Starting phenix.real_space_refine on Mon Jun 16 16:53:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tno_26016/06_2025/7tno_26016.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tno_26016/06_2025/7tno_26016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tno_26016/06_2025/7tno_26016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tno_26016/06_2025/7tno_26016.map" model { file = "/net/cci-nas-00/data/ceres_data/7tno_26016/06_2025/7tno_26016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tno_26016/06_2025/7tno_26016.cif" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 136 5.16 5 Cl 4 4.86 5 C 12198 2.51 5 N 3044 2.21 5 O 3428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18810 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4673 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 585} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4667 Classifications: {'peptide': 600} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 584} Chain breaks: 4 Chain: "C" Number of atoms: 4673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4673 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 585} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4671 Classifications: {'peptide': 600} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 584} Chain breaks: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 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: 12.03, per 1000 atoms: 0.64 Number of scatterers: 18810 At special positions: 0 Unit cell: (125.33, 115.37, 136.95, 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 3428 8.00 N 3044 7.00 C 12198 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=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.04 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.02 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.02 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.36 Conformation dependent library (CDL) restraints added in 2.3 seconds 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4390 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 24 sheets defined 55.6% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 416 through 419 removed outlier: 4.327A 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 469 removed outlier: 3.542A pdb=" N TYR A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 488 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.613A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.740A pdb=" N THR A 568 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 569' Processing helix chain 'A' and resid 573 through 585 Processing helix chain 'A' and resid 595 through 626 removed outlier: 3.570A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 642 Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.645A pdb=" N ARG A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 removed outlier: 3.744A pdb=" N TYR A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.535A pdb=" N LYS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.514A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.672A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 767 removed outlier: 3.616A pdb=" N LYS A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 822 removed outlier: 4.358A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG A 819 " --> pdb=" O CYS A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1029 removed outlier: 3.812A pdb=" N LEU A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1103 removed outlier: 3.597A pdb=" N LEU A1097 " --> pdb=" O ALA A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1123 Processing helix chain 'A' and resid 1132 through 1160 removed outlier: 3.617A pdb=" N VAL A1142 " --> pdb=" O GLY A1138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A1145 " --> pdb=" O PHE A1141 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A1155 " --> pdb=" O GLY A1151 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A1160 " --> pdb=" O ILE A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1207 removed outlier: 3.597A pdb=" N GLY A1182 " --> pdb=" O SER A1178 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A1187 " --> pdb=" O ALA A1183 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A1197 " --> pdb=" O GLY A1193 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.595A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.695A pdb=" N VAL B 468 " --> pdb=" O VAL B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.651A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.516A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 545 removed outlier: 3.574A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 597 through 617 removed outlier: 4.157A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.504A pdb=" N PHE B 623 " --> pdb=" O ASN B 619 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 619 through 624' Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.827A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 4.375A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP B 671 " --> pdb=" O PHE B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 695 removed outlier: 3.505A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 743 through 756 removed outlier: 4.251A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 770 removed outlier: 3.502A pdb=" N TRP B 767 " --> pdb=" O LYS B 763 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 770 " --> pdb=" O TRP B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 777 removed outlier: 3.508A pdb=" N LYS B 776 " --> pdb=" O CYS B 773 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP B 777 " --> pdb=" O GLY B 774 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 773 through 777' Processing helix chain 'B' and resid 793 through 819 removed outlier: 3.543A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 819 " --> pdb=" O CYS B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1028 removed outlier: 3.858A pdb=" N GLN B1008 " --> pdb=" O ASP B1004 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET B1009 " --> pdb=" O ARG B1005 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B1010 " --> pdb=" O GLY B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1104 Processing helix chain 'B' and resid 1104 through 1123 removed outlier: 3.525A pdb=" N CYS B1120 " --> pdb=" O MET B1116 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1160 removed outlier: 3.593A pdb=" N VAL B1154 " --> pdb=" O ILE B1150 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B1158 " --> pdb=" O VAL B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1209 removed outlier: 3.709A pdb=" N TYR B1180 " --> pdb=" O GLY B1176 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B1187 " --> pdb=" O ALA B1183 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B1197 " --> pdb=" O GLY B1193 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 462 through 469 removed outlier: 3.571A pdb=" N GLU C 466 " --> pdb=" O GLY C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.520A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.589A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 545 removed outlier: 3.805A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 569 removed outlier: 3.673A pdb=" N ASN C 569 " --> pdb=" O GLU C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 623 removed outlier: 3.876A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 621 " --> pdb=" O THR C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 641 removed outlier: 3.516A pdb=" N LYS C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 664 through 676 removed outlier: 3.749A pdb=" N TYR C 673 " --> pdb=" O LYS C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 697 Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.592A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 756 Processing helix chain 'C' and resid 757 through 767 Processing helix chain 'C' and resid 792 through 822 removed outlier: 4.082A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1029 removed outlier: 3.622A pdb=" N THR C1012 " --> pdb=" O GLN C1008 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE C1017 " --> pdb=" O THR C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1104 Processing helix chain 'C' and resid 1104 through 1126 removed outlier: 3.904A pdb=" N LEU C1114 " --> pdb=" O SER C1110 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU C1125 " --> pdb=" O ILE C1121 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE C1126 " --> pdb=" O ALA C1122 " (cutoff:3.500A) Processing helix chain 'C' and resid 1132 through 1160 removed outlier: 3.678A pdb=" N PHE C1140 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C1145 " --> pdb=" O PHE C1141 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C1150 " --> pdb=" O LEU C1146 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C1158 " --> pdb=" O VAL C1154 " (cutoff:3.500A) Processing helix chain 'C' and resid 1177 through 1208 removed outlier: 3.549A pdb=" N ILE C1187 " --> pdb=" O ALA C1183 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C1189 " --> pdb=" O SER C1185 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C1197 " --> pdb=" O GLY C1193 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.761A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.594A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 458 Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.507A pdb=" N GLU D 486 " --> pdb=" O THR D 482 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 482 through 487' Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 545 removed outlier: 3.642A pdb=" N SER D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 616 removed outlier: 3.736A pdb=" N ILE D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 625 removed outlier: 3.670A pdb=" N PHE D 623 " --> pdb=" O ASN D 619 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 4.124A pdb=" N GLN D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.581A pdb=" N PHE D 658 " --> pdb=" O SER D 654 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.871A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.614A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.578A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU D 755 " --> pdb=" O LEU D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 removed outlier: 3.711A pdb=" N ASN D 764 " --> pdb=" O ASP D 760 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 765 " --> pdb=" O LYS D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 819 Processing helix chain 'D' and resid 1007 through 1029 Processing helix chain 'D' and resid 1092 through 1103 removed outlier: 3.994A pdb=" N VAL D1100 " --> pdb=" O PHE D1096 " (cutoff:3.500A) Processing helix chain 'D' and resid 1104 through 1123 removed outlier: 3.592A pdb=" N LEU D1114 " --> pdb=" O SER D1110 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS D1120 " --> pdb=" O MET D1116 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA D1122 " --> pdb=" O GLY D1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1161 removed outlier: 3.554A pdb=" N PHE D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL D1142 " --> pdb=" O GLY D1138 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE D1150 " --> pdb=" O LEU D1146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY D1161 " --> pdb=" O SER D1157 " (cutoff:3.500A) Processing helix chain 'D' and resid 1176 through 1208 removed outlier: 3.531A pdb=" N ILE D1187 " --> pdb=" O ALA D1183 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D1197 " --> pdb=" O GLY D1193 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS D1204 " --> pdb=" O PHE D1200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 398 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 489 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.974A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.265A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1033 through 1036 removed outlier: 3.582A pdb=" N SER A1035 " --> pdb=" O THR A1058 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1064 through 1067 removed outlier: 3.874A pdb=" N LEU A1075 " --> pdb=" O CYS A1067 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 440 through 444 removed outlier: 6.801A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) 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 489 through 491 Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 removed outlier: 5.893A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 646 through 648 removed outlier: 5.893A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1076 through 1078 Processing sheet with id=AB5, first strand: chain 'C' and resid 397 through 399 removed outlier: 6.084A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 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 489 through 498 removed outlier: 5.241A pdb=" N ILE C 734 " --> pdb=" O SER C 492 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR C 732 " --> pdb=" O PRO C 494 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET C 496 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS C 730 " --> pdb=" O MET C 496 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.269A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1064 through 1065 Processing sheet with id=AC1, first strand: chain 'D' and resid 440 through 444 Processing sheet with id=AC2, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC3, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC4, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.686A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 646 through 648 removed outlier: 3.637A pdb=" N LEU D 703 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 1077 through 1078 removed outlier: 3.871A pdb=" N CYS D1066 " --> pdb=" O HIS D1059 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER D1035 " --> pdb=" O THR D1058 " (cutoff:3.500A) 962 hydrogen bonds defined for protein. 2811 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: 6.45 Time building geometry restraints manager: 5.20 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: 5732 1.34 - 1.47: 4929 1.47 - 1.59: 8338 1.59 - 1.71: 8 1.71 - 1.83: 220 Bond restraints: 19227 Sorted by residual: bond pdb=" N LYS C 449 " pdb=" CA LYS C 449 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.17e-02 7.31e+03 9.03e+00 bond pdb=" N ILE C 459 " pdb=" CA ILE C 459 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.72e+00 bond pdb=" N ARG C 453 " pdb=" CA ARG C 453 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.49e+00 bond pdb=" N ASP C 454 " pdb=" CA ASP C 454 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.78e+00 bond pdb=" N LYS A 449 " pdb=" CA LYS A 449 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.33e-02 5.65e+03 6.78e+00 ... (remaining 19222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 25331 2.48 - 4.96: 524 4.96 - 7.44: 95 7.44 - 9.92: 20 9.92 - 12.40: 5 Bond angle restraints: 25975 Sorted by residual: angle pdb=" C PRO D 507 " pdb=" N GLN D 508 " pdb=" CA GLN D 508 " ideal model delta sigma weight residual 121.54 133.70 -12.16 1.91e+00 2.74e-01 4.05e+01 angle pdb=" C GLN D 508 " pdb=" N LYS D 509 " pdb=" CA LYS D 509 " ideal model delta sigma weight residual 121.54 132.92 -11.38 1.91e+00 2.74e-01 3.55e+01 angle pdb=" C ALA D1086 " pdb=" N ASP D1087 " pdb=" CA ASP D1087 " ideal model delta sigma weight residual 121.54 131.82 -10.28 1.91e+00 2.74e-01 2.90e+01 angle pdb=" C ARG D1130 " pdb=" N HIS D1131 " pdb=" CA HIS D1131 " ideal model delta sigma weight residual 122.08 129.44 -7.36 1.47e+00 4.63e-01 2.51e+01 angle pdb=" N ASN B1132 " pdb=" CA ASN B1132 " pdb=" C ASN B1132 " ideal model delta sigma weight residual 114.75 108.86 5.89 1.26e+00 6.30e-01 2.19e+01 ... (remaining 25970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.44: 10969 24.44 - 48.87: 354 48.87 - 73.31: 24 73.31 - 97.74: 12 97.74 - 122.18: 9 Dihedral angle restraints: 11368 sinusoidal: 4488 harmonic: 6880 Sorted by residual: dihedral pdb=" CA GLN D 508 " pdb=" C GLN D 508 " pdb=" N LYS D 509 " pdb=" CA LYS D 509 " ideal model delta harmonic sigma weight residual 180.00 138.33 41.67 0 5.00e+00 4.00e-02 6.95e+01 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 166.76 -73.76 1 1.00e+01 1.00e-02 6.92e+01 dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 166.46 -73.46 1 1.00e+01 1.00e-02 6.87e+01 ... (remaining 11365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2321 0.059 - 0.118: 483 0.118 - 0.178: 95 0.178 - 0.237: 7 0.237 - 0.296: 5 Chirality restraints: 2911 Sorted by residual: chirality pdb=" C1 CYZ A1302 " pdb=" C2 CYZ A1302 " pdb=" C6 CYZ A1302 " pdb=" C8 CYZ A1302 " both_signs ideal model delta sigma weight residual False 2.79 2.50 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C1 CYZ D1301 " pdb=" C2 CYZ D1301 " pdb=" C6 CYZ D1301 " pdb=" C8 CYZ D1301 " both_signs ideal model delta sigma weight residual False 2.79 2.51 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C8 CYZ C1302 " pdb=" C1 CYZ C1302 " pdb=" N1 CYZ C1302 " pdb=" N2 CYZ C1302 " both_signs ideal model delta sigma weight residual False 2.20 2.48 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 2908 not shown) Planarity restraints: 3188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 447 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C ASP C 447 " -0.057 2.00e-02 2.50e+03 pdb=" O ASP C 447 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY C 448 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 566 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C GLU D 566 " 0.041 2.00e-02 2.50e+03 pdb=" O GLU D 566 " -0.015 2.00e-02 2.50e+03 pdb=" N SER D 567 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 716 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO C 717 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 717 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 717 " -0.028 5.00e-02 4.00e+02 ... (remaining 3185 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 113 2.60 - 3.17: 15425 3.17 - 3.75: 28580 3.75 - 4.32: 39920 4.32 - 4.90: 64209 Nonbonded interactions: 148247 Sorted by model distance: nonbonded pdb=" OD1 ASP B 760 " pdb="CL CYZ B1302 " model vdw 2.023 3.270 nonbonded pdb=" O PHE B 517 " pdb=" OH TYR B 616 " model vdw 2.302 3.040 nonbonded pdb=" OG SER A 597 " pdb=" O ALA B 806 " model vdw 2.310 3.040 nonbonded pdb=" O SER B 564 " pdb=" OG1 THR B 568 " model vdw 2.313 3.040 nonbonded pdb=" O PHE D 517 " pdb=" OH TYR D 616 " model vdw 2.315 3.040 ... (remaining 148242 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 394 through 819 or resid 1002 through 1169 or resid 1171 t \ hrough 1208 or resid 1302)) selection = (chain 'B' and (resid 394 through 548 or (resid 563 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 819 or resid 1002 through 1041 \ or resid 1056 through 1208 or resid 1302)) selection = (chain 'C' and (resid 394 through 819 or resid 1002 through 1169 or resid 1171 t \ hrough 1208 or resid 1302)) selection = (chain 'D' and (resid 394 through 548 or (resid 563 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 1041 or resid 1056 through 116 \ 9 or resid 1171 through 1208 or resid 1301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.460 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: 0.030 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.150 Process input model: 44.390 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 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 : 0.004 0.060 19239 Z= 0.229 Angle : 0.939 12.405 25999 Z= 0.525 Chirality : 0.051 0.296 2911 Planarity : 0.006 0.058 3188 Dihedral : 12.110 122.178 6942 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.68 % Favored : 96.15 % Rotamer: Outliers : 0.65 % Allowed : 5.24 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.12 (0.11), residues: 2362 helix: -3.93 (0.06), residues: 1303 sheet: -2.15 (0.39), residues: 156 loop : -2.42 (0.16), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A1032 HIS 0.006 0.002 HIS B1081 PHE 0.028 0.002 PHE B1072 TYR 0.028 0.002 TYR B1031 ARG 0.005 0.001 ARG A 692 Details of bonding type rmsd hydrogen bonds : bond 0.29804 ( 958) hydrogen bonds : angle 9.37486 ( 2811) SS BOND : bond 0.00556 ( 12) SS BOND : angle 1.38411 ( 24) covalent geometry : bond 0.00445 (19227) covalent geometry : angle 0.93867 (25975) *********************** 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 724 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 711 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7270 (mtmt) REVERT: A 511 LYS cc_start: 0.6826 (mttp) cc_final: 0.6082 (tptt) REVERT: A 600 ILE cc_start: 0.9378 (mt) cc_final: 0.9124 (mm) REVERT: A 654 SER cc_start: 0.8564 (p) cc_final: 0.8192 (m) REVERT: A 680 SER cc_start: 0.6957 (p) cc_final: 0.6362 (t) REVERT: A 723 VAL cc_start: 0.8267 (m) cc_final: 0.8025 (t) REVERT: A 1030 ASP cc_start: 0.5668 (p0) cc_final: 0.4402 (p0) REVERT: A 1063 TRP cc_start: 0.7834 (m100) cc_final: 0.7435 (m-10) REVERT: A 1130 ARG cc_start: 0.7809 (mmp-170) cc_final: 0.7474 (mmm160) REVERT: A 1147 SER cc_start: 0.8542 (t) cc_final: 0.8316 (p) REVERT: A 1148 ASN cc_start: 0.8342 (t0) cc_final: 0.7951 (t0) REVERT: B 498 LEU cc_start: 0.8853 (pt) cc_final: 0.8584 (pp) REVERT: B 519 ASP cc_start: 0.8442 (m-30) cc_final: 0.7887 (t70) REVERT: B 524 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7139 (pt0) REVERT: B 537 SER cc_start: 0.8966 (m) cc_final: 0.8597 (m) REVERT: B 585 MET cc_start: 0.8381 (mmt) cc_final: 0.8166 (mmm) REVERT: B 620 LEU cc_start: 0.8065 (tp) cc_final: 0.7752 (tp) REVERT: B 661 ARG cc_start: 0.5955 (mmp80) cc_final: 0.5689 (ptp90) REVERT: B 1021 SER cc_start: 0.8411 (m) cc_final: 0.8102 (p) REVERT: B 1022 LEU cc_start: 0.8408 (mt) cc_final: 0.8193 (mp) REVERT: B 1148 ASN cc_start: 0.8770 (t0) cc_final: 0.8553 (t0) REVERT: B 1187 ILE cc_start: 0.9218 (mt) cc_final: 0.8990 (mt) REVERT: C 438 PHE cc_start: 0.5883 (p90) cc_final: 0.5582 (p90) REVERT: C 460 TRP cc_start: 0.5889 (m100) cc_final: 0.5576 (m100) REVERT: C 498 LEU cc_start: 0.8354 (pp) cc_final: 0.7740 (pp) REVERT: C 501 SER cc_start: 0.8390 (p) cc_final: 0.8086 (t) REVERT: C 683 VAL cc_start: 0.7310 (m) cc_final: 0.6873 (m) REVERT: C 699 LYS cc_start: 0.8011 (mptt) cc_final: 0.7675 (mmmt) REVERT: C 711 TYR cc_start: 0.7413 (t80) cc_final: 0.7211 (t80) REVERT: C 732 TYR cc_start: 0.7976 (m-10) cc_final: 0.7639 (m-10) REVERT: C 764 ASN cc_start: 0.7857 (m-40) cc_final: 0.7571 (t0) REVERT: C 817 LYS cc_start: 0.7905 (mmpt) cc_final: 0.7644 (mmmt) REVERT: C 1031 TYR cc_start: 0.3906 (p90) cc_final: 0.3598 (p90) REVERT: C 1036 ARG cc_start: 0.6959 (mmt180) cc_final: 0.6704 (mmt-90) REVERT: C 1096 PHE cc_start: 0.7793 (t80) cc_final: 0.7495 (t80) REVERT: C 1120 CYS cc_start: 0.7700 (m) cc_final: 0.7256 (m) REVERT: C 1126 PHE cc_start: 0.6414 (m-10) cc_final: 0.5863 (m-80) REVERT: C 1169 LYS cc_start: 0.2793 (tptp) cc_final: 0.1150 (ptmt) REVERT: D 425 CYS cc_start: 0.7947 (m) cc_final: 0.7681 (m) REVERT: D 476 ILE cc_start: 0.8670 (mt) cc_final: 0.8432 (mp) REVERT: D 533 TYR cc_start: 0.8753 (t80) cc_final: 0.8484 (t80) REVERT: D 637 GLU cc_start: 0.8196 (pp20) cc_final: 0.7684 (pp20) REVERT: D 639 LEU cc_start: 0.7958 (tp) cc_final: 0.7574 (tp) REVERT: D 720 THR cc_start: 0.8009 (p) cc_final: 0.7643 (p) REVERT: D 764 ASN cc_start: 0.7839 (p0) cc_final: 0.7545 (p0) REVERT: D 770 LYS cc_start: 0.7155 (mmmt) cc_final: 0.6659 (mmtt) REVERT: D 1170 LYS cc_start: 0.5128 (tptp) cc_final: 0.4853 (ptpp) REVERT: D 1173 TYR cc_start: 0.6761 (p90) cc_final: 0.6477 (p90) outliers start: 13 outliers final: 2 residues processed: 721 average time/residue: 0.3486 time to fit residues: 374.4160 Evaluate side-chains 426 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 423 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 7.9990 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 188 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN A 619 ASN A1204 HIS B 411 ASN B 587 GLN B 791 ASN B1131 HIS B1204 HIS C1059 HIS ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 ASN D 791 ASN ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 ASN ** D1159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1204 HIS D1206 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.128485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102115 restraints weight = 39220.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.104636 restraints weight = 23471.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.106310 restraints weight = 17077.733| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19239 Z= 0.175 Angle : 0.653 11.024 25999 Z= 0.346 Chirality : 0.042 0.230 2911 Planarity : 0.005 0.063 3188 Dihedral : 8.976 105.896 2697 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Rotamer: Outliers : 0.25 % Allowed : 4.09 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.15), residues: 2362 helix: -0.94 (0.12), residues: 1306 sheet: -1.87 (0.37), residues: 183 loop : -2.13 (0.18), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 766 HIS 0.005 0.001 HIS B1081 PHE 0.020 0.002 PHE D 574 TYR 0.023 0.002 TYR C1031 ARG 0.005 0.001 ARG D 594 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 958) hydrogen bonds : angle 4.43156 ( 2811) SS BOND : bond 0.01112 ( 12) SS BOND : angle 2.49084 ( 24) covalent geometry : bond 0.00398 (19227) covalent geometry : angle 0.64887 (25975) *********************** 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 497 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 492 time to evaluate : 2.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7948 (mt) cc_final: 0.7497 (pt) REVERT: A 487 GLU cc_start: 0.7571 (tp30) cc_final: 0.7141 (pt0) REVERT: A 511 LYS cc_start: 0.6988 (mttp) cc_final: 0.6298 (tptt) REVERT: A 732 TYR cc_start: 0.7928 (m-10) cc_final: 0.7190 (m-80) REVERT: A 1063 TRP cc_start: 0.7913 (m100) cc_final: 0.7481 (m-10) REVERT: A 1130 ARG cc_start: 0.8061 (mmp-170) cc_final: 0.7561 (mmm160) REVERT: A 1199 MET cc_start: 0.7868 (mmm) cc_final: 0.7550 (mmt) REVERT: B 500 ILE cc_start: 0.8937 (mt) cc_final: 0.8642 (mm) REVERT: B 519 ASP cc_start: 0.8514 (m-30) cc_final: 0.8274 (t70) REVERT: B 620 LEU cc_start: 0.8182 (tp) cc_final: 0.7905 (tp) REVERT: B 637 GLU cc_start: 0.6601 (mp0) cc_final: 0.6380 (mp0) REVERT: B 1008 GLN cc_start: 0.7085 (pt0) cc_final: 0.6553 (pt0) REVERT: B 1021 SER cc_start: 0.8387 (m) cc_final: 0.8114 (p) REVERT: B 1023 MET cc_start: 0.8489 (tpp) cc_final: 0.7719 (tpt) REVERT: C 438 PHE cc_start: 0.6227 (p90) cc_final: 0.5679 (p90) REVERT: C 683 VAL cc_start: 0.7366 (m) cc_final: 0.7040 (p) REVERT: C 711 TYR cc_start: 0.7598 (t80) cc_final: 0.7346 (t80) REVERT: C 817 LYS cc_start: 0.7964 (mmpt) cc_final: 0.7643 (mmmt) REVERT: C 1020 PHE cc_start: 0.8179 (t80) cc_final: 0.7886 (t80) REVERT: C 1031 TYR cc_start: 0.4611 (p90) cc_final: 0.3588 (p90) REVERT: C 1092 THR cc_start: 0.6873 (p) cc_final: 0.6650 (t) REVERT: C 1139 ILE cc_start: 0.8971 (mt) cc_final: 0.8762 (pt) REVERT: C 1169 LYS cc_start: 0.3136 (tptp) cc_final: 0.1559 (ptmt) REVERT: D 425 CYS cc_start: 0.7991 (m) cc_final: 0.7642 (m) REVERT: D 533 TYR cc_start: 0.8814 (t80) cc_final: 0.8427 (t80) REVERT: D 580 SER cc_start: 0.9325 (m) cc_final: 0.8805 (p) REVERT: D 713 GLU cc_start: 0.7221 (tt0) cc_final: 0.6888 (tp30) REVERT: D 1064 ARG cc_start: 0.7170 (ptp-170) cc_final: 0.6955 (ptp90) REVERT: D 1136 SER cc_start: 0.8959 (p) cc_final: 0.8709 (p) REVERT: D 1139 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8185 (tt) outliers start: 5 outliers final: 1 residues processed: 495 average time/residue: 0.3021 time to fit residues: 227.9130 Evaluate side-chains 359 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 357 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 190 optimal weight: 0.7980 chunk 172 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 234 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 4 optimal weight: 0.0870 chunk 217 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 overall best weight: 1.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1059 HIS D 412 HIS D 726 ASN ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.126755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.100656 restraints weight = 39259.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.102962 restraints weight = 23978.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.104628 restraints weight = 17596.896| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19239 Z= 0.184 Angle : 0.649 10.281 25999 Z= 0.339 Chirality : 0.043 0.260 2911 Planarity : 0.004 0.046 3188 Dihedral : 8.361 100.695 2697 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.94 % Favored : 96.02 % Rotamer: Outliers : 0.20 % Allowed : 4.24 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.16), residues: 2362 helix: 0.34 (0.14), residues: 1313 sheet: -1.81 (0.38), residues: 183 loop : -1.96 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 460 HIS 0.009 0.001 HIS B1204 PHE 0.023 0.002 PHE C1200 TYR 0.026 0.002 TYR A 647 ARG 0.005 0.001 ARG D 594 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 958) hydrogen bonds : angle 4.18777 ( 2811) SS BOND : bond 0.00967 ( 12) SS BOND : angle 2.89085 ( 24) covalent geometry : bond 0.00426 (19227) covalent geometry : angle 0.64337 (25975) *********************** 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 453 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 449 time to evaluate : 3.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7947 (mt) cc_final: 0.7517 (pt) REVERT: A 425 CYS cc_start: 0.8388 (p) cc_final: 0.8089 (p) REVERT: A 511 LYS cc_start: 0.7061 (mttp) cc_final: 0.6361 (tptt) REVERT: A 600 ILE cc_start: 0.9315 (mt) cc_final: 0.8987 (mm) REVERT: A 714 GLN cc_start: 0.7513 (mm-40) cc_final: 0.7227 (tp40) REVERT: A 732 TYR cc_start: 0.8032 (m-10) cc_final: 0.7410 (m-80) REVERT: A 1008 GLN cc_start: 0.7826 (pt0) cc_final: 0.7424 (pt0) REVERT: A 1063 TRP cc_start: 0.7891 (m100) cc_final: 0.7447 (m-10) REVERT: A 1130 ARG cc_start: 0.7979 (mmp-170) cc_final: 0.7587 (mmm160) REVERT: A 1199 MET cc_start: 0.7895 (mmm) cc_final: 0.7408 (tpp) REVERT: B 500 ILE cc_start: 0.8969 (mt) cc_final: 0.8716 (mm) REVERT: B 519 ASP cc_start: 0.8490 (m-30) cc_final: 0.8279 (t70) REVERT: B 585 MET cc_start: 0.8483 (mmm) cc_final: 0.8216 (mmm) REVERT: B 620 LEU cc_start: 0.8263 (tp) cc_final: 0.8009 (tp) REVERT: B 675 ARG cc_start: 0.6736 (ttp-110) cc_final: 0.6347 (ptp90) REVERT: B 1021 SER cc_start: 0.8445 (m) cc_final: 0.8126 (p) REVERT: C 438 PHE cc_start: 0.6272 (p90) cc_final: 0.5629 (p90) REVERT: C 501 SER cc_start: 0.8049 (p) cc_final: 0.7720 (t) REVERT: C 585 MET cc_start: 0.9017 (mmm) cc_final: 0.8690 (mmm) REVERT: C 671 TRP cc_start: 0.7106 (t-100) cc_final: 0.6833 (t-100) REVERT: C 817 LYS cc_start: 0.7996 (mmpt) cc_final: 0.7690 (mmmt) REVERT: C 1020 PHE cc_start: 0.8150 (t80) cc_final: 0.7894 (t80) REVERT: C 1072 PHE cc_start: 0.6023 (m-10) cc_final: 0.5667 (m-80) REVERT: C 1075 LEU cc_start: 0.6173 (mm) cc_final: 0.5563 (tp) REVERT: D 425 CYS cc_start: 0.8121 (m) cc_final: 0.7819 (m) REVERT: D 580 SER cc_start: 0.9404 (m) cc_final: 0.8817 (p) REVERT: D 589 CYS cc_start: 0.6863 (t) cc_final: 0.6572 (p) REVERT: D 713 GLU cc_start: 0.7176 (tt0) cc_final: 0.6848 (tp30) REVERT: D 1064 ARG cc_start: 0.7213 (ptp-170) cc_final: 0.6939 (ptp90) REVERT: D 1139 ILE cc_start: 0.8492 (mp) cc_final: 0.8254 (tt) outliers start: 4 outliers final: 0 residues processed: 452 average time/residue: 0.3430 time to fit residues: 240.1558 Evaluate side-chains 346 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 231 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 22 optimal weight: 0.0000 chunk 189 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 233 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 412 HIS D 435 HIS ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN D1204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.127019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101148 restraints weight = 39284.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.103617 restraints weight = 23517.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.105320 restraints weight = 17132.460| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19239 Z= 0.155 Angle : 0.617 9.710 25999 Z= 0.321 Chirality : 0.042 0.285 2911 Planarity : 0.004 0.069 3188 Dihedral : 7.855 96.293 2697 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Rotamer: Outliers : 0.10 % Allowed : 3.64 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2362 helix: 0.93 (0.14), residues: 1319 sheet: -1.79 (0.40), residues: 164 loop : -1.92 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 460 HIS 0.006 0.001 HIS D 435 PHE 0.021 0.002 PHE A1200 TYR 0.022 0.001 TYR C 732 ARG 0.004 0.000 ARG D 594 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 958) hydrogen bonds : angle 4.02534 ( 2811) SS BOND : bond 0.01280 ( 12) SS BOND : angle 3.32366 ( 24) covalent geometry : bond 0.00360 (19227) covalent geometry : angle 0.60930 (25975) *********************** 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 451 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 449 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7991 (mt) cc_final: 0.7504 (pt) REVERT: A 425 CYS cc_start: 0.8382 (p) cc_final: 0.8136 (p) REVERT: A 487 GLU cc_start: 0.7725 (tp30) cc_final: 0.7163 (pt0) REVERT: A 511 LYS cc_start: 0.7054 (mttp) cc_final: 0.6366 (tptt) REVERT: A 600 ILE cc_start: 0.9263 (mt) cc_final: 0.8926 (mm) REVERT: A 714 GLN cc_start: 0.7444 (mm-40) cc_final: 0.7220 (tp40) REVERT: A 732 TYR cc_start: 0.8039 (m-10) cc_final: 0.7294 (m-80) REVERT: A 1008 GLN cc_start: 0.7618 (pt0) cc_final: 0.7341 (pt0) REVERT: A 1063 TRP cc_start: 0.7658 (m100) cc_final: 0.7318 (m-10) REVERT: A 1199 MET cc_start: 0.7829 (mmm) cc_final: 0.7406 (tpp) REVERT: B 500 ILE cc_start: 0.9057 (mt) cc_final: 0.8734 (mm) REVERT: B 519 ASP cc_start: 0.8463 (m-30) cc_final: 0.8242 (t70) REVERT: B 585 MET cc_start: 0.8523 (mmm) cc_final: 0.8315 (mmm) REVERT: B 637 GLU cc_start: 0.6453 (mp0) cc_final: 0.6233 (mp0) REVERT: B 708 MET cc_start: 0.6995 (mpp) cc_final: 0.6661 (mpp) REVERT: B 1021 SER cc_start: 0.8437 (m) cc_final: 0.8110 (p) REVERT: B 1023 MET cc_start: 0.8681 (tpt) cc_final: 0.8438 (tpt) REVERT: B 1065 THR cc_start: 0.7066 (t) cc_final: 0.6205 (m) REVERT: C 438 PHE cc_start: 0.6191 (p90) cc_final: 0.5593 (p90) REVERT: C 501 SER cc_start: 0.8066 (p) cc_final: 0.7769 (t) REVERT: C 682 PHE cc_start: 0.5121 (m-80) cc_final: 0.4794 (m-80) REVERT: C 817 LYS cc_start: 0.8013 (mmpt) cc_final: 0.7697 (mmmt) REVERT: C 1020 PHE cc_start: 0.8113 (t80) cc_final: 0.7876 (t80) REVERT: C 1031 TYR cc_start: 0.3889 (p90) cc_final: 0.3299 (p90) REVERT: D 422 GLU cc_start: 0.6817 (pp20) cc_final: 0.6574 (pm20) REVERT: D 425 CYS cc_start: 0.8053 (m) cc_final: 0.7801 (m) REVERT: D 580 SER cc_start: 0.9364 (m) cc_final: 0.8777 (p) REVERT: D 644 GLU cc_start: 0.7201 (mp0) cc_final: 0.6556 (tm-30) REVERT: D 713 GLU cc_start: 0.7119 (tt0) cc_final: 0.6826 (tp30) REVERT: D 1139 ILE cc_start: 0.8489 (mp) cc_final: 0.8205 (tt) outliers start: 2 outliers final: 0 residues processed: 450 average time/residue: 0.2810 time to fit residues: 197.0890 Evaluate side-chains 352 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 99 optimal weight: 3.9990 chunk 168 optimal weight: 0.0870 chunk 82 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN D 587 GLN ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN D1204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.104104 restraints weight = 39921.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.105576 restraints weight = 24219.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.105816 restraints weight = 17533.484| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19239 Z= 0.132 Angle : 0.601 10.818 25999 Z= 0.310 Chirality : 0.042 0.266 2911 Planarity : 0.004 0.048 3188 Dihedral : 7.271 91.801 2697 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2362 helix: 1.43 (0.14), residues: 1287 sheet: -1.93 (0.44), residues: 146 loop : -1.64 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 460 HIS 0.011 0.001 HIS D1059 PHE 0.024 0.001 PHE C1200 TYR 0.020 0.001 TYR C 732 ARG 0.003 0.000 ARG D 594 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 958) hydrogen bonds : angle 3.90122 ( 2811) SS BOND : bond 0.01520 ( 12) SS BOND : angle 3.40465 ( 24) covalent geometry : bond 0.00303 (19227) covalent geometry : angle 0.59224 (25975) *********************** 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 469 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 467 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7985 (mt) cc_final: 0.7434 (pt) REVERT: A 476 ILE cc_start: 0.9070 (mt) cc_final: 0.8762 (pt) REVERT: A 487 GLU cc_start: 0.7673 (tp30) cc_final: 0.7140 (pt0) REVERT: A 511 LYS cc_start: 0.7052 (mttp) cc_final: 0.6361 (tptt) REVERT: A 519 ASP cc_start: 0.7992 (m-30) cc_final: 0.7747 (t0) REVERT: A 714 GLN cc_start: 0.7445 (mm-40) cc_final: 0.7244 (tp40) REVERT: A 732 TYR cc_start: 0.7903 (m-10) cc_final: 0.7292 (m-80) REVERT: A 1008 GLN cc_start: 0.7581 (pt0) cc_final: 0.7327 (pt0) REVERT: A 1063 TRP cc_start: 0.7707 (m100) cc_final: 0.7337 (m-10) REVERT: A 1130 ARG cc_start: 0.7888 (mmt-90) cc_final: 0.7511 (mmt-90) REVERT: A 1199 MET cc_start: 0.7807 (mmm) cc_final: 0.7424 (tpp) REVERT: B 445 VAL cc_start: 0.6981 (p) cc_final: 0.6764 (t) REVERT: B 481 ILE cc_start: 0.8717 (mt) cc_final: 0.8433 (mt) REVERT: B 500 ILE cc_start: 0.9034 (mt) cc_final: 0.8740 (mm) REVERT: B 519 ASP cc_start: 0.8463 (m-30) cc_final: 0.8167 (t70) REVERT: B 637 GLU cc_start: 0.6531 (mp0) cc_final: 0.6252 (mp0) REVERT: B 708 MET cc_start: 0.6840 (mpp) cc_final: 0.6605 (mpp) REVERT: B 1021 SER cc_start: 0.8349 (m) cc_final: 0.7943 (p) REVERT: B 1023 MET cc_start: 0.8663 (tpt) cc_final: 0.8430 (tpt) REVERT: B 1065 THR cc_start: 0.6954 (t) cc_final: 0.6020 (m) REVERT: C 432 ILE cc_start: 0.8014 (mm) cc_final: 0.7706 (tp) REVERT: C 438 PHE cc_start: 0.6092 (p90) cc_final: 0.5397 (p90) REVERT: C 473 ASP cc_start: 0.7010 (m-30) cc_final: 0.5146 (t70) REVERT: C 474 ILE cc_start: 0.8505 (pt) cc_final: 0.8230 (pt) REVERT: C 497 SER cc_start: 0.8551 (t) cc_final: 0.8218 (m) REVERT: C 501 SER cc_start: 0.8104 (p) cc_final: 0.7739 (t) REVERT: C 654 SER cc_start: 0.7678 (p) cc_final: 0.7372 (p) REVERT: C 682 PHE cc_start: 0.5169 (m-80) cc_final: 0.4946 (m-80) REVERT: C 817 LYS cc_start: 0.8080 (mmpt) cc_final: 0.7750 (mmmt) REVERT: C 1020 PHE cc_start: 0.8117 (t80) cc_final: 0.7852 (t80) REVERT: C 1031 TYR cc_start: 0.3980 (p90) cc_final: 0.3291 (p90) REVERT: D 422 GLU cc_start: 0.6836 (pp20) cc_final: 0.6452 (pm20) REVERT: D 425 CYS cc_start: 0.8023 (m) cc_final: 0.7755 (m) REVERT: D 541 PHE cc_start: 0.7906 (t80) cc_final: 0.7623 (t80) REVERT: D 580 SER cc_start: 0.9315 (m) cc_final: 0.8751 (p) REVERT: D 713 GLU cc_start: 0.7081 (tt0) cc_final: 0.6746 (tp30) outliers start: 2 outliers final: 0 residues processed: 468 average time/residue: 0.2712 time to fit residues: 200.1639 Evaluate side-chains 359 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 34 optimal weight: 6.9990 chunk 76 optimal weight: 0.0040 chunk 43 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 201 optimal weight: 0.0070 chunk 142 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 236 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 192 optimal weight: 0.9990 overall best weight: 0.7814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1059 HIS D 586 GLN D1159 ASN D1204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.129396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103865 restraints weight = 39697.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.106430 restraints weight = 23911.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.108088 restraints weight = 17354.566| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19239 Z= 0.121 Angle : 0.604 12.960 25999 Z= 0.309 Chirality : 0.041 0.265 2911 Planarity : 0.004 0.067 3188 Dihedral : 6.820 87.457 2697 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2362 helix: 1.62 (0.14), residues: 1302 sheet: -1.79 (0.45), residues: 145 loop : -1.60 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D1177 HIS 0.007 0.001 HIS D1059 PHE 0.022 0.001 PHE C1200 TYR 0.016 0.001 TYR C 732 ARG 0.004 0.000 ARG C 675 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 958) hydrogen bonds : angle 3.82669 ( 2811) SS BOND : bond 0.01189 ( 12) SS BOND : angle 3.51008 ( 24) covalent geometry : bond 0.00275 (19227) covalent geometry : angle 0.59470 (25975) *********************** 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 452 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7943 (mt) cc_final: 0.7320 (pt) REVERT: A 405 TYR cc_start: 0.7507 (m-80) cc_final: 0.7287 (m-80) REVERT: A 476 ILE cc_start: 0.8998 (mt) cc_final: 0.8752 (pt) REVERT: A 487 GLU cc_start: 0.7576 (tp30) cc_final: 0.7100 (pt0) REVERT: A 511 LYS cc_start: 0.7013 (mttp) cc_final: 0.6343 (tptt) REVERT: A 519 ASP cc_start: 0.7977 (m-30) cc_final: 0.7747 (t0) REVERT: A 674 MET cc_start: 0.6732 (mmm) cc_final: 0.6513 (mmt) REVERT: A 1063 TRP cc_start: 0.7682 (m100) cc_final: 0.7367 (m-10) REVERT: B 500 ILE cc_start: 0.9029 (mt) cc_final: 0.8764 (mm) REVERT: B 519 ASP cc_start: 0.8414 (m-30) cc_final: 0.8097 (t70) REVERT: B 566 GLU cc_start: 0.6018 (mt-10) cc_final: 0.5794 (mt-10) REVERT: B 592 SER cc_start: 0.8191 (t) cc_final: 0.7916 (p) REVERT: C 432 ILE cc_start: 0.7924 (mm) cc_final: 0.7648 (tp) REVERT: C 438 PHE cc_start: 0.5948 (p90) cc_final: 0.5263 (p90) REVERT: C 473 ASP cc_start: 0.6939 (m-30) cc_final: 0.5165 (t70) REVERT: C 501 SER cc_start: 0.8144 (p) cc_final: 0.7778 (t) REVERT: C 683 VAL cc_start: 0.7458 (p) cc_final: 0.7212 (t) REVERT: C 817 LYS cc_start: 0.8069 (mmpt) cc_final: 0.7719 (mmmt) REVERT: C 1020 PHE cc_start: 0.8108 (t80) cc_final: 0.7855 (t80) REVERT: C 1031 TYR cc_start: 0.3592 (p90) cc_final: 0.2956 (p90) REVERT: C 1156 ILE cc_start: 0.8601 (mt) cc_final: 0.8333 (mp) REVERT: C 1179 PHE cc_start: 0.8422 (t80) cc_final: 0.8178 (t80) REVERT: D 425 CYS cc_start: 0.7965 (m) cc_final: 0.7706 (m) REVERT: D 527 MET cc_start: 0.6745 (mmt) cc_final: 0.6514 (mtt) REVERT: D 580 SER cc_start: 0.9260 (m) cc_final: 0.8671 (p) REVERT: D 644 GLU cc_start: 0.7142 (mp0) cc_final: 0.6430 (tm-30) REVERT: D 645 ILE cc_start: 0.7713 (mt) cc_final: 0.7466 (mt) REVERT: D 713 GLU cc_start: 0.7074 (tt0) cc_final: 0.6708 (tp30) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.2804 time to fit residues: 198.1138 Evaluate side-chains 358 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 192 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 195 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS D 435 HIS D 714 GLN ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN D1204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.128025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102175 restraints weight = 39319.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.104679 restraints weight = 23830.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.106339 restraints weight = 17459.816| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19239 Z= 0.141 Angle : 0.613 14.832 25999 Z= 0.315 Chirality : 0.042 0.242 2911 Planarity : 0.004 0.055 3188 Dihedral : 6.623 85.771 2697 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2362 helix: 1.65 (0.14), residues: 1295 sheet: -1.79 (0.45), residues: 146 loop : -1.60 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D1032 HIS 0.007 0.001 HIS D1059 PHE 0.019 0.001 PHE B1200 TYR 0.019 0.001 TYR A 533 ARG 0.003 0.000 ARG C1036 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 958) hydrogen bonds : angle 3.87085 ( 2811) SS BOND : bond 0.00773 ( 12) SS BOND : angle 2.76087 ( 24) covalent geometry : bond 0.00329 (19227) covalent geometry : angle 0.60727 (25975) *********************** 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 436 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 436 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7839 (mt) cc_final: 0.7292 (pt) REVERT: A 425 CYS cc_start: 0.8263 (p) cc_final: 0.8044 (p) REVERT: A 463 MET cc_start: 0.7646 (tpp) cc_final: 0.7281 (tpp) REVERT: A 476 ILE cc_start: 0.9126 (mt) cc_final: 0.8784 (pt) REVERT: A 487 GLU cc_start: 0.7450 (tp30) cc_final: 0.7039 (pt0) REVERT: A 511 LYS cc_start: 0.7054 (mttp) cc_final: 0.6419 (tptt) REVERT: A 519 ASP cc_start: 0.8002 (m-30) cc_final: 0.7734 (t0) REVERT: A 600 ILE cc_start: 0.9203 (mt) cc_final: 0.8805 (mm) REVERT: A 629 MET cc_start: 0.3954 (mpp) cc_final: 0.3189 (tpt) REVERT: A 1063 TRP cc_start: 0.7673 (m100) cc_final: 0.7394 (m-10) REVERT: A 1199 MET cc_start: 0.7944 (mmt) cc_final: 0.7661 (mmm) REVERT: B 500 ILE cc_start: 0.9061 (mt) cc_final: 0.8780 (mm) REVERT: B 519 ASP cc_start: 0.8460 (m-30) cc_final: 0.8128 (t70) REVERT: B 592 SER cc_start: 0.8206 (t) cc_final: 0.7927 (p) REVERT: B 655 THR cc_start: 0.6326 (t) cc_final: 0.5914 (t) REVERT: B 715 ARG cc_start: 0.6870 (ttp-170) cc_final: 0.6581 (tpm170) REVERT: B 1020 PHE cc_start: 0.7598 (t80) cc_final: 0.7394 (t80) REVERT: B 1115 PHE cc_start: 0.6993 (t80) cc_final: 0.6326 (t80) REVERT: C 438 PHE cc_start: 0.5945 (p90) cc_final: 0.5342 (p90) REVERT: C 501 SER cc_start: 0.8173 (p) cc_final: 0.7791 (t) REVERT: C 585 MET cc_start: 0.8832 (mtp) cc_final: 0.8593 (mtp) REVERT: C 817 LYS cc_start: 0.8083 (mmpt) cc_final: 0.7761 (mmmt) REVERT: C 1020 PHE cc_start: 0.8089 (t80) cc_final: 0.7797 (t80) REVERT: C 1031 TYR cc_start: 0.3942 (p90) cc_final: 0.3626 (p90) REVERT: D 425 CYS cc_start: 0.8025 (m) cc_final: 0.7791 (m) REVERT: D 518 LEU cc_start: 0.8638 (mt) cc_final: 0.8415 (mt) REVERT: D 541 PHE cc_start: 0.7830 (t80) cc_final: 0.7619 (t80) REVERT: D 580 SER cc_start: 0.9328 (m) cc_final: 0.8739 (p) REVERT: D 644 GLU cc_start: 0.7318 (mp0) cc_final: 0.6937 (tt0) outliers start: 0 outliers final: 0 residues processed: 436 average time/residue: 0.2677 time to fit residues: 183.6617 Evaluate side-chains 351 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 134 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 221 optimal weight: 0.0970 chunk 122 optimal weight: 0.6980 chunk 44 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 chunk 231 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1081 HIS D1159 ASN D1204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.130059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104380 restraints weight = 39060.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106971 restraints weight = 23304.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108650 restraints weight = 16919.883| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19239 Z= 0.116 Angle : 0.596 13.931 25999 Z= 0.305 Chirality : 0.041 0.246 2911 Planarity : 0.004 0.082 3188 Dihedral : 6.339 81.209 2697 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.18), residues: 2362 helix: 1.79 (0.15), residues: 1306 sheet: -1.45 (0.47), residues: 144 loop : -1.55 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 671 HIS 0.007 0.001 HIS A1204 PHE 0.016 0.001 PHE A1082 TYR 0.018 0.001 TYR C 424 ARG 0.003 0.000 ARG C1036 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 958) hydrogen bonds : angle 3.77635 ( 2811) SS BOND : bond 0.00829 ( 12) SS BOND : angle 2.35371 ( 24) covalent geometry : bond 0.00260 (19227) covalent geometry : angle 0.59229 (25975) *********************** 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 464 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 2.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7782 (mt) cc_final: 0.7274 (pt) REVERT: A 425 CYS cc_start: 0.8230 (p) cc_final: 0.7978 (p) REVERT: A 487 GLU cc_start: 0.7211 (tp30) cc_final: 0.6982 (pt0) REVERT: A 511 LYS cc_start: 0.7014 (mttp) cc_final: 0.6371 (tptt) REVERT: A 600 ILE cc_start: 0.9177 (mt) cc_final: 0.8785 (mm) REVERT: A 629 MET cc_start: 0.3925 (mpp) cc_final: 0.3191 (tpt) REVERT: A 1063 TRP cc_start: 0.7660 (m100) cc_final: 0.7409 (m-10) REVERT: B 500 ILE cc_start: 0.9072 (mt) cc_final: 0.8773 (mm) REVERT: B 519 ASP cc_start: 0.8371 (m-30) cc_final: 0.8027 (t70) REVERT: B 592 SER cc_start: 0.8126 (t) cc_final: 0.7859 (p) REVERT: B 637 GLU cc_start: 0.7647 (tp30) cc_final: 0.7416 (tp30) REVERT: B 1023 MET cc_start: 0.8668 (tpt) cc_final: 0.8031 (tpt) REVERT: B 1065 THR cc_start: 0.7040 (t) cc_final: 0.6176 (m) REVERT: B 1115 PHE cc_start: 0.6924 (t80) cc_final: 0.6313 (t80) REVERT: C 438 PHE cc_start: 0.5862 (p90) cc_final: 0.5175 (p90) REVERT: C 473 ASP cc_start: 0.6878 (m-30) cc_final: 0.5165 (t70) REVERT: C 501 SER cc_start: 0.8219 (p) cc_final: 0.7865 (t) REVERT: C 817 LYS cc_start: 0.8060 (mmpt) cc_final: 0.7741 (mmmt) REVERT: C 1020 PHE cc_start: 0.8098 (t80) cc_final: 0.7847 (t80) REVERT: C 1031 TYR cc_start: 0.3700 (p90) cc_final: 0.2964 (p90) REVERT: C 1156 ILE cc_start: 0.8587 (mt) cc_final: 0.8339 (mp) REVERT: D 425 CYS cc_start: 0.8133 (m) cc_final: 0.7846 (m) REVERT: D 518 LEU cc_start: 0.8600 (mt) cc_final: 0.8380 (mt) REVERT: D 527 MET cc_start: 0.6700 (mmt) cc_final: 0.6471 (mtt) REVERT: D 541 PHE cc_start: 0.7805 (t80) cc_final: 0.7573 (t80) REVERT: D 580 SER cc_start: 0.9280 (m) cc_final: 0.8670 (p) REVERT: D 644 GLU cc_start: 0.7312 (mp0) cc_final: 0.6931 (tt0) REVERT: D 713 GLU cc_start: 0.7026 (tt0) cc_final: 0.6666 (tp30) REVERT: D 752 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7911 (ttmm) outliers start: 0 outliers final: 0 residues processed: 464 average time/residue: 0.2884 time to fit residues: 209.7178 Evaluate side-chains 352 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 130 optimal weight: 2.9990 chunk 211 optimal weight: 0.0570 chunk 63 optimal weight: 0.8980 chunk 82 optimal weight: 0.3980 chunk 18 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 167 optimal weight: 0.0970 chunk 155 optimal weight: 0.7980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A1198 HIS B1204 HIS ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN D1204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.131627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.106050 restraints weight = 38986.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108627 restraints weight = 23297.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110299 restraints weight = 16856.094| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 19239 Z= 0.113 Angle : 0.593 14.033 25999 Z= 0.303 Chirality : 0.040 0.254 2911 Planarity : 0.004 0.072 3188 Dihedral : 6.156 76.988 2697 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.05 % Allowed : 0.65 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.17), residues: 2362 helix: 1.89 (0.14), residues: 1304 sheet: -1.39 (0.46), residues: 143 loop : -1.49 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 671 HIS 0.006 0.001 HIS D1059 PHE 0.019 0.001 PHE B1200 TYR 0.019 0.001 TYR A 533 ARG 0.004 0.000 ARG B 675 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 958) hydrogen bonds : angle 3.73539 ( 2811) SS BOND : bond 0.00681 ( 12) SS BOND : angle 2.40737 ( 24) covalent geometry : bond 0.00252 (19227) covalent geometry : angle 0.58845 (25975) *********************** 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 459 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 458 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7735 (mt) cc_final: 0.7269 (pt) REVERT: A 511 LYS cc_start: 0.6985 (mttp) cc_final: 0.6376 (tptt) REVERT: A 541 PHE cc_start: 0.8629 (t80) cc_final: 0.8318 (t80) REVERT: A 600 ILE cc_start: 0.9169 (mt) cc_final: 0.8749 (mm) REVERT: A 629 MET cc_start: 0.3868 (mpp) cc_final: 0.3222 (tpt) REVERT: A 1063 TRP cc_start: 0.7615 (m100) cc_final: 0.7388 (m-10) REVERT: B 402 GLU cc_start: 0.7195 (pp20) cc_final: 0.6880 (mm-30) REVERT: B 498 LEU cc_start: 0.8554 (pt) cc_final: 0.8340 (pp) REVERT: B 500 ILE cc_start: 0.9092 (mt) cc_final: 0.8805 (mm) REVERT: B 592 SER cc_start: 0.8132 (t) cc_final: 0.7888 (p) REVERT: B 655 THR cc_start: 0.6270 (t) cc_final: 0.5935 (t) REVERT: B 1023 MET cc_start: 0.8635 (tpt) cc_final: 0.8410 (tpt) REVERT: B 1115 PHE cc_start: 0.6867 (t80) cc_final: 0.6237 (t80) REVERT: C 438 PHE cc_start: 0.5785 (p90) cc_final: 0.5068 (p90) REVERT: C 473 ASP cc_start: 0.6829 (m-30) cc_final: 0.5076 (t70) REVERT: C 541 PHE cc_start: 0.8220 (t80) cc_final: 0.7878 (t80) REVERT: C 722 LYS cc_start: 0.8303 (tttm) cc_final: 0.7985 (ptmm) REVERT: C 817 LYS cc_start: 0.8054 (mmpt) cc_final: 0.7740 (mmmt) REVERT: C 1020 PHE cc_start: 0.8084 (t80) cc_final: 0.7866 (t80) REVERT: C 1031 TYR cc_start: 0.3743 (p90) cc_final: 0.3121 (p90) REVERT: C 1156 ILE cc_start: 0.8565 (mt) cc_final: 0.8309 (mp) REVERT: D 405 TYR cc_start: 0.7404 (m-80) cc_final: 0.7163 (m-80) REVERT: D 425 CYS cc_start: 0.8180 (m) cc_final: 0.7838 (m) REVERT: D 463 MET cc_start: 0.6394 (mtm) cc_final: 0.5997 (mtm) REVERT: D 527 MET cc_start: 0.6639 (mmt) cc_final: 0.6435 (mtt) REVERT: D 541 PHE cc_start: 0.7846 (t80) cc_final: 0.7625 (t80) REVERT: D 580 SER cc_start: 0.9266 (m) cc_final: 0.8652 (p) REVERT: D 644 GLU cc_start: 0.7233 (mp0) cc_final: 0.6643 (tm-30) REVERT: D 645 ILE cc_start: 0.7688 (mt) cc_final: 0.7376 (mt) REVERT: D 713 GLU cc_start: 0.6966 (tt0) cc_final: 0.6647 (tp30) REVERT: D 752 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7875 (ttmm) outliers start: 1 outliers final: 0 residues processed: 459 average time/residue: 0.2860 time to fit residues: 206.4901 Evaluate side-chains 357 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 170 optimal weight: 0.2980 chunk 106 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1148 ASN B1159 ASN D1081 HIS D1159 ASN D1204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.126312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100011 restraints weight = 39663.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.102479 restraints weight = 23961.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.104128 restraints weight = 17506.940| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19239 Z= 0.202 Angle : 0.693 14.897 25999 Z= 0.357 Chirality : 0.044 0.257 2911 Planarity : 0.004 0.067 3188 Dihedral : 6.564 79.981 2697 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.17), residues: 2362 helix: 1.39 (0.14), residues: 1313 sheet: -1.42 (0.47), residues: 134 loop : -1.63 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 671 HIS 0.007 0.002 HIS C1059 PHE 0.020 0.002 PHE A1082 TYR 0.023 0.002 TYR B1031 ARG 0.007 0.001 ARG A1130 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 958) hydrogen bonds : angle 4.15244 ( 2811) SS BOND : bond 0.00782 ( 12) SS BOND : angle 2.31392 ( 24) covalent geometry : bond 0.00473 (19227) covalent geometry : angle 0.68927 (25975) ********************** 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 433 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7733 (mt) cc_final: 0.7309 (pt) REVERT: A 463 MET cc_start: 0.7788 (tpp) cc_final: 0.7431 (tpp) REVERT: A 511 LYS cc_start: 0.7041 (mttp) cc_final: 0.6401 (tptt) REVERT: A 600 ILE cc_start: 0.9245 (mt) cc_final: 0.8926 (mm) REVERT: A 629 MET cc_start: 0.3993 (mpp) cc_final: 0.3301 (tpt) REVERT: A 670 MET cc_start: 0.7734 (mmt) cc_final: 0.7506 (mmt) REVERT: A 674 MET cc_start: 0.7123 (mmt) cc_final: 0.6737 (mmt) REVERT: A 1063 TRP cc_start: 0.7762 (m100) cc_final: 0.7438 (m-10) REVERT: A 1115 PHE cc_start: 0.8283 (t80) cc_final: 0.7678 (t80) REVERT: B 500 ILE cc_start: 0.9127 (mt) cc_final: 0.8744 (mm) REVERT: B 592 SER cc_start: 0.8253 (t) cc_final: 0.7964 (p) REVERT: B 670 MET cc_start: 0.7122 (mpp) cc_final: 0.6902 (mpp) REVERT: B 1023 MET cc_start: 0.8675 (tpt) cc_final: 0.8239 (tpt) REVERT: B 1065 THR cc_start: 0.7219 (t) cc_final: 0.6490 (m) REVERT: B 1115 PHE cc_start: 0.6911 (t80) cc_final: 0.6375 (t80) REVERT: C 438 PHE cc_start: 0.6101 (p90) cc_final: 0.5488 (p90) REVERT: C 501 SER cc_start: 0.8303 (p) cc_final: 0.7982 (t) REVERT: C 541 PHE cc_start: 0.8314 (t80) cc_final: 0.8070 (t80) REVERT: C 585 MET cc_start: 0.8655 (mmm) cc_final: 0.8363 (mmm) REVERT: C 817 LYS cc_start: 0.8074 (mmpt) cc_final: 0.7768 (mmmt) REVERT: C 1020 PHE cc_start: 0.8145 (t80) cc_final: 0.7785 (t80) REVERT: C 1031 TYR cc_start: 0.4083 (p90) cc_final: 0.3851 (p90) REVERT: C 1060 SER cc_start: 0.7747 (t) cc_final: 0.7405 (p) REVERT: D 425 CYS cc_start: 0.8071 (m) cc_final: 0.7825 (m) REVERT: D 580 SER cc_start: 0.9421 (m) cc_final: 0.8884 (p) REVERT: D 644 GLU cc_start: 0.7300 (mp0) cc_final: 0.7007 (tt0) REVERT: D 713 GLU cc_start: 0.7227 (tt0) cc_final: 0.6734 (tp30) outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.2770 time to fit residues: 187.8209 Evaluate side-chains 334 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 178 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.0770 chunk 9 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 176 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 196 optimal weight: 3.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1198 HIS B1159 ASN ** C 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN D1204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.130519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104450 restraints weight = 39069.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.107069 restraints weight = 23529.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108724 restraints weight = 17135.453| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19239 Z= 0.117 Angle : 0.620 14.332 25999 Z= 0.315 Chirality : 0.041 0.251 2911 Planarity : 0.004 0.061 3188 Dihedral : 6.238 77.164 2697 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2362 helix: 1.71 (0.14), residues: 1303 sheet: -1.32 (0.47), residues: 130 loop : -1.50 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 671 HIS 0.006 0.001 HIS A1204 PHE 0.026 0.001 PHE B1020 TYR 0.019 0.001 TYR A 533 ARG 0.005 0.000 ARG A1130 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 958) hydrogen bonds : angle 3.84751 ( 2811) SS BOND : bond 0.00687 ( 12) SS BOND : angle 2.18956 ( 24) covalent geometry : bond 0.00260 (19227) covalent geometry : angle 0.61622 (25975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6852.40 seconds wall clock time: 120 minutes 24.91 seconds (7224.91 seconds total)