Starting phenix.real_space_refine on Thu Mar 5 03:41:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tnj_26011/03_2026/7tnj_26011.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnj_26011/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tnj_26011/03_2026/7tnj_26011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnj_26011/03_2026/7tnj_26011.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tnj_26011/03_2026/7tnj_26011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnj_26011/03_2026/7tnj_26011.map" } 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-5986/lib/python3.9/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: 4.22, per 1000 atoms: 0.22 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: 1.49 Conformation dependent library (CDL) restraints added in 833.7 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: 0.47 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: 3.21 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5722 1.34 - 1.46: 4829 1.46 - 1.58: 8455 1.58 - 1.70: 8 1.70 - 1.82: 220 Bond restraints: 19234 Sorted by residual: bond pdb=" N3 CYZ C1301 " pdb=" S2 CYZ C1301 " ideal model delta sigma weight residual 1.644 1.601 0.043 2.00e-02 2.50e+03 4.57e+00 bond pdb=" N3 CYZ B1301 " pdb=" S2 CYZ B1301 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" N3 CYZ A1301 " pdb=" S2 CYZ A1301 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" N3 CYZ D1301 " pdb=" S2 CYZ D1301 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.37e+00 bond pdb=" C ASP B 519 " pdb=" N PRO B 520 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.25e-02 6.40e+03 3.53e+00 ... (remaining 19229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 25075 2.11 - 4.23: 745 4.23 - 6.34: 118 6.34 - 8.46: 39 8.46 - 10.57: 9 Bond angle restraints: 25986 Sorted by residual: angle pdb=" N ASN D1132 " pdb=" CA ASN D1132 " pdb=" C ASN D1132 " ideal model delta sigma weight residual 114.56 107.79 6.77 1.27e+00 6.20e-01 2.84e+01 angle pdb=" C ASP A1091 " pdb=" N THR A1092 " pdb=" CA THR A1092 " ideal model delta sigma weight residual 121.54 131.65 -10.11 1.91e+00 2.74e-01 2.80e+01 angle pdb=" N ASN B1132 " pdb=" CA ASN B1132 " pdb=" C ASN B1132 " ideal model delta sigma weight residual 114.56 107.84 6.72 1.27e+00 6.20e-01 2.80e+01 angle pdb=" C LYS C1128 " pdb=" N THR C1129 " pdb=" CA THR C1129 " ideal model delta sigma weight residual 122.74 130.36 -7.62 1.44e+00 4.82e-01 2.80e+01 angle pdb=" C LYS A1128 " pdb=" N THR A1129 " pdb=" CA THR A1129 " ideal model delta sigma weight residual 122.74 130.35 -7.61 1.44e+00 4.82e-01 2.79e+01 ... (remaining 25981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 11038 24.42 - 48.84: 290 48.84 - 73.27: 18 73.27 - 97.69: 11 97.69 - 122.11: 9 Dihedral angle restraints: 11366 sinusoidal: 4488 harmonic: 6878 Sorted by residual: dihedral pdb=" CB CYS B1039 " pdb=" SG CYS B1039 " pdb=" SG CYS B1067 " pdb=" CB CYS B1067 " ideal model delta sinusoidal sigma weight residual 93.00 40.68 52.32 1 1.00e+01 1.00e-02 3.73e+01 dihedral pdb=" CB CYS D1039 " pdb=" SG CYS D1039 " pdb=" SG CYS D1067 " pdb=" CB CYS D1067 " ideal model delta sinusoidal sigma weight residual 93.00 40.74 52.26 1 1.00e+01 1.00e-02 3.72e+01 dihedral pdb=" CA PRO D 632 " pdb=" C PRO D 632 " pdb=" N ILE D 633 " pdb=" CA ILE D 633 " ideal model delta harmonic sigma weight residual 180.00 -152.42 -27.58 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 11363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2367 0.061 - 0.121: 439 0.121 - 0.182: 83 0.182 - 0.243: 13 0.243 - 0.304: 6 Chirality restraints: 2908 Sorted by residual: chirality pdb=" CB ILE D 525 " pdb=" CA ILE D 525 " pdb=" CG1 ILE D 525 " pdb=" CG2 ILE D 525 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB ILE B 525 " pdb=" CA ILE B 525 " pdb=" CG1 ILE B 525 " pdb=" CG2 ILE B 525 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C8 CYZ A1301 " pdb=" C1 CYZ A1301 " pdb=" N1 CYZ A1301 " pdb=" N2 CYZ A1301 " both_signs ideal model delta sigma weight residual False 2.20 2.47 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 2905 not shown) Planarity restraints: 3184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D1088 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.98e+00 pdb=" C TYR D1088 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR D1088 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU D1089 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B1088 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.91e+00 pdb=" C TYR B1088 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR B1088 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU B1089 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 477 " -0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO C 478 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 478 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 478 " -0.037 5.00e-02 4.00e+02 ... (remaining 3181 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4404 2.78 - 3.31: 17338 3.31 - 3.84: 30296 3.84 - 4.37: 36016 4.37 - 4.90: 60875 Nonbonded interactions: 148929 Sorted by model distance: nonbonded pdb=" OG SER C 597 " pdb=" O ALA D 806 " model vdw 2.246 3.040 nonbonded pdb=" OD1 ASP C 760 " pdb="CL CYZ C1301 " model vdw 2.286 3.270 nonbonded pdb=" O THR D 643 " pdb=" OH TYR D 673 " model vdw 2.291 3.040 nonbonded pdb=" O THR B 643 " pdb=" OH TYR B 673 " model vdw 2.292 3.040 nonbonded pdb=" O PHE B 517 " pdb=" OH TYR B 616 " model vdw 2.299 3.040 ... (remaining 148924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 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: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.960 Find NCS groups from input model: 0.080 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 19246 Z= 0.248 Angle : 0.941 10.572 26010 Z= 0.527 Chirality : 0.052 0.304 2908 Planarity : 0.007 0.067 3184 Dihedral : 11.627 122.110 6946 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.20 % Allowed : 4.69 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 covalent geometry : bond 0.00543 (19234) covalent geometry : angle 0.94112 (25986) SS BOND : bond 0.00551 ( 12) SS BOND : angle 1.24805 ( 24) hydrogen bonds : bond 0.29210 ( 1014) hydrogen bonds : angle 9.39770 ( 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 : 0.675 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: 0.1439 time to fit residues: 150.9578 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 : 0.687 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3849 r_free = 0.3849 target = 0.138492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.110883 restraints weight = 38002.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.111784 restraints weight = 31392.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113022 restraints weight = 23397.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.113160 restraints weight = 19172.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113552 restraints weight = 17866.800| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3325 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= 0.154 Angle : 0.637 20.425 26010 Z= 0.337 Chirality : 0.043 0.646 2908 Planarity : 0.005 0.048 3184 Dihedral : 9.208 106.618 2698 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.15 % Allowed : 3.14 % Favored : 96.71 % 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: -1.74 (0.15), residues: 2362 helix: -0.60 (0.12), residues: 1344 sheet: -1.62 (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 D1036 TYR 0.018 0.002 TYR A1031 PHE 0.032 0.002 PHE B1017 TRP 0.027 0.002 TRP C1032 HIS 0.006 0.001 HIS B1198 Details of bonding type rmsd covalent geometry : bond 0.00340 (19234) covalent geometry : angle 0.63697 (25986) SS BOND : bond 0.00511 ( 12) SS BOND : angle 0.99283 ( 24) hydrogen bonds : bond 0.04730 ( 1014) hydrogen bonds : angle 4.42203 ( 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 540 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 537 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 449 LYS cc_start: 0.6634 (mptt) cc_final: 0.6306 (mtmt) REVERT: A 460 TRP cc_start: 0.4913 (m100) cc_final: 0.4010 (m100) REVERT: A 474 ILE cc_start: 0.8345 (tt) cc_final: 0.8003 (mp) REVERT: A 490 ASP cc_start: 0.6910 (m-30) cc_final: 0.6707 (t70) REVERT: A 568 THR cc_start: 0.6654 (p) cc_final: 0.6150 (t) REVERT: A 575 ASN cc_start: 0.8050 (m-40) cc_final: 0.7735 (m-40) REVERT: A 697 LYS cc_start: 0.7582 (mttm) cc_final: 0.6665 (pttp) REVERT: A 710 GLU cc_start: 0.7244 (mt-10) cc_final: 0.7012 (mt-10) REVERT: A 808 LEU cc_start: 0.7149 (mt) cc_final: 0.6869 (mp) REVERT: A 814 PHE cc_start: 0.6887 (t80) cc_final: 0.6635 (t80) REVERT: A 1009 MET cc_start: 0.7795 (tmm) cc_final: 0.7296 (tmm) REVERT: A 1142 VAL cc_start: 0.8090 (t) cc_final: 0.7847 (m) REVERT: A 1195 LEU cc_start: 0.8286 (mt) cc_final: 0.8035 (mt) REVERT: A 1201 ILE cc_start: 0.8178 (mm) cc_final: 0.7904 (mm) REVERT: B 432 ILE cc_start: 0.8588 (mm) cc_final: 0.8386 (tp) REVERT: B 496 MET cc_start: 0.8156 (ttp) cc_final: 0.7855 (ttp) REVERT: B 545 ARG cc_start: 0.6651 (mmt180) cc_final: 0.6379 (mmt180) REVERT: B 752 LYS cc_start: 0.8015 (ttmm) cc_final: 0.7698 (ttpt) REVERT: B 754 SER cc_start: 0.7679 (t) cc_final: 0.7461 (p) REVERT: B 772 GLU cc_start: 0.7127 (pt0) cc_final: 0.6216 (mm-30) REVERT: C 460 TRP cc_start: 0.4287 (m100) cc_final: 0.3667 (m100) REVERT: C 644 GLU cc_start: 0.5400 (tt0) cc_final: 0.5162 (tt0) REVERT: C 697 LYS cc_start: 0.7137 (mttm) cc_final: 0.6555 (pttp) REVERT: C 710 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6652 (mt-10) REVERT: C 1022 LEU cc_start: 0.6754 (mt) cc_final: 0.6482 (mt) REVERT: C 1128 LYS cc_start: 0.5863 (ttmm) cc_final: 0.5225 (tptp) REVERT: C 1191 MET cc_start: 0.5855 (tpt) cc_final: 0.5486 (tpt) REVERT: C 1194 VAL cc_start: 0.7782 (t) cc_final: 0.7553 (p) REVERT: D 508 GLN cc_start: 0.7083 (pm20) cc_final: 0.6249 (tt0) REVERT: D 570 GLU cc_start: 0.7279 (pm20) cc_final: 0.6828 (pt0) REVERT: D 645 ILE cc_start: 0.6944 (mm) cc_final: 0.6514 (tt) REVERT: D 709 ASN cc_start: 0.8703 (t0) cc_final: 0.8390 (t0) REVERT: D 713 GLU cc_start: 0.7404 (tt0) cc_final: 0.7037 (tm-30) REVERT: D 772 GLU cc_start: 0.6783 (pt0) cc_final: 0.6090 (mm-30) REVERT: D 1023 MET cc_start: 0.7347 (tpt) cc_final: 0.6524 (mtp) REVERT: D 1027 VAL cc_start: 0.8131 (t) cc_final: 0.7863 (m) REVERT: D 1031 TYR cc_start: 0.6198 (m-80) cc_final: 0.5929 (m-80) REVERT: D 1139 ILE cc_start: 0.8253 (pt) cc_final: 0.7871 (mt) REVERT: D 1179 PHE cc_start: 0.8045 (t80) cc_final: 0.7636 (t80) REVERT: D 1190 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7524 (mm-30) REVERT: D 1206 GLN cc_start: 0.3836 (mp10) cc_final: 0.2634 (tp40) outliers start: 3 outliers final: 0 residues processed: 539 average time/residue: 0.1294 time to fit residues: 108.4124 Evaluate side-chains 382 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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: 2.9990 chunk 99 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 216 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 206 optimal weight: 0.8980 chunk 75 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.138208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111120 restraints weight = 38328.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.111814 restraints weight = 28424.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112638 restraints weight = 24086.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.113116 restraints weight = 20205.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.113384 restraints weight = 18950.894| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19246 Z= 0.135 Angle : 0.571 6.602 26010 Z= 0.302 Chirality : 0.040 0.200 2908 Planarity : 0.004 0.047 3184 Dihedral : 8.602 101.828 2698 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.20 % Allowed : 3.19 % Favored : 96.61 % 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: -0.38 (0.16), residues: 2362 helix: 0.76 (0.14), residues: 1348 sheet: -1.72 (0.36), residues: 162 loop : -1.55 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 684 TYR 0.020 0.001 TYR C1031 PHE 0.027 0.002 PHE B1017 TRP 0.018 0.001 TRP A 767 HIS 0.005 0.001 HIS B1198 Details of bonding type rmsd covalent geometry : bond 0.00299 (19234) covalent geometry : angle 0.57073 (25986) SS BOND : bond 0.00455 ( 12) SS BOND : angle 0.85652 ( 24) hydrogen bonds : bond 0.03854 ( 1014) hydrogen bonds : angle 4.05365 ( 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 485 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 481 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 449 LYS cc_start: 0.6674 (mptt) cc_final: 0.6308 (mtmt) REVERT: A 460 TRP cc_start: 0.4999 (m100) cc_final: 0.3961 (m100) REVERT: A 490 ASP cc_start: 0.6948 (m-30) cc_final: 0.6720 (t70) REVERT: A 568 THR cc_start: 0.6450 (p) cc_final: 0.6005 (t) REVERT: A 575 ASN cc_start: 0.7881 (m-40) cc_final: 0.7618 (m-40) REVERT: A 697 LYS cc_start: 0.7418 (mttm) cc_final: 0.6491 (pttp) REVERT: A 814 PHE cc_start: 0.7172 (t80) cc_final: 0.6884 (t80) REVERT: A 1009 MET cc_start: 0.7816 (tmm) cc_final: 0.7336 (tmm) REVERT: B 772 GLU cc_start: 0.7009 (pt0) cc_final: 0.6143 (mm-30) REVERT: B 1188 ILE cc_start: 0.7578 (mm) cc_final: 0.7374 (mm) REVERT: B 1191 MET cc_start: 0.5395 (tpp) cc_final: 0.5147 (tpp) REVERT: C 460 TRP cc_start: 0.4504 (m100) cc_final: 0.3651 (m100) REVERT: C 467 LEU cc_start: 0.7896 (tp) cc_final: 0.7680 (tt) REVERT: C 596 LEU cc_start: 0.8206 (tt) cc_final: 0.7980 (tp) REVERT: C 697 LYS cc_start: 0.7199 (mttm) cc_final: 0.6577 (pttp) REVERT: C 1022 LEU cc_start: 0.6696 (mt) cc_final: 0.6430 (mt) REVERT: C 1128 LYS cc_start: 0.5754 (ttmm) cc_final: 0.5167 (tptp) REVERT: C 1191 MET cc_start: 0.6055 (tpt) cc_final: 0.5676 (tpt) REVERT: C 1194 VAL cc_start: 0.8019 (t) cc_final: 0.7788 (p) REVERT: D 508 GLN cc_start: 0.7061 (pm20) cc_final: 0.6175 (tt0) REVERT: D 570 GLU cc_start: 0.7321 (pm20) cc_final: 0.6769 (pt0) REVERT: D 645 ILE cc_start: 0.6891 (mm) cc_final: 0.6414 (tt) REVERT: D 709 ASN cc_start: 0.8627 (t0) cc_final: 0.8403 (t0) REVERT: D 713 GLU cc_start: 0.7431 (tt0) cc_final: 0.7043 (tm-30) REVERT: D 772 GLU cc_start: 0.6399 (pt0) cc_final: 0.5897 (mm-30) REVERT: D 1023 MET cc_start: 0.7261 (tpt) cc_final: 0.6465 (mtp) REVERT: D 1027 VAL cc_start: 0.8157 (t) cc_final: 0.7902 (m) REVERT: D 1139 ILE cc_start: 0.8222 (pt) cc_final: 0.7918 (mt) REVERT: D 1179 PHE cc_start: 0.8028 (t80) cc_final: 0.7794 (t80) outliers start: 4 outliers final: 0 residues processed: 483 average time/residue: 0.1154 time to fit residues: 89.9640 Evaluate side-chains 362 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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: 0.8980 chunk 229 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 642 GLN A1059 HIS B1132 ASN B1148 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.134327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.107803 restraints weight = 38715.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107397 restraints weight = 30216.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108697 restraints weight = 27245.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109398 restraints weight = 21118.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109647 restraints weight = 19665.466| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 19246 Z= 0.208 Angle : 0.647 9.814 26010 Z= 0.343 Chirality : 0.043 0.285 2908 Planarity : 0.005 0.051 3184 Dihedral : 8.432 96.125 2698 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.25 % Allowed : 3.44 % Favored : 96.31 % 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: -0.11 (0.17), residues: 2362 helix: 0.98 (0.14), residues: 1358 sheet: -1.60 (0.36), residues: 172 loop : -1.46 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1064 TYR 0.022 0.002 TYR C1031 PHE 0.032 0.002 PHE D 574 TRP 0.019 0.002 TRP A 767 HIS 0.005 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00478 (19234) covalent geometry : angle 0.64467 (25986) SS BOND : bond 0.01461 ( 12) SS BOND : angle 1.86736 ( 24) hydrogen bonds : bond 0.04189 ( 1014) hydrogen bonds : angle 4.29507 ( 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 435 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 430 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 490 ASP cc_start: 0.7216 (m-30) cc_final: 0.6868 (m-30) REVERT: A 568 THR cc_start: 0.6217 (p) cc_final: 0.5846 (t) REVERT: A 575 ASN cc_start: 0.8097 (m-40) cc_final: 0.7824 (m-40) REVERT: A 697 LYS cc_start: 0.7388 (mttm) cc_final: 0.6463 (pttp) REVERT: A 713 GLU cc_start: 0.7090 (tt0) cc_final: 0.6805 (tt0) REVERT: A 772 GLU cc_start: 0.6552 (pm20) cc_final: 0.5520 (mm-30) REVERT: A 814 PHE cc_start: 0.7324 (t80) cc_final: 0.7037 (t80) REVERT: A 1032 TRP cc_start: 0.8082 (m-10) cc_final: 0.7841 (m-10) REVERT: B 542 LEU cc_start: 0.8483 (tt) cc_final: 0.8130 (tp) REVERT: B 772 GLU cc_start: 0.6561 (pt0) cc_final: 0.5856 (mm-30) REVERT: B 1020 PHE cc_start: 0.6729 (t80) cc_final: 0.6506 (t80) REVERT: B 1111 VAL cc_start: 0.6597 (t) cc_final: 0.6213 (p) REVERT: B 1191 MET cc_start: 0.5730 (tpp) cc_final: 0.5397 (tpp) REVERT: C 460 TRP cc_start: 0.4746 (m100) cc_final: 0.3734 (m100) REVERT: C 575 ASN cc_start: 0.8500 (t0) cc_final: 0.8263 (t0) REVERT: C 697 LYS cc_start: 0.7229 (mttm) cc_final: 0.6527 (pttp) REVERT: C 772 GLU cc_start: 0.6570 (pm20) cc_final: 0.5361 (mm-30) REVERT: C 1098 ARG cc_start: 0.7023 (mtp180) cc_final: 0.6434 (ptm160) REVERT: C 1128 LYS cc_start: 0.5779 (ttmm) cc_final: 0.5192 (tptp) REVERT: C 1191 MET cc_start: 0.6287 (tpt) cc_final: 0.5833 (tpt) REVERT: D 508 GLN cc_start: 0.6896 (pm20) cc_final: 0.6126 (tt0) REVERT: D 713 GLU cc_start: 0.7566 (tt0) cc_final: 0.7055 (tm-30) REVERT: D 772 GLU cc_start: 0.6293 (pt0) cc_final: 0.5994 (mm-30) REVERT: D 1023 MET cc_start: 0.7168 (tpt) cc_final: 0.6221 (ttm) REVERT: D 1027 VAL cc_start: 0.8254 (t) cc_final: 0.7973 (m) REVERT: D 1139 ILE cc_start: 0.8222 (pt) cc_final: 0.7737 (mt) REVERT: D 1179 PHE cc_start: 0.8058 (t80) cc_final: 0.7841 (t80) REVERT: D 1188 ILE cc_start: 0.7941 (mm) cc_final: 0.7724 (mm) outliers start: 5 outliers final: 0 residues processed: 434 average time/residue: 0.1240 time to fit residues: 86.2937 Evaluate side-chains 342 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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: 0.9990 chunk 175 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 0.0020 chunk 148 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 5 optimal weight: 0.0670 chunk 201 optimal weight: 5.9990 overall best weight: 0.5328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 HIS C 575 ASN C 642 GLN ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.137514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.111570 restraints weight = 38487.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.111571 restraints weight = 31055.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.112752 restraints weight = 26600.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.113120 restraints weight = 20995.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.113274 restraints weight = 20483.330| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19246 Z= 0.115 Angle : 0.563 8.939 26010 Z= 0.292 Chirality : 0.040 0.195 2908 Planarity : 0.004 0.040 3184 Dihedral : 7.633 90.854 2698 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.05 % Allowed : 2.30 % Favored : 97.65 % 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: 0.46 (0.17), residues: 2362 helix: 1.57 (0.14), residues: 1340 sheet: -1.34 (0.35), residues: 180 loop : -1.40 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1203 TYR 0.021 0.001 TYR C1175 PHE 0.020 0.001 PHE B1141 TRP 0.020 0.001 TRP C 767 HIS 0.004 0.001 HIS C1059 Details of bonding type rmsd covalent geometry : bond 0.00252 (19234) covalent geometry : angle 0.56154 (25986) SS BOND : bond 0.00633 ( 12) SS BOND : angle 1.30995 ( 24) hydrogen bonds : bond 0.03393 ( 1014) hydrogen bonds : angle 3.92691 ( 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: 1 poor density : 451 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7212 (p90) cc_final: 0.6841 (p90) REVERT: A 460 TRP cc_start: 0.4961 (m100) cc_final: 0.3987 (m100) REVERT: A 490 ASP cc_start: 0.7137 (m-30) cc_final: 0.6685 (t70) REVERT: A 568 THR cc_start: 0.6065 (p) cc_final: 0.5702 (t) REVERT: A 599 ARG cc_start: 0.7998 (mtt-85) cc_final: 0.7442 (mtt90) REVERT: A 639 LEU cc_start: 0.8007 (tp) cc_final: 0.7763 (tp) REVERT: A 697 LYS cc_start: 0.7301 (mttm) cc_final: 0.6420 (pttp) REVERT: A 713 GLU cc_start: 0.7474 (tt0) cc_final: 0.7227 (tt0) REVERT: A 772 GLU cc_start: 0.6291 (pm20) cc_final: 0.5315 (mm-30) REVERT: A 814 PHE cc_start: 0.7295 (t80) cc_final: 0.7059 (t80) REVERT: A 1096 PHE cc_start: 0.7411 (m-10) cc_final: 0.7183 (m-10) REVERT: B 772 GLU cc_start: 0.6489 (pt0) cc_final: 0.5792 (mm-30) REVERT: C 440 TYR cc_start: 0.7212 (p90) cc_final: 0.7005 (p90) REVERT: C 460 TRP cc_start: 0.4639 (m100) cc_final: 0.3659 (m100) REVERT: C 697 LYS cc_start: 0.7235 (mttm) cc_final: 0.6590 (pttp) REVERT: C 708 MET cc_start: 0.7855 (tpp) cc_final: 0.7629 (tpp) REVERT: C 772 GLU cc_start: 0.6381 (pm20) cc_final: 0.5126 (mm-30) REVERT: C 1032 TRP cc_start: 0.7093 (m-10) cc_final: 0.6608 (m-10) REVERT: C 1057 MET cc_start: 0.5863 (ttt) cc_final: 0.5454 (ttm) REVERT: C 1098 ARG cc_start: 0.7039 (mtp180) cc_final: 0.6460 (ptm160) REVERT: C 1128 LYS cc_start: 0.5763 (ttmm) cc_final: 0.5169 (tptp) REVERT: C 1152 ILE cc_start: 0.8565 (mm) cc_final: 0.8362 (mt) REVERT: D 431 GLU cc_start: 0.6741 (tp30) cc_final: 0.6536 (tp30) REVERT: D 500 ILE cc_start: 0.8551 (mm) cc_final: 0.8185 (mm) REVERT: D 508 GLN cc_start: 0.6993 (pm20) cc_final: 0.6188 (tt0) REVERT: D 570 GLU cc_start: 0.7344 (pm20) cc_final: 0.6697 (pt0) REVERT: D 645 ILE cc_start: 0.6569 (mm) cc_final: 0.6160 (tt) REVERT: D 709 ASN cc_start: 0.8651 (t0) cc_final: 0.8359 (t0) REVERT: D 713 GLU cc_start: 0.7482 (tt0) cc_final: 0.6983 (tm-30) REVERT: D 772 GLU cc_start: 0.6351 (pt0) cc_final: 0.5991 (mm-30) REVERT: D 1023 MET cc_start: 0.6993 (tpt) cc_final: 0.6289 (mtp) REVERT: D 1027 VAL cc_start: 0.8293 (t) cc_final: 0.8040 (m) REVERT: D 1063 TRP cc_start: 0.4662 (m100) cc_final: 0.4210 (m100) REVERT: D 1116 MET cc_start: 0.6716 (mpp) cc_final: 0.6454 (mtt) REVERT: D 1179 PHE cc_start: 0.8073 (t80) cc_final: 0.7671 (t80) outliers start: 1 outliers final: 0 residues processed: 451 average time/residue: 0.1222 time to fit residues: 88.8011 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 : 0.660 ------------------------------------------------------------------------------- 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: 9.9990 chunk 6 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 chunk 122 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 173 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1204 HIS B1132 ASN ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** 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 = 0.3770 r_free = 0.3770 target = 0.132898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.106186 restraints weight = 39477.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106611 restraints weight = 31164.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107498 restraints weight = 28460.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107938 restraints weight = 22509.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.108178 restraints weight = 21145.733| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 19246 Z= 0.211 Angle : 0.653 7.106 26010 Z= 0.345 Chirality : 0.044 0.226 2908 Planarity : 0.004 0.049 3184 Dihedral : 7.646 94.724 2698 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.36 % 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: 0.33 (0.17), residues: 2362 helix: 1.38 (0.14), residues: 1338 sheet: -1.31 (0.36), residues: 178 loop : -1.33 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 628 TYR 0.029 0.002 TYR C1031 PHE 0.020 0.002 PHE D 623 TRP 0.021 0.002 TRP C1032 HIS 0.007 0.001 HIS A1204 Details of bonding type rmsd covalent geometry : bond 0.00488 (19234) covalent geometry : angle 0.65258 (25986) SS BOND : bond 0.00576 ( 12) SS BOND : angle 1.20189 ( 24) hydrogen bonds : bond 0.04107 ( 1014) hydrogen bonds : angle 4.28233 ( 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 408 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 407 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7224 (p90) cc_final: 0.6865 (p90) REVERT: A 460 TRP cc_start: 0.5299 (m100) cc_final: 0.3954 (m100) REVERT: A 464 VAL cc_start: 0.7981 (t) cc_final: 0.7643 (p) REVERT: A 490 ASP cc_start: 0.7295 (m-30) cc_final: 0.6894 (m-30) REVERT: A 568 THR cc_start: 0.5922 (p) cc_final: 0.5665 (t) REVERT: A 697 LYS cc_start: 0.7406 (mttm) cc_final: 0.6525 (pttp) REVERT: A 772 GLU cc_start: 0.6431 (pm20) cc_final: 0.5605 (mm-30) REVERT: A 814 PHE cc_start: 0.7434 (t80) cc_final: 0.7217 (t80) REVERT: A 816 TYR cc_start: 0.5872 (t80) cc_final: 0.5606 (t80) REVERT: B 542 LEU cc_start: 0.8522 (tt) cc_final: 0.8080 (tp) REVERT: B 772 GLU cc_start: 0.6419 (pt0) cc_final: 0.5768 (mm-30) REVERT: C 440 TYR cc_start: 0.7336 (p90) cc_final: 0.7056 (p90) REVERT: C 460 TRP cc_start: 0.4730 (m100) cc_final: 0.3583 (m100) REVERT: C 697 LYS cc_start: 0.7220 (mttm) cc_final: 0.6569 (pttp) REVERT: C 772 GLU cc_start: 0.6473 (pm20) cc_final: 0.5645 (mm-30) REVERT: C 1098 ARG cc_start: 0.7114 (mtp180) cc_final: 0.6507 (ptm160) REVERT: C 1128 LYS cc_start: 0.5764 (ttmm) cc_final: 0.5049 (tptp) REVERT: D 500 ILE cc_start: 0.8679 (mm) cc_final: 0.8198 (mm) REVERT: D 508 GLN cc_start: 0.6931 (pm20) cc_final: 0.6038 (tt0) REVERT: D 570 GLU cc_start: 0.7482 (pm20) cc_final: 0.6916 (pt0) REVERT: D 591 ILE cc_start: 0.8271 (pt) cc_final: 0.7991 (pt) REVERT: D 713 GLU cc_start: 0.7587 (tt0) cc_final: 0.7229 (tm-30) REVERT: D 772 GLU cc_start: 0.6458 (pt0) cc_final: 0.6022 (mm-30) REVERT: D 1023 MET cc_start: 0.7177 (tpt) cc_final: 0.6209 (ttm) REVERT: D 1027 VAL cc_start: 0.8371 (t) cc_final: 0.8095 (m) REVERT: D 1077 LYS cc_start: 0.6680 (tmtt) cc_final: 0.5855 (tptt) REVERT: D 1175 TYR cc_start: 0.5737 (m-80) cc_final: 0.5458 (m-10) REVERT: D 1179 PHE cc_start: 0.8171 (t80) cc_final: 0.7618 (t80) outliers start: 1 outliers final: 1 residues processed: 408 average time/residue: 0.1195 time to fit residues: 77.8197 Evaluate side-chains 333 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 332 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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: 0.6980 chunk 73 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 131 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 196 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.131389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.104003 restraints weight = 39897.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.104580 restraints weight = 31552.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105023 restraints weight = 27811.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105612 restraints weight = 23867.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.105821 restraints weight = 22179.146| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 19246 Z= 0.224 Angle : 0.692 9.048 26010 Z= 0.368 Chirality : 0.045 0.213 2908 Planarity : 0.005 0.059 3184 Dihedral : 7.730 96.064 2698 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.05 % Allowed : 2.50 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.08 (0.17), residues: 2362 helix: 1.18 (0.14), residues: 1336 sheet: -1.35 (0.37), residues: 168 loop : -1.43 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 692 TYR 0.028 0.002 TYR C1031 PHE 0.019 0.002 PHE B1186 TRP 0.020 0.002 TRP C1032 HIS 0.021 0.002 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00521 (19234) covalent geometry : angle 0.68804 (25986) SS BOND : bond 0.00912 ( 12) SS BOND : angle 2.41752 ( 24) hydrogen bonds : bond 0.04315 ( 1014) hydrogen bonds : angle 4.46121 ( 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 390 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 389 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7279 (p90) cc_final: 0.6937 (p90) REVERT: A 460 TRP cc_start: 0.5482 (m100) cc_final: 0.4018 (m100) REVERT: A 568 THR cc_start: 0.5649 (p) cc_final: 0.5443 (t) REVERT: A 673 TYR cc_start: 0.6933 (t80) cc_final: 0.6658 (t80) REVERT: A 697 LYS cc_start: 0.7289 (mttm) cc_final: 0.6458 (pttp) REVERT: A 772 GLU cc_start: 0.6384 (pm20) cc_final: 0.5857 (mm-30) REVERT: A 814 PHE cc_start: 0.7419 (t80) cc_final: 0.7195 (t80) REVERT: A 816 TYR cc_start: 0.6024 (t80) cc_final: 0.5724 (t80) REVERT: B 772 GLU cc_start: 0.6366 (pt0) cc_final: 0.5697 (mm-30) REVERT: B 1023 MET cc_start: 0.6995 (mmm) cc_final: 0.6242 (mtt) REVERT: C 440 TYR cc_start: 0.7353 (p90) cc_final: 0.7008 (p90) REVERT: C 531 PHE cc_start: 0.7995 (m-10) cc_final: 0.7476 (m-80) REVERT: C 673 TYR cc_start: 0.6575 (t80) cc_final: 0.6316 (t80) REVERT: C 697 LYS cc_start: 0.7099 (mttm) cc_final: 0.6478 (pttp) REVERT: C 772 GLU cc_start: 0.6420 (pm20) cc_final: 0.5748 (mm-30) REVERT: C 1017 PHE cc_start: 0.7410 (t80) cc_final: 0.6965 (m-10) REVERT: C 1032 TRP cc_start: 0.7957 (m-10) cc_final: 0.7614 (m-10) REVERT: C 1098 ARG cc_start: 0.7198 (mtp180) cc_final: 0.6635 (ptm160) REVERT: C 1128 LYS cc_start: 0.5692 (ttmm) cc_final: 0.5028 (tptp) REVERT: D 500 ILE cc_start: 0.8666 (mm) cc_final: 0.8195 (mm) REVERT: D 645 ILE cc_start: 0.6129 (mm) cc_final: 0.5799 (tt) REVERT: D 713 GLU cc_start: 0.7623 (tt0) cc_final: 0.7276 (tm-30) REVERT: D 1023 MET cc_start: 0.7077 (tpt) cc_final: 0.6179 (ttm) REVERT: D 1027 VAL cc_start: 0.8372 (t) cc_final: 0.8079 (m) REVERT: D 1175 TYR cc_start: 0.5834 (m-80) cc_final: 0.5310 (m-10) outliers start: 1 outliers final: 0 residues processed: 389 average time/residue: 0.1182 time to fit residues: 74.4246 Evaluate side-chains 323 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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: 5.9990 chunk 141 optimal weight: 0.0870 chunk 108 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 237 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1206 GLN ** 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 = 0.3796 r_free = 0.3796 target = 0.134787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.107650 restraints weight = 39631.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.108224 restraints weight = 32384.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.109203 restraints weight = 26217.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.109555 restraints weight = 22087.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.109838 restraints weight = 20310.985| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.5568 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= 0.122 Angle : 0.603 12.191 26010 Z= 0.314 Chirality : 0.041 0.209 2908 Planarity : 0.004 0.042 3184 Dihedral : 7.006 89.017 2698 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.05 % Allowed : 1.10 % Favored : 98.85 % 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: 1.66 (0.14), residues: 1324 sheet: -1.46 (0.36), residues: 172 loop : -1.36 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 715 TYR 0.024 0.001 TYR A 700 PHE 0.027 0.002 PHE D1096 TRP 0.030 0.002 TRP B1177 HIS 0.003 0.001 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00274 (19234) covalent geometry : angle 0.60028 (25986) SS BOND : bond 0.00549 ( 12) SS BOND : angle 1.85838 ( 24) hydrogen bonds : bond 0.03535 ( 1014) hydrogen bonds : angle 4.08754 ( 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 418 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 417 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7191 (p90) cc_final: 0.6872 (p90) REVERT: A 460 TRP cc_start: 0.5274 (m100) cc_final: 0.4055 (m100) REVERT: A 490 ASP cc_start: 0.7926 (m-30) cc_final: 0.6514 (t70) REVERT: A 568 THR cc_start: 0.5772 (p) cc_final: 0.5530 (t) REVERT: A 639 LEU cc_start: 0.7726 (tp) cc_final: 0.7519 (tp) REVERT: A 697 LYS cc_start: 0.7345 (mttm) cc_final: 0.6561 (pttp) REVERT: A 772 GLU cc_start: 0.6291 (pm20) cc_final: 0.5624 (mm-30) REVERT: A 788 SER cc_start: 0.8241 (p) cc_final: 0.7962 (p) REVERT: A 814 PHE cc_start: 0.7406 (t80) cc_final: 0.7112 (t80) REVERT: A 816 TYR cc_start: 0.6067 (t80) cc_final: 0.5781 (t80) REVERT: B 570 GLU cc_start: 0.7103 (pm20) cc_final: 0.6641 (pt0) REVERT: B 709 ASN cc_start: 0.8605 (t0) cc_final: 0.8349 (t0) REVERT: B 772 GLU cc_start: 0.6374 (pt0) cc_final: 0.5669 (mm-30) REVERT: B 1023 MET cc_start: 0.7050 (mmm) cc_final: 0.6111 (mtt) REVERT: B 1175 TYR cc_start: 0.5258 (m-80) cc_final: 0.4867 (m-10) REVERT: C 440 TYR cc_start: 0.7315 (p90) cc_final: 0.6941 (p90) REVERT: C 460 TRP cc_start: 0.4848 (m100) cc_final: 0.3756 (m100) REVERT: C 673 TYR cc_start: 0.6436 (t80) cc_final: 0.6190 (t80) REVERT: C 697 LYS cc_start: 0.7068 (mttm) cc_final: 0.6491 (pttp) REVERT: C 772 GLU cc_start: 0.6073 (pm20) cc_final: 0.5246 (mm-30) REVERT: C 1032 TRP cc_start: 0.7800 (m-10) cc_final: 0.7523 (m-10) REVERT: C 1098 ARG cc_start: 0.7087 (mtp180) cc_final: 0.6552 (ptm160) REVERT: C 1128 LYS cc_start: 0.5576 (ttmm) cc_final: 0.4948 (tptp) REVERT: C 1191 MET cc_start: 0.6189 (tpt) cc_final: 0.5538 (tpp) REVERT: D 570 GLU cc_start: 0.7487 (pm20) cc_final: 0.6949 (pt0) REVERT: D 591 ILE cc_start: 0.8128 (pt) cc_final: 0.7869 (pt) REVERT: D 709 ASN cc_start: 0.8690 (t0) cc_final: 0.8394 (t0) REVERT: D 713 GLU cc_start: 0.7606 (tt0) cc_final: 0.7081 (tm-30) REVERT: D 754 SER cc_start: 0.7714 (t) cc_final: 0.7414 (p) REVERT: D 1023 MET cc_start: 0.7131 (tpt) cc_final: 0.6233 (mtp) REVERT: D 1027 VAL cc_start: 0.8382 (t) cc_final: 0.8090 (m) REVERT: D 1077 LYS cc_start: 0.6572 (tmtt) cc_final: 0.5732 (tptt) REVERT: D 1175 TYR cc_start: 0.5687 (m-80) cc_final: 0.5119 (m-10) REVERT: D 1179 PHE cc_start: 0.8160 (t80) cc_final: 0.7491 (t80) REVERT: D 1188 ILE cc_start: 0.7886 (mm) cc_final: 0.7635 (mm) REVERT: D 1191 MET cc_start: 0.7050 (mtp) cc_final: 0.5631 (tpp) outliers start: 1 outliers final: 0 residues processed: 418 average time/residue: 0.1171 time to fit residues: 78.4917 Evaluate side-chains 343 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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: 2.9990 chunk 167 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 205 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 131 optimal weight: 0.0070 chunk 183 optimal weight: 2.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** A1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.133192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.105814 restraints weight = 39560.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.106313 restraints weight = 32248.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.107208 restraints weight = 26692.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.107561 restraints weight = 22794.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107641 restraints weight = 21909.242| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 19246 Z= 0.157 Angle : 0.623 12.588 26010 Z= 0.326 Chirality : 0.042 0.232 2908 Planarity : 0.004 0.041 3184 Dihedral : 7.005 90.565 2698 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.05 % Allowed : 0.60 % Favored : 99.35 % 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: 0.47 (0.17), residues: 2362 helix: 1.60 (0.14), residues: 1338 sheet: -1.41 (0.37), residues: 170 loop : -1.41 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 485 TYR 0.025 0.002 TYR C1031 PHE 0.028 0.002 PHE C1082 TRP 0.024 0.001 TRP B1177 HIS 0.005 0.001 HIS A1204 Details of bonding type rmsd covalent geometry : bond 0.00367 (19234) covalent geometry : angle 0.62089 (25986) SS BOND : bond 0.00520 ( 12) SS BOND : angle 1.80789 ( 24) hydrogen bonds : bond 0.03764 ( 1014) hydrogen bonds : angle 4.17274 ( 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 391 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 390 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7204 (p90) cc_final: 0.6886 (p90) REVERT: A 460 TRP cc_start: 0.5330 (m100) cc_final: 0.3754 (m100) REVERT: A 464 VAL cc_start: 0.7881 (t) cc_final: 0.7507 (p) REVERT: A 490 ASP cc_start: 0.7902 (m-30) cc_final: 0.6449 (t70) REVERT: A 568 THR cc_start: 0.5655 (p) cc_final: 0.5439 (t) REVERT: A 639 LEU cc_start: 0.7856 (tp) cc_final: 0.7550 (tp) REVERT: A 697 LYS cc_start: 0.7381 (mttm) cc_final: 0.6600 (pttp) REVERT: A 814 PHE cc_start: 0.7403 (t80) cc_final: 0.7185 (t80) REVERT: A 816 TYR cc_start: 0.6109 (t80) cc_final: 0.5816 (t80) REVERT: B 570 GLU cc_start: 0.7161 (pm20) cc_final: 0.6707 (pt0) REVERT: B 770 LYS cc_start: 0.7829 (mmtp) cc_final: 0.7135 (ttmt) REVERT: B 772 GLU cc_start: 0.6352 (pt0) cc_final: 0.5675 (mm-30) REVERT: B 1023 MET cc_start: 0.7024 (mmm) cc_final: 0.6145 (mtt) REVERT: B 1175 TYR cc_start: 0.5314 (m-80) cc_final: 0.4861 (m-10) REVERT: C 440 TYR cc_start: 0.7283 (p90) cc_final: 0.6908 (p90) REVERT: C 460 TRP cc_start: 0.5037 (m100) cc_final: 0.3779 (m100) REVERT: C 673 TYR cc_start: 0.6475 (t80) cc_final: 0.6243 (t80) REVERT: C 697 LYS cc_start: 0.7119 (mttm) cc_final: 0.6566 (pttp) REVERT: C 772 GLU cc_start: 0.6042 (pm20) cc_final: 0.5367 (mm-30) REVERT: C 1003 PHE cc_start: 0.4318 (p90) cc_final: 0.3843 (m-80) REVERT: C 1032 TRP cc_start: 0.7846 (m-10) cc_final: 0.7540 (m-10) REVERT: C 1098 ARG cc_start: 0.7187 (mtp180) cc_final: 0.6648 (ptm160) REVERT: C 1128 LYS cc_start: 0.5616 (ttmm) cc_final: 0.4938 (tptp) REVERT: C 1191 MET cc_start: 0.6199 (tpt) cc_final: 0.5903 (tpt) REVERT: D 570 GLU cc_start: 0.7434 (pm20) cc_final: 0.6829 (pt0) REVERT: D 709 ASN cc_start: 0.8755 (t0) cc_final: 0.8456 (t0) REVERT: D 713 GLU cc_start: 0.7724 (tt0) cc_final: 0.7167 (tm-30) REVERT: D 754 SER cc_start: 0.7789 (t) cc_final: 0.7533 (p) REVERT: D 1023 MET cc_start: 0.7128 (tpt) cc_final: 0.6162 (ttm) REVERT: D 1027 VAL cc_start: 0.8441 (t) cc_final: 0.8136 (m) REVERT: D 1077 LYS cc_start: 0.6620 (tmtt) cc_final: 0.5822 (tptt) REVERT: D 1175 TYR cc_start: 0.5689 (m-80) cc_final: 0.5256 (m-10) REVERT: D 1179 PHE cc_start: 0.8172 (t80) cc_final: 0.7548 (t80) REVERT: D 1188 ILE cc_start: 0.7879 (mm) cc_final: 0.7645 (mm) REVERT: D 1191 MET cc_start: 0.7037 (mtp) cc_final: 0.5646 (tpp) outliers start: 1 outliers final: 0 residues processed: 391 average time/residue: 0.1228 time to fit residues: 77.0959 Evaluate side-chains 328 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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: 3.9990 chunk 20 optimal weight: 0.7980 chunk 205 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 102 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN B1132 ASN ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** 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 = 0.3788 r_free = 0.3788 target = 0.134384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.106789 restraints weight = 39283.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.108001 restraints weight = 31380.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.108381 restraints weight = 27934.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.109028 restraints weight = 23661.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109664 restraints weight = 21793.146| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19246 Z= 0.128 Angle : 0.610 12.070 26010 Z= 0.317 Chirality : 0.041 0.218 2908 Planarity : 0.004 0.041 3184 Dihedral : 6.676 86.219 2698 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.05 % Allowed : 0.30 % Favored : 99.65 % 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: 1.68 (0.14), residues: 1338 sheet: -1.46 (0.37), residues: 170 loop : -1.42 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 692 TYR 0.027 0.001 TYR B 647 PHE 0.031 0.002 PHE D1096 TRP 0.024 0.001 TRP A 767 HIS 0.004 0.001 HIS C1204 Details of bonding type rmsd covalent geometry : bond 0.00292 (19234) covalent geometry : angle 0.60828 (25986) SS BOND : bond 0.00608 ( 12) SS BOND : angle 1.57966 ( 24) hydrogen bonds : bond 0.03535 ( 1014) hydrogen bonds : angle 4.07639 ( 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 397 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 396 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7119 (p90) cc_final: 0.6760 (p90) REVERT: A 460 TRP cc_start: 0.5254 (m100) cc_final: 0.3924 (m100) REVERT: A 490 ASP cc_start: 0.7887 (m-30) cc_final: 0.6454 (t70) REVERT: A 568 THR cc_start: 0.5753 (p) cc_final: 0.5527 (t) REVERT: A 697 LYS cc_start: 0.7326 (mttm) cc_final: 0.6591 (pttp) REVERT: A 710 GLU cc_start: 0.7278 (mm-30) cc_final: 0.7077 (mt-10) REVERT: A 788 SER cc_start: 0.8259 (p) cc_final: 0.7987 (p) REVERT: A 814 PHE cc_start: 0.7444 (t80) cc_final: 0.7196 (t80) REVERT: B 570 GLU cc_start: 0.7105 (pm20) cc_final: 0.6653 (pt0) REVERT: B 770 LYS cc_start: 0.7761 (mmtp) cc_final: 0.7020 (ttmt) REVERT: B 772 GLU cc_start: 0.6224 (pt0) cc_final: 0.5559 (mm-30) REVERT: B 1008 GLN cc_start: 0.7038 (mt0) cc_final: 0.6723 (mt0) REVERT: B 1023 MET cc_start: 0.7029 (mmm) cc_final: 0.6015 (mtt) REVERT: C 440 TYR cc_start: 0.7216 (p90) cc_final: 0.6862 (p90) REVERT: C 460 TRP cc_start: 0.4955 (m100) cc_final: 0.3757 (m100) REVERT: C 697 LYS cc_start: 0.7155 (mttm) cc_final: 0.6602 (pttp) REVERT: C 772 GLU cc_start: 0.5892 (pm20) cc_final: 0.5398 (mm-30) REVERT: C 1003 PHE cc_start: 0.4289 (p90) cc_final: 0.3866 (m-80) REVERT: C 1032 TRP cc_start: 0.7803 (m-10) cc_final: 0.7518 (m-10) REVERT: C 1098 ARG cc_start: 0.7173 (mtp180) cc_final: 0.6640 (ptm160) REVERT: C 1128 LYS cc_start: 0.5591 (ttmm) cc_final: 0.4906 (tptp) REVERT: C 1191 MET cc_start: 0.6202 (tpt) cc_final: 0.5921 (tpt) REVERT: D 570 GLU cc_start: 0.7502 (pm20) cc_final: 0.6910 (pt0) REVERT: D 591 ILE cc_start: 0.8164 (pt) cc_final: 0.7879 (pt) REVERT: D 709 ASN cc_start: 0.8716 (t0) cc_final: 0.8427 (t0) REVERT: D 713 GLU cc_start: 0.7721 (tt0) cc_final: 0.7279 (tm-30) REVERT: D 754 SER cc_start: 0.7663 (t) cc_final: 0.7365 (p) REVERT: D 1023 MET cc_start: 0.7098 (tpt) cc_final: 0.6201 (mtp) REVERT: D 1027 VAL cc_start: 0.8423 (t) cc_final: 0.8097 (m) REVERT: D 1077 LYS cc_start: 0.6598 (tmtt) cc_final: 0.5843 (tptt) REVERT: D 1175 TYR cc_start: 0.5541 (m-80) cc_final: 0.4266 (m-80) REVERT: D 1179 PHE cc_start: 0.8144 (t80) cc_final: 0.7602 (t80) REVERT: D 1188 ILE cc_start: 0.7848 (mm) cc_final: 0.7646 (mm) REVERT: D 1191 MET cc_start: 0.7021 (mtp) cc_final: 0.5631 (tpp) outliers start: 1 outliers final: 0 residues processed: 397 average time/residue: 0.1187 time to fit residues: 76.0943 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 : 0.561 ------------------------------------------------------------------------------- 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: 3.9990 chunk 231 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 219 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.131873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105183 restraints weight = 39712.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.105527 restraints weight = 31853.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.106496 restraints weight = 27113.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.106862 restraints weight = 22555.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.106935 restraints weight = 21533.240| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.5830 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= 0.167 Angle : 0.630 12.444 26010 Z= 0.331 Chirality : 0.042 0.232 2908 Planarity : 0.004 0.042 3184 Dihedral : 6.774 88.108 2698 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.05 % Allowed : 0.35 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.45 (0.17), residues: 2362 helix: 1.57 (0.14), residues: 1338 sheet: -1.43 (0.38), residues: 170 loop : -1.39 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 694 TYR 0.025 0.002 TYR C1031 PHE 0.031 0.002 PHE C1082 TRP 0.023 0.001 TRP A 767 HIS 0.006 0.001 HIS A1204 Details of bonding type rmsd covalent geometry : bond 0.00390 (19234) covalent geometry : angle 0.62846 (25986) SS BOND : bond 0.00594 ( 12) SS BOND : angle 1.54911 ( 24) hydrogen bonds : bond 0.03851 ( 1014) hydrogen bonds : angle 4.18839 ( 2964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3069.18 seconds wall clock time: 54 minutes 8.47 seconds (3248.47 seconds total)