: 0.7406 (tt0) cc_final: 0.7122 (tm-30) REVERT: D 772 GLU cc_start: 0.6236 (pt0) cc_final: 0.5908 (mm-30) REVERT: D 1023 MET cc_start: 0.7225 (tpt) cc_final: 0.6302 (ttm) REVERT: D 1027 VAL cc_start: 0.8245 (t) cc_final: 0.7953 (m) REVERT: D 1033 LEU cc_start: 0.6737 (tp) cc_final: 0.6442 (tp) REVERT: D 1139 ILE cc_start: 0.8206 (pt) cc_final: 0.7739 (mt) REVERT: D 1179 PHE cc_start: 0.8062 (t80) cc_final: 0.7787 (t80) outliers start: 4 outliers final: 0 residues processed: 454 average time/residue: 0.1249 time to fit residues: 90.5824 Evaluate side-chains 357 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 220 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 86 optimal weight: 0.0070 chunk 148 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 201 optimal weight: 0.0980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN B1132 ASN B1148 ASN C 575 ASN D1206 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.138213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.111487 restraints weight = 38450.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.112665 restraints weight = 29559.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.113633 restraints weight = 23997.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.115120 restraints weight = 19279.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.115113 restraints weight = 16559.543| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19246 Z= 0.113 Angle : 0.548 8.490 26010 Z= 0.285 Chirality : 0.039 0.189 2908 Planarity : 0.004 0.040 3184 Dihedral : 5.295 73.094 2602 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.10 % Allowed : 1.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.17), residues: 2362 helix: 1.60 (0.14), residues: 1350 sheet: -1.37 (0.35), residues: 180 loop : -1.35 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1203 TYR 0.018 0.001 TYR C 533 PHE 0.023 0.001 PHE D 623 TRP 0.012 0.001 TRP C1032 HIS 0.003 0.001 HIS C1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (19234) covalent geometry : angle 0.54672 / 0.28 (25986) SS BOND : bond 0.00538 / 0.29 ( 12) SS BOND : angle 1.27009 / 0.79 ( 24) hydrogen bonds : bond 0.03372 / 2.23 ( 1014) hydrogen bonds : angle 3.82928 / 2.64 ( 2964) *********************** 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 452 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 450 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 TRP cc_start: 0.4840 (m100) cc_final: 0.3844 (m100) REVERT: A 568 THR cc_start: 0.6201 (p) cc_final: 0.5767 (t) REVERT: A 639 LEU cc_start: 0.7959 (tp) cc_final: 0.7754 (tp) REVERT: A 673 TYR cc_start: 0.6726 (t80) cc_final: 0.6450 (t80) REVERT: A 697 LYS cc_start: 0.7308 (mttm) cc_final: 0.6453 (pttp) REVERT: A 772 GLU cc_start: 0.6321 (pm20) cc_final: 0.5285 (mm-30) REVERT: A 788 SER cc_start: 0.8129 (p) cc_final: 0.7884 (p) REVERT: A 814 PHE cc_start: 0.7283 (t80) cc_final: 0.6911 (t80) REVERT: A 1009 MET cc_start: 0.7737 (tmm) cc_final: 0.7458 (tmm) REVERT: B 546 PHE cc_start: 0.7234 (p90) cc_final: 0.6642 (m-10) REVERT: B 772 GLU cc_start: 0.6501 (pt0) cc_final: 0.5811 (mm-30) REVERT: B 1191 MET cc_start: 0.5555 (tpp) cc_final: 0.5293 (tpp) REVERT: C 460 TRP cc_start: 0.4496 (m100) cc_final: 0.3614 (m100) REVERT: C 575 ASN cc_start: 0.8426 (t160) cc_final: 0.8050 (t0) REVERT: C 600 ILE cc_start: 0.8100 (mt) cc_final: 0.7899 (mp) REVERT: C 697 LYS cc_start: 0.7297 (mttm) cc_final: 0.6612 (pttp) REVERT: C 772 GLU cc_start: 0.6592 (pm20) cc_final: 0.5268 (mm-30) REVERT: C 1057 MET cc_start: 0.5839 (ttt) cc_final: 0.5461 (ttp) REVERT: C 1105 ILE cc_start: 0.8086 (pt) cc_final: 0.7787 (tp) REVERT: C 1128 LYS cc_start: 0.5712 (ttmm) cc_final: 0.5151 (tptp) REVERT: D 508 GLN cc_start: 0.7013 (pm20) cc_final: 0.6156 (tt0) REVERT: D 527 MET cc_start: 0.7808 (tmm) cc_final: 0.7320 (ttp) REVERT: D 570 GLU cc_start: 0.7366 (pm20) cc_final: 0.6752 (pt0) REVERT: D 645 ILE cc_start: 0.6569 (mm) cc_final: 0.6089 (tt) REVERT: D 709 ASN cc_start: 0.8649 (t0) cc_final: 0.8377 (t0) REVERT: D 713 GLU cc_start: 0.7406 (tt0) cc_final: 0.7129 (tm-30) REVERT: D 772 GLU cc_start: 0.6117 (pt0) cc_final: 0.5798 (mm-30) REVERT: D 1023 MET cc_start: 0.7087 (tpt) cc_final: 0.6310 (mtp) REVERT: D 1027 VAL cc_start: 0.8232 (t) cc_final: 0.8014 (m) REVERT: D 1063 TRP cc_start: 0.4768 (m100) cc_final: 0.4358 (m100) REVERT: D 1077 LYS cc_start: 0.7160 (tmmt) cc_final: 0.6382 (tptt) REVERT: D 1116 MET cc_start: 0.6672 (mpp) cc_final: 0.6425 (mtt) REVERT: D 1179 PHE cc_start: 0.8064 (t80) cc_final: 0.7595 (t80) REVERT: D 1188 ILE cc_start: 0.7909 (mm) cc_final: 0.7650 (mm) outliers start: 2 outliers final: 0 residues processed: 452 average time/residue: 0.1111 time to fit residues: 80.8132 Evaluate side-chains 361 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 57 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 6 optimal weight: 0.0040 chunk 40 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 0.0050 chunk 122 optimal weight: 6.9990 chunk 147 optimal weight: 0.0970 chunk 173 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN C 575 ASN D1206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.137574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.110997 restraints weight = 38604.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111157 restraints weight = 30726.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111832 restraints weight = 28113.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.112441 restraints weight = 23270.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112731 restraints weight = 21169.575| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19246 Z= 0.107 Angle : 0.534 9.394 26010 Z= 0.278 Chirality : 0.039 0.170 2908 Planarity : 0.003 0.041 3184 Dihedral : 5.126 71.315 2602 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.17), residues: 2362 helix: 1.84 (0.14), residues: 1350 sheet: -1.28 (0.36), residues: 170 loop : -1.37 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1203 TYR 0.022 0.001 TYR C 533 PHE 0.018 0.001 PHE B1141 TRP 0.012 0.001 TRP D1177 HIS 0.017 0.001 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (19234) covalent geometry : angle 0.53353 / 0.28 (25986) SS BOND : bond 0.00477 / 0.31 ( 12) SS BOND : angle 1.00728 / 0.68 ( 24) hydrogen bonds : bond 0.03224 / 2.13 ( 1014) hydrogen bonds : angle 3.72911 / 2.58 ( 2964) *********************** 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 458 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7150 (p90) cc_final: 0.6777 (p90) REVERT: A 460 TRP cc_start: 0.4769 (m100) cc_final: 0.3650 (m100) REVERT: A 568 THR cc_start: 0.6052 (p) cc_final: 0.5727 (t) REVERT: A 599 ARG cc_start: 0.8018 (mtt-85) cc_final: 0.7422 (mtt90) REVERT: A 639 LEU cc_start: 0.7832 (tp) cc_final: 0.7593 (tp) REVERT: A 673 TYR cc_start: 0.6640 (t80) cc_final: 0.6434 (t80) REVERT: A 697 LYS cc_start: 0.7286 (mttm) cc_final: 0.6492 (pttp) REVERT: A 772 GLU cc_start: 0.6255 (pm20) cc_final: 0.5297 (mm-30) REVERT: A 788 SER cc_start: 0.8167 (p) cc_final: 0.7913 (p) REVERT: A 814 PHE cc_start: 0.7348 (t80) cc_final: 0.6966 (t80) REVERT: A 1009 MET cc_start: 0.7695 (tmm) cc_final: 0.7406 (tmm) REVERT: B 546 PHE cc_start: 0.7449 (p90) cc_final: 0.6864 (m-10) REVERT: B 772 GLU cc_start: 0.6530 (pt0) cc_final: 0.5767 (mm-30) REVERT: B 1023 MET cc_start: 0.7372 (mmm) cc_final: 0.6950 (mmt) REVERT: C 460 TRP cc_start: 0.4442 (m100) cc_final: 0.3571 (m100) REVERT: C 575 ASN cc_start: 0.8345 (t160) cc_final: 0.8106 (t0) REVERT: C 642 GLN cc_start: 0.6276 (pp30) cc_final: 0.6070 (pp30) REVERT: C 697 LYS cc_start: 0.7247 (mttm) cc_final: 0.6647 (pttp) REVERT: C 708 MET cc_start: 0.7630 (tpp) cc_final: 0.7395 (tpp) REVERT: C 772 GLU cc_start: 0.6372 (pm20) cc_final: 0.5144 (mm-30) REVERT: C 1057 MET cc_start: 0.5905 (ttt) cc_final: 0.5442 (ttm) REVERT: C 1098 ARG cc_start: 0.6712 (mtp180) cc_final: 0.6412 (mtp85) REVERT: C 1105 ILE cc_start: 0.7981 (pt) cc_final: 0.7716 (tp) REVERT: C 1128 LYS cc_start: 0.5690 (ttmm) cc_final: 0.5096 (tptp) REVERT: D 464 VAL cc_start: 0.8159 (t) cc_final: 0.7907 (t) REVERT: D 500 ILE cc_start: 0.8541 (mm) cc_final: 0.8186 (mm) REVERT: D 508 GLN cc_start: 0.6945 (pm20) cc_final: 0.6055 (tt0) REVERT: D 527 MET cc_start: 0.7870 (tmm) cc_final: 0.7490 (ttp) REVERT: D 570 GLU cc_start: 0.7397 (pm20) cc_final: 0.6797 (pt0) REVERT: D 645 ILE cc_start: 0.6557 (mm) cc_final: 0.6107 (tt) REVERT: D 709 ASN cc_start: 0.8619 (t0) cc_final: 0.8379 (t0) REVERT: D 713 GLU cc_start: 0.7336 (tt0) cc_final: 0.7015 (tm-30) REVERT: D 772 GLU cc_start: 0.5955 (pt0) cc_final: 0.5732 (mm-30) REVERT: D 1023 MET cc_start: 0.7049 (tpt) cc_final: 0.6250 (mtp) REVERT: D 1027 VAL cc_start: 0.8282 (t) cc_final: 0.8002 (m) REVERT: D 1179 PHE cc_start: 0.8016 (t80) cc_final: 0.7644 (t80) REVERT: D 1191 MET cc_start: 0.7006 (mtp) cc_final: 0.5498 (tpp) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.1146 time to fit residues: 83.9904 Evaluate side-chains 354 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 0.4980 chunk 73 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 222 optimal weight: 0.0770 chunk 51 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 642 GLN B1132 ASN ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.136756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.110644 restraints weight = 38943.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.109869 restraints weight = 34267.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110936 restraints weight = 29134.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111497 restraints weight = 23491.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111719 restraints weight = 22460.159| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19246 Z= 0.119 Angle : 0.553 7.727 26010 Z= 0.289 Chirality : 0.039 0.170 2908 Planarity : 0.003 0.042 3184 Dihedral : 5.135 71.027 2602 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.10 % Allowed : 1.60 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.17), residues: 2362 helix: 1.86 (0.14), residues: 1352 sheet: -1.44 (0.33), residues: 204 loop : -1.41 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 692 TYR 0.017 0.001 TYR C1031 PHE 0.032 0.001 PHE D 574 TRP 0.017 0.001 TRP B1177 HIS 0.005 0.001 HIS C1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (19234) covalent geometry : angle 0.55154 / 0.29 (25986) SS BOND : bond 0.00567 / 0.35 ( 12) SS BOND : angle 1.61764 / 0.93 ( 24) hydrogen bonds : bond 0.03298 / 2.18 ( 1014) hydrogen bonds : angle 3.76643 / 2.60 ( 2964) *********************** 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 431 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 429 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7126 (p90) cc_final: 0.6705 (p90) REVERT: A 460 TRP cc_start: 0.4762 (m100) cc_final: 0.3664 (m100) REVERT: A 568 THR cc_start: 0.5936 (p) cc_final: 0.5715 (t) REVERT: A 599 ARG cc_start: 0.7987 (mtt-85) cc_final: 0.7458 (mtt90) REVERT: A 655 THR cc_start: 0.8335 (p) cc_final: 0.8126 (p) REVERT: A 673 TYR cc_start: 0.6616 (t80) cc_final: 0.6409 (t80) REVERT: A 697 LYS cc_start: 0.7220 (mttm) cc_final: 0.6463 (pttp) REVERT: A 772 GLU cc_start: 0.6306 (pm20) cc_final: 0.5339 (mm-30) REVERT: A 788 SER cc_start: 0.8215 (p) cc_final: 0.7889 (p) REVERT: A 814 PHE cc_start: 0.7416 (t80) cc_final: 0.7034 (t80) REVERT: A 1009 MET cc_start: 0.7672 (tmm) cc_final: 0.7395 (tmm) REVERT: B 546 PHE cc_start: 0.7479 (p90) cc_final: 0.6872 (m-10) REVERT: B 772 GLU cc_start: 0.6466 (pt0) cc_final: 0.5662 (mm-30) REVERT: B 1023 MET cc_start: 0.7519 (mmm) cc_final: 0.6428 (mmt) REVERT: B 1179 PHE cc_start: 0.8336 (t80) cc_final: 0.8000 (t80) REVERT: B 1191 MET cc_start: 0.5558 (tpp) cc_final: 0.5269 (tpp) REVERT: C 460 TRP cc_start: 0.4579 (m100) cc_final: 0.3567 (m100) REVERT: C 697 LYS cc_start: 0.7067 (mttm) cc_final: 0.6536 (pttp) REVERT: C 708 MET cc_start: 0.7588 (tpp) cc_final: 0.7297 (tpp) REVERT: C 772 GLU cc_start: 0.6331 (pm20) cc_final: 0.5138 (mm-30) REVERT: C 1098 ARG cc_start: 0.6702 (mtp180) cc_final: 0.6239 (ptm160) REVERT: C 1105 ILE cc_start: 0.7991 (pt) cc_final: 0.7707 (tp) REVERT: C 1128 LYS cc_start: 0.5483 (ttmm) cc_final: 0.4890 (tptp) REVERT: D 464 VAL cc_start: 0.8085 (t) cc_final: 0.7862 (t) REVERT: D 500 ILE cc_start: 0.8580 (mm) cc_final: 0.8273 (mm) REVERT: D 508 GLN cc_start: 0.6981 (pm20) cc_final: 0.6030 (tt0) REVERT: D 527 MET cc_start: 0.7919 (tmm) cc_final: 0.7512 (ttp) REVERT: D 570 GLU cc_start: 0.7440 (pm20) cc_final: 0.6792 (pt0) REVERT: D 645 ILE cc_start: 0.6508 (mm) cc_final: 0.6051 (tt) REVERT: D 709 ASN cc_start: 0.8670 (t0) cc_final: 0.8365 (t0) REVERT: D 713 GLU cc_start: 0.7376 (tt0) cc_final: 0.6934 (tm-30) REVERT: D 772 GLU cc_start: 0.6048 (pt0) cc_final: 0.5802 (mm-30) REVERT: D 1023 MET cc_start: 0.7001 (tpt) cc_final: 0.6225 (mtp) REVERT: D 1027 VAL cc_start: 0.8288 (t) cc_final: 0.8026 (m) REVERT: D 1063 TRP cc_start: 0.4871 (m100) cc_final: 0.4499 (m100) REVERT: D 1179 PHE cc_start: 0.7967 (t80) cc_final: 0.7551 (t80) REVERT: D 1191 MET cc_start: 0.6943 (mtp) cc_final: 0.5443 (tpp) outliers start: 2 outliers final: 0 residues processed: 431 average time/residue: 0.1095 time to fit residues: 76.1399 Evaluate side-chains 357 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 162 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 237 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 154 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN B 714 GLN D1206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.135609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109006 restraints weight = 39379.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109429 restraints weight = 31251.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110184 restraints weight = 27787.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.110572 restraints weight = 23077.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.110763 restraints weight = 21738.873| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19246 Z= 0.141 Angle : 0.584 14.464 26010 Z= 0.305 Chirality : 0.040 0.216 2908 Planarity : 0.004 0.042 3184 Dihedral : 5.196 72.363 2602 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.17), residues: 2362 helix: 1.81 (0.14), residues: 1340 sheet: -1.19 (0.36), residues: 186 loop : -1.28 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 692 TYR 0.018 0.001 TYR C1031 PHE 0.021 0.002 PHE A1115 TRP 0.013 0.001 TRP B1177 HIS 0.005 0.001 HIS C1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (19234) covalent geometry : angle 0.58261 / 0.30 (25986) SS BOND : bond 0.00502 / 0.30 ( 12) SS BOND : angle 1.50099 / 0.87 ( 24) hydrogen bonds : bond 0.03497 / 2.33 ( 1014) hydrogen bonds : angle 3.88942 / 2.69 ( 2964) *********************** 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 427 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 427 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7126 (p90) cc_final: 0.6800 (p90) REVERT: A 460 TRP cc_start: 0.4807 (m100) cc_final: 0.3678 (m100) REVERT: A 568 THR cc_start: 0.6010 (p) cc_final: 0.5695 (t) REVERT: A 697 LYS cc_start: 0.7350 (mttm) cc_final: 0.6507 (pttp) REVERT: A 772 GLU cc_start: 0.6222 (pm20) cc_final: 0.5379 (mm-30) REVERT: A 788 SER cc_start: 0.8209 (p) cc_final: 0.7881 (p) REVERT: A 814 PHE cc_start: 0.7359 (t80) cc_final: 0.7116 (t80) REVERT: A 1009 MET cc_start: 0.7663 (tmm) cc_final: 0.7395 (tmm) REVERT: B 542 LEU cc_start: 0.8504 (tt) cc_final: 0.8042 (tp) REVERT: B 772 GLU cc_start: 0.6389 (pt0) cc_final: 0.5623 (mm-30) REVERT: B 1179 PHE cc_start: 0.8311 (t80) cc_final: 0.8012 (t80) REVERT: C 460 TRP cc_start: 0.4514 (m100) cc_final: 0.3547 (m100) REVERT: C 642 GLN cc_start: 0.6814 (pp30) cc_final: 0.6508 (pp30) REVERT: C 697 LYS cc_start: 0.7029 (mttm) cc_final: 0.6583 (pttp) REVERT: C 1057 MET cc_start: 0.6232 (ttt) cc_final: 0.5765 (ttm) REVERT: C 1098 ARG cc_start: 0.6747 (mtp180) cc_final: 0.6412 (mtp85) REVERT: C 1105 ILE cc_start: 0.8024 (pt) cc_final: 0.7774 (tp) REVERT: C 1128 LYS cc_start: 0.5671 (ttmm) cc_final: 0.5070 (tptp) REVERT: D 500 ILE cc_start: 0.8585 (mm) cc_final: 0.8333 (mm) REVERT: D 508 GLN cc_start: 0.7010 (pm20) cc_final: 0.6125 (tt0) REVERT: D 570 GLU cc_start: 0.7560 (pm20) cc_final: 0.6963 (pt0) REVERT: D 645 ILE cc_start: 0.6304 (mm) cc_final: 0.5902 (tt) REVERT: D 709 ASN cc_start: 0.8681 (t0) cc_final: 0.8464 (t0) REVERT: D 713 GLU cc_start: 0.7450 (tt0) cc_final: 0.6963 (tm-30) REVERT: D 1023 MET cc_start: 0.7112 (tpt) cc_final: 0.6270 (mtt) REVERT: D 1027 VAL cc_start: 0.8301 (t) cc_final: 0.7979 (m) REVERT: D 1063 TRP cc_start: 0.4871 (m100) cc_final: 0.4476 (m100) REVERT: D 1111 VAL cc_start: 0.6969 (t) cc_final: 0.6578 (p) REVERT: D 1179 PHE cc_start: 0.8033 (t80) cc_final: 0.7676 (t80) REVERT: D 1188 ILE cc_start: 0.7806 (mm) cc_final: 0.7586 (mm) REVERT: D 1191 MET cc_start: 0.6951 (mtp) cc_final: 0.5504 (tpp) outliers start: 0 outliers final: 0 residues processed: 427 average time/residue: 0.1102 time to fit residues: 75.5344 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 : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 192 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 642 GLN ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106278 restraints weight = 39424.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.107019 restraints weight = 34073.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107910 restraints weight = 27154.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108274 restraints weight = 22501.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.108445 restraints weight = 21223.813| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 19246 Z= 0.180 Angle : 0.628 14.000 26010 Z= 0.330 Chirality : 0.042 0.195 2908 Planarity : 0.004 0.042 3184 Dihedral : 5.379 70.903 2602 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.10 % Allowed : 0.70 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.17), residues: 2362 helix: 1.60 (0.14), residues: 1348 sheet: -1.16 (0.38), residues: 168 loop : -1.36 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1064 TYR 0.021 0.002 TYR C1031 PHE 0.031 0.002 PHE D 574 TRP 0.024 0.001 TRP D1177 HIS 0.006 0.001 HIS C1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (19234) covalent geometry : angle 0.62710 / 0.33 (25986) SS BOND : bond 0.00449 / 0.28 ( 12) SS BOND : angle 1.36755 / 0.85 ( 24) hydrogen bonds : bond 0.03838 / 2.56 ( 1014) hydrogen bonds : angle 4.07611 / 2.82 ( 2964) *********************** 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 395 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 393 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7170 (p90) cc_final: 0.6814 (p90) REVERT: A 568 THR cc_start: 0.5871 (p) cc_final: 0.5611 (t) REVERT: A 697 LYS cc_start: 0.7249 (mttm) cc_final: 0.6518 (pttp) REVERT: A 772 GLU cc_start: 0.6320 (pm20) cc_final: 0.5618 (mm-30) REVERT: A 814 PHE cc_start: 0.7430 (t80) cc_final: 0.7118 (t80) REVERT: A 1009 MET cc_start: 0.7839 (tmm) cc_final: 0.7624 (tmm) REVERT: B 542 LEU cc_start: 0.8438 (tt) cc_final: 0.7911 (tp) REVERT: B 772 GLU cc_start: 0.6323 (pt0) cc_final: 0.5653 (mm-30) REVERT: B 1023 MET cc_start: 0.7218 (mmm) cc_final: 0.6229 (mtt) REVERT: B 1179 PHE cc_start: 0.8313 (t80) cc_final: 0.7997 (t80) REVERT: B 1191 MET cc_start: 0.5816 (tpp) cc_final: 0.5484 (tpp) REVERT: C 460 TRP cc_start: 0.4537 (m100) cc_final: 0.3553 (m100) REVERT: C 642 GLN cc_start: 0.6655 (pp30) cc_final: 0.6321 (pp30) REVERT: C 697 LYS cc_start: 0.7090 (mttm) cc_final: 0.6594 (pttp) REVERT: C 772 GLU cc_start: 0.6133 (pm20) cc_final: 0.5352 (mm-30) REVERT: C 1098 ARG cc_start: 0.6828 (mtp180) cc_final: 0.6380 (ptm160) REVERT: C 1105 ILE cc_start: 0.8117 (pt) cc_final: 0.7811 (tp) REVERT: C 1128 LYS cc_start: 0.5702 (ttmm) cc_final: 0.5004 (tptp) REVERT: D 500 ILE cc_start: 0.8626 (mm) cc_final: 0.8360 (mm) REVERT: D 508 GLN cc_start: 0.6978 (pm20) cc_final: 0.6019 (tt0) REVERT: D 570 GLU cc_start: 0.7519 (pm20) cc_final: 0.6904 (pt0) REVERT: D 709 ASN cc_start: 0.8765 (t0) cc_final: 0.8448 (t0) REVERT: D 713 GLU cc_start: 0.7469 (tt0) cc_final: 0.7200 (tm-30) REVERT: D 1023 MET cc_start: 0.7122 (tpt) cc_final: 0.6400 (mtt) REVERT: D 1027 VAL cc_start: 0.8373 (t) cc_final: 0.8086 (m) REVERT: D 1179 PHE cc_start: 0.8008 (t80) cc_final: 0.7672 (t80) REVERT: D 1188 ILE cc_start: 0.7904 (mm) cc_final: 0.7668 (mm) REVERT: D 1191 MET cc_start: 0.6991 (mtp) cc_final: 0.5543 (tpp) outliers start: 2 outliers final: 1 residues processed: 395 average time/residue: 0.1027 time to fit residues: 66.0863 Evaluate side-chains 324 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 217 optimal weight: 0.7980 chunk 196 optimal weight: 0.0570 chunk 20 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 208 optimal weight: 0.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 642 GLN ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.135325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.107941 restraints weight = 38987.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109473 restraints weight = 30827.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.110335 restraints weight = 23078.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.110816 restraints weight = 20205.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.110926 restraints weight = 19697.016| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19246 Z= 0.120 Angle : 0.583 13.144 26010 Z= 0.304 Chirality : 0.040 0.229 2908 Planarity : 0.004 0.042 3184 Dihedral : 5.202 67.987 2602 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.05 % Allowed : 0.80 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.17), residues: 2362 helix: 1.82 (0.14), residues: 1336 sheet: -1.10 (0.38), residues: 158 loop : -1.42 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 628 TYR 0.019 0.001 TYR C1031 PHE 0.027 0.001 PHE A1115 TRP 0.031 0.001 TRP B1177 HIS 0.017 0.001 HIS C 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (19234) covalent geometry : angle 0.58055 / 0.30 (25986) SS BOND : bond 0.00469 / 0.32 ( 12) SS BOND : angle 1.71785 / 1.16 ( 24) hydrogen bonds : bond 0.03408 / 2.26 ( 1014) hydrogen bonds : angle 3.88460 / 2.69 ( 2964) ********************** 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 422 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 421 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7211 (p90) cc_final: 0.6828 (p90) REVERT: A 460 TRP cc_start: 0.4922 (m100) cc_final: 0.3741 (m100) REVERT: A 568 THR cc_start: 0.5970 (p) cc_final: 0.5705 (t) REVERT: A 697 LYS cc_start: 0.7289 (mttm) cc_final: 0.6625 (pttp) REVERT: A 772 GLU cc_start: 0.6278 (pm20) cc_final: 0.5561 (mm-30) REVERT: A 788 SER cc_start: 0.8195 (p) cc_final: 0.7913 (p) REVERT: A 814 PHE cc_start: 0.7383 (t80) cc_final: 0.7067 (t80) REVERT: B 770 LYS cc_start: 0.7744 (mmtp) cc_final: 0.7281 (tppt) REVERT: B 772 GLU cc_start: 0.6272 (pt0) cc_final: 0.5606 (mm-30) REVERT: B 1023 MET cc_start: 0.7320 (mmm) cc_final: 0.6275 (mpp) REVERT: B 1191 MET cc_start: 0.5855 (tpp) cc_final: 0.5498 (tpp) REVERT: C 460 TRP cc_start: 0.4464 (m100) cc_final: 0.3527 (m100) REVERT: C 697 LYS cc_start: 0.7206 (mttm) cc_final: 0.6647 (pttp) REVERT: C 772 GLU cc_start: 0.5917 (pm20) cc_final: 0.5235 (mm-30) REVERT: C 1057 MET cc_start: 0.6110 (ttt) cc_final: 0.5608 (ttm) REVERT: C 1098 ARG cc_start: 0.6833 (mtp180) cc_final: 0.6533 (mtp85) REVERT: C 1105 ILE cc_start: 0.8097 (pt) cc_final: 0.7871 (tp) REVERT: C 1128 LYS cc_start: 0.5654 (ttmm) cc_final: 0.5001 (tptp) REVERT: D 508 GLN cc_start: 0.7069 (pm20) cc_final: 0.6136 (tt0) REVERT: D 570 GLU cc_start: 0.7526 (pm20) cc_final: 0.6946 (pt0) REVERT: D 591 ILE cc_start: 0.8158 (pt) cc_final: 0.7930 (pt) REVERT: D 709 ASN cc_start: 0.8730 (t0) cc_final: 0.8453 (t0) REVERT: D 713 GLU cc_start: 0.7469 (tt0) cc_final: 0.7225 (tm-30) REVERT: D 1023 MET cc_start: 0.7078 (tpt) cc_final: 0.6195 (mtt) REVERT: D 1027 VAL cc_start: 0.8365 (t) cc_final: 0.8086 (m) REVERT: D 1063 TRP cc_start: 0.4696 (m100) cc_final: 0.4283 (m100) REVERT: D 1179 PHE cc_start: 0.8004 (t80) cc_final: 0.7676 (t80) REVERT: D 1191 MET cc_start: 0.6967 (mtp) cc_final: 0.5502 (tpp) outliers start: 1 outliers final: 0 residues processed: 422 average time/residue: 0.1073 time to fit residues: 72.4392 Evaluate side-chains 337 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 28 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 236 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 chunk 194 optimal weight: 0.0770 chunk 219 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 overall best weight: 0.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 642 GLN ** A1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.136183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.108615 restraints weight = 39262.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.110832 restraints weight = 31986.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.111324 restraints weight = 24961.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111726 restraints weight = 21809.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.111750 restraints weight = 20392.643| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.5774 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= 0.122 Angle : 0.601 12.935 26010 Z= 0.313 Chirality : 0.040 0.240 2908 Planarity : 0.004 0.042 3184 Dihedral : 5.158 67.549 2602 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.15 % Allowed : 0.25 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.17), residues: 2362 helix: 1.80 (0.14), residues: 1348 sheet: -1.10 (0.39), residues: 154 loop : -1.34 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 692 TYR 0.027 0.001 TYR C1031 PHE 0.044 0.002 PHE D 574 TRP 0.026 0.001 TRP B1177 HIS 0.007 0.001 HIS A1204 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (19234) covalent geometry : angle 0.59926 / 0.31 (25986) SS BOND : bond 0.00480 / 0.31 ( 12) SS BOND : angle 1.73350 / 1.12 ( 24) hydrogen bonds : bond 0.03380 / 2.25 ( 1014) hydrogen bonds : angle 3.86586 / 2.67 ( 2964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2963.63 seconds wall clock time: 52 minutes 6.58 seconds (3126.58 seconds total)