Starting phenix.real_space_refine on Sun Oct 25 23:33:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tno_26016/10_2026/7tno_26016.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tno_26016/10_2026/7tno_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_26016/10_2026/7tno_26016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tno_26016/10_2026/7tno_26016.map" model { file = "/net/cci-nas-00/data/ceres_data/7tno_26016/10_2026/7tno_26016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tno_26016/10_2026/7tno_26016.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tno_26016/10_2026/7tno_26016.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tno_26016/10_2026/7tno_26016.cif" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 136 5.16 5 Cl 4 4.86 5 C 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/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: 4.27, per 1000 atoms: 0.23 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: 1.47 Conformation dependent library (CDL) restraints added in 832.5 milliseconds 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 0.51 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: 3.12 Time building geometry restraints manager: 2.02 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 - 19.69: 10781 19.69 - 39.37: 407 39.37 - 59.06: 68 59.06 - 78.75: 12 78.75 - 98.43: 4 Dihedral angle restraints: 11272 sinusoidal: 4392 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 11269 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: 0.000 Normalize map: mean=0, sd=1: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.780 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 : 11.143 98.432 6846 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.38 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.005 0.001 ARG A 692 TYR 0.028 0.002 TYR B1031 PHE 0.028 0.002 PHE B1072 TRP 0.029 0.003 TRP A1032 HIS 0.006 0.002 HIS B1081 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.23 (19227) covalent geometry : angle 0.93867 / 0.53 (25975) SS BOND : bond 0.00556 / 0.46 ( 12) SS BOND : angle 1.38411 / 0.80 ( 24) hydrogen bonds : bond 0.29804 / 19.66 ( 958) hydrogen bonds : angle 9.37486 / 6.42 ( 2811) *********************** 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 : 0.676 Fit side-chains 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: 0.7272 (mtmt) REVERT: A 511 LYS cc_start: 0.6826 (mttp) cc_final: 0.6082 (tptt) REVERT: A 600 ILE cc_start: 0.9377 (mt) cc_final: 0.9123 (mm) REVERT: A 654 SER cc_start: 0.8564 (p) cc_final: 0.8195 (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: 0.4400 (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: 0.7472 (mmm160) REVERT: A 1147 SER cc_start: 0.8542 (t) cc_final: 0.8318 (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: 0.7140 (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: 0.8167 (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: 0.5687 (ptp90) REVERT: B 1021 SER cc_start: 0.8410 (m) cc_final: 0.8101 (p) REVERT: B 1022 LEU cc_start: 0.8408 (mt) cc_final: 0.8192 (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: 0.5581 (p90) REVERT: C 460 TRP cc_start: 0.5889 (m100) cc_final: 0.5573 (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: 0.8080 (t) REVERT: C 683 VAL cc_start: 0.7310 (m) cc_final: 0.6258 (m) REVERT: C 699 LYS cc_start: 0.8011 (mptt) cc_final: 0.7672 (mmmt) REVERT: C 711 TYR cc_start: 0.7413 (t80) cc_final: 0.7208 (t80) REVERT: C 732 TYR cc_start: 0.7976 (m-10) cc_final: 0.7644 (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: 0.7646 (mmmt) REVERT: C 1031 TYR cc_start: 0.3906 (p90) cc_final: 0.3599 (p90) REVERT: C 1036 ARG cc_start: 0.6959 (mmt180) cc_final: 0.6702 (mmt-90) REVERT: C 1096 PHE cc_start: 0.7792 (t80) cc_final: 0.7494 (t80) REVERT: C 1120 CYS cc_start: 0.7700 (m) cc_final: 0.7255 (m) REVERT: C 1126 PHE cc_start: 0.6413 (m-10) cc_final: 0.5863 (m-80) REVERT: C 1169 LYS cc_start: 0.2793 (tptp) cc_final: 0.1149 (ptmt) REVERT: D 425 CYS cc_start: 0.7947 (m) cc_final: 0.7683 (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: 0.8010 (p) cc_final: 0.7641 (p) REVERT: D 764 ASN cc_start: 0.7839 (p0) cc_final: 0.7548 (p0) REVERT: D 770 LYS cc_start: 0.7155 (mmmt) cc_final: 0.6657 (mmtt) REVERT: D 1170 LYS cc_start: 0.5128 (tptp) cc_final: 0.4851 (ptpp) REVERT: D 1173 TYR cc_start: 0.6761 (p90) cc_final: 0.6479 (p90) outliers start: 13 outliers final: 2 residues processed: 721 average time/residue: 0.1402 time to fit residues: 152.7522 Evaluate side-chains 422 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 419 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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 = 0.3719 r_free = 0.3719 target = 0.130663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.105024 restraints weight = 38786.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.107416 restraints weight = 24006.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.109010 restraints weight = 17765.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109861 restraints weight = 14741.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110204 restraints weight = 13239.210| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19239 Z= 0.139 Angle : 0.618 10.997 25999 Z= 0.327 Chirality : 0.041 0.204 2911 Planarity : 0.005 0.062 3188 Dihedral : 6.267 84.520 2601 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.32 % Rotamer: Outliers : 0.20 % Allowed : 3.79 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.15), residues: 2362 helix: -0.92 (0.12), residues: 1308 sheet: -1.86 (0.37), residues: 181 loop : -2.06 (0.18), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1005 TYR 0.020 0.001 TYR C1031 PHE 0.019 0.002 PHE B1072 TRP 0.020 0.002 TRP C 766 HIS 0.004 0.001 HIS B1081 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (19227) covalent geometry : angle 0.61414 / 0.33 (25975) SS BOND : bond 0.00915 / 0.68 ( 12) SS BOND : angle 2.28720 / 1.57 ( 24) hydrogen bonds : bond 0.04341 / 2.83 ( 958) hydrogen bonds : angle 4.32966 / 2.98 ( 2811) *********************** 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 519 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 515 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7955 (mt) cc_final: 0.7415 (pt) REVERT: A 511 LYS cc_start: 0.6865 (mttp) cc_final: 0.6169 (tptt) REVERT: A 600 ILE cc_start: 0.9270 (mt) cc_final: 0.8961 (mm) REVERT: A 732 TYR cc_start: 0.7848 (m-10) cc_final: 0.7086 (m-80) REVERT: A 1063 TRP cc_start: 0.7811 (m100) cc_final: 0.7424 (m-10) REVERT: A 1130 ARG cc_start: 0.8063 (mmp-170) cc_final: 0.7672 (mmm160) REVERT: A 1199 MET cc_start: 0.7799 (mmm) cc_final: 0.7441 (mmt) REVERT: B 500 ILE cc_start: 0.8888 (mt) cc_final: 0.8589 (mm) REVERT: B 637 GLU cc_start: 0.6518 (mp0) cc_final: 0.6269 (mp0) REVERT: B 776 LYS cc_start: 0.4126 (tttt) cc_final: 0.3923 (tttm) REVERT: B 1008 GLN cc_start: 0.6985 (pt0) cc_final: 0.6686 (pt0) REVERT: B 1021 SER cc_start: 0.8446 (m) cc_final: 0.8158 (p) REVERT: B 1023 MET cc_start: 0.8443 (tpp) cc_final: 0.7805 (tpt) REVERT: B 1065 THR cc_start: 0.6944 (t) cc_final: 0.6148 (m) REVERT: C 400 ILE cc_start: 0.8931 (tp) cc_final: 0.8667 (tp) REVERT: C 432 ILE cc_start: 0.7955 (mm) cc_final: 0.7541 (tp) REVERT: C 438 PHE cc_start: 0.6130 (p90) cc_final: 0.5499 (p90) REVERT: C 711 TYR cc_start: 0.7536 (t80) cc_final: 0.7330 (t80) REVERT: C 817 LYS cc_start: 0.7944 (mmpt) cc_final: 0.7656 (mmmt) REVERT: C 1020 PHE cc_start: 0.8112 (t80) cc_final: 0.7816 (t80) REVERT: C 1031 TYR cc_start: 0.4479 (p90) cc_final: 0.3529 (p90) REVERT: C 1092 THR cc_start: 0.6738 (p) cc_final: 0.6474 (t) REVERT: C 1130 ARG cc_start: 0.7169 (tpm170) cc_final: 0.6139 (tpt-90) REVERT: C 1169 LYS cc_start: 0.2972 (tptp) cc_final: 0.1457 (ptmt) REVERT: D 420 ARG cc_start: 0.6807 (mtm110) cc_final: 0.6546 (mtm110) REVERT: D 425 CYS cc_start: 0.7805 (m) cc_final: 0.7506 (m) REVERT: D 594 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8080 (ttp80) REVERT: D 639 LEU cc_start: 0.7890 (tp) cc_final: 0.7648 (tt) REVERT: D 712 ILE cc_start: 0.8382 (mm) cc_final: 0.8145 (mt) REVERT: D 1136 SER cc_start: 0.8979 (p) cc_final: 0.8701 (p) REVERT: D 1139 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.7973 (tt) outliers start: 4 outliers final: 0 residues processed: 517 average time/residue: 0.1268 time to fit residues: 101.4915 Evaluate side-chains 374 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [8, 99, 69, 9, 216, 194, 237, 206, 75, 52, 14] chunk 8 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 9 optimal weight: 0.0970 chunk 216 optimal weight: 0.0570 chunk 194 optimal weight: 0.9980 chunk 237 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1198 HIS B1148 ASN C1059 HIS D 412 HIS D 726 ASN ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.131828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.106363 restraints weight = 39340.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.108730 restraints weight = 24437.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110405 restraints weight = 18043.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.111441 restraints weight = 14907.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111701 restraints weight = 13245.890| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19239 Z= 0.118 Angle : 0.580 10.234 25999 Z= 0.300 Chirality : 0.040 0.237 2911 Planarity : 0.004 0.043 3188 Dihedral : 5.861 86.590 2601 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.35 % Allowed : 3.49 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.16), residues: 2362 helix: 0.57 (0.14), residues: 1303 sheet: -1.52 (0.39), residues: 177 loop : -1.78 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 420 TYR 0.023 0.001 TYR C 732 PHE 0.022 0.001 PHE C1200 TRP 0.018 0.001 TRP C 767 HIS 0.008 0.001 HIS D1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (19227) covalent geometry : angle 0.57414 / 0.30 (25975) SS BOND : bond 0.01205 / 0.93 ( 12) SS BOND : angle 2.82420 / 1.82 ( 24) hydrogen bonds : bond 0.03653 / 2.40 ( 958) hydrogen bonds : angle 3.87977 / 2.69 ( 2811) *********************** 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 501 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 494 time to evaluate : 0.688 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: 0.7916 (mt) cc_final: 0.7352 (pt) REVERT: A 425 CYS cc_start: 0.8302 (p) cc_final: 0.8048 (p) REVERT: A 511 LYS cc_start: 0.6935 (mttp) cc_final: 0.6296 (tptt) REVERT: A 671 TRP cc_start: 0.7752 (t-100) cc_final: 0.7531 (t-100) REVERT: A 732 TYR cc_start: 0.7838 (m-10) cc_final: 0.7260 (m-80) REVERT: A 1063 TRP cc_start: 0.7786 (m100) cc_final: 0.7338 (m-10) REVERT: A 1130 ARG cc_start: 0.8010 (mmp-170) cc_final: 0.7712 (mmm160) REVERT: A 1131 HIS cc_start: 0.6984 (m-70) cc_final: 0.6692 (m-70) REVERT: A 1198 HIS cc_start: 0.8272 (OUTLIER) cc_final: 0.7567 (m90) REVERT: B 500 ILE cc_start: 0.8974 (mt) cc_final: 0.8625 (mm) REVERT: B 635 SER cc_start: 0.7563 (p) cc_final: 0.7234 (t) REVERT: B 637 GLU cc_start: 0.6599 (mp0) cc_final: 0.6331 (mp0) REVERT: B 1008 GLN cc_start: 0.7092 (pt0) cc_final: 0.6675 (pt0) REVERT: B 1021 SER cc_start: 0.8438 (m) cc_final: 0.7842 (p) REVERT: B 1022 LEU cc_start: 0.8576 (mt) cc_final: 0.8318 (mp) REVERT: C 432 ILE cc_start: 0.7981 (mm) cc_final: 0.7622 (tp) REVERT: C 438 PHE cc_start: 0.5865 (p90) cc_final: 0.5128 (p90) REVERT: C 817 LYS cc_start: 0.7979 (mmpt) cc_final: 0.7672 (mmmt) REVERT: C 1031 TYR cc_start: 0.3748 (p90) cc_final: 0.3027 (p90) REVERT: C 1072 PHE cc_start: 0.5885 (m-10) cc_final: 0.5669 (m-80) REVERT: C 1075 LEU cc_start: 0.6062 (mm) cc_final: 0.5417 (tp) REVERT: C 1130 ARG cc_start: 0.7098 (tpm170) cc_final: 0.6068 (tpt-90) REVERT: C 1169 LYS cc_start: 0.2677 (tptp) cc_final: 0.1086 (ptmt) REVERT: D 425 CYS cc_start: 0.7914 (m) cc_final: 0.7568 (m) REVERT: D 469 TYR cc_start: 0.6404 (m-80) cc_final: 0.5462 (m-10) REVERT: D 476 ILE cc_start: 0.8579 (mt) cc_final: 0.8354 (mt) REVERT: D 541 PHE cc_start: 0.8099 (t80) cc_final: 0.7727 (t80) REVERT: D 594 ARG cc_start: 0.8402 (ttp80) cc_final: 0.8173 (ttp80) REVERT: D 637 GLU cc_start: 0.8206 (pp20) cc_final: 0.7711 (pp20) REVERT: D 1139 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8112 (tt) outliers start: 7 outliers final: 0 residues processed: 499 average time/residue: 0.1204 time to fit residues: 94.5697 Evaluate side-chains 378 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 376 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [22, 229, 167, 134, 182, 178, 158, 15, 147, 5, 127] chunk 22 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 182 optimal weight: 0.0570 chunk 178 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1059 HIS D 412 HIS D 435 HIS ** D1008 GLN ** 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 = 0.3725 r_free = 0.3725 target = 0.130912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.105011 restraints weight = 39153.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107592 restraints weight = 23440.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109263 restraints weight = 16953.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.110302 restraints weight = 13967.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.110819 restraints weight = 12416.973| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4361 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= 0.118 Angle : 0.579 9.791 25999 Z= 0.300 Chirality : 0.040 0.272 2911 Planarity : 0.004 0.047 3188 Dihedral : 5.664 86.309 2601 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.15 % Allowed : 3.14 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2362 helix: 1.24 (0.14), residues: 1298 sheet: -1.42 (0.42), residues: 158 loop : -1.66 (0.18), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 594 TYR 0.018 0.001 TYR A 673 PHE 0.019 0.001 PHE C1200 TRP 0.015 0.001 TRP B 460 HIS 0.006 0.001 HIS D 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (19227) covalent geometry : angle 0.57037 / 0.30 (25975) SS BOND : bond 0.01285 / 0.94 ( 12) SS BOND : angle 3.26143 / 2.13 ( 24) hydrogen bonds : bond 0.03406 / 2.23 ( 958) hydrogen bonds : angle 3.73781 / 2.59 ( 2811) *********************** 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 507 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 504 time to evaluate : 0.716 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: 0.7916 (mt) cc_final: 0.7359 (pt) REVERT: A 476 ILE cc_start: 0.9096 (mt) cc_final: 0.8769 (pt) REVERT: A 511 LYS cc_start: 0.6921 (mttp) cc_final: 0.6262 (tptt) REVERT: A 600 ILE cc_start: 0.9250 (mt) cc_final: 0.8914 (mm) REVERT: A 673 TYR cc_start: 0.7280 (t80) cc_final: 0.6955 (t80) REVERT: A 732 TYR cc_start: 0.7808 (m-10) cc_final: 0.6012 (m-80) REVERT: A 1063 TRP cc_start: 0.7675 (m100) cc_final: 0.7259 (m-10) REVERT: A 1199 MET cc_start: 0.7708 (mmm) cc_final: 0.7505 (mmt) REVERT: B 500 ILE cc_start: 0.9055 (mt) cc_final: 0.8725 (mm) REVERT: B 519 ASP cc_start: 0.8568 (m-30) cc_final: 0.8159 (t70) REVERT: B 675 ARG cc_start: 0.6799 (ttp-110) cc_final: 0.6268 (ptp-170) REVERT: B 1008 GLN cc_start: 0.7168 (pt0) cc_final: 0.6633 (pt0) REVERT: B 1115 PHE cc_start: 0.7128 (t80) cc_final: 0.6377 (t80) REVERT: B 1119 LEU cc_start: 0.8851 (mt) cc_final: 0.8577 (mt) REVERT: C 473 ASP cc_start: 0.7004 (m-30) cc_final: 0.5141 (t70) REVERT: C 682 PHE cc_start: 0.5141 (m-80) cc_final: 0.4771 (m-80) REVERT: C 722 LYS cc_start: 0.8452 (tttm) cc_final: 0.8196 (ptmm) REVERT: C 817 LYS cc_start: 0.8087 (mmpt) cc_final: 0.7741 (mmmt) REVERT: C 1020 PHE cc_start: 0.8066 (t80) cc_final: 0.7817 (t80) REVERT: C 1031 TYR cc_start: 0.4082 (p90) cc_final: 0.3340 (p90) REVERT: C 1075 LEU cc_start: 0.6334 (mm) cc_final: 0.5602 (tp) REVERT: C 1130 ARG cc_start: 0.7021 (tpm170) cc_final: 0.5944 (tpt-90) REVERT: C 1169 LYS cc_start: 0.2890 (tptp) cc_final: 0.1266 (ptmt) REVERT: C 1179 PHE cc_start: 0.8713 (t80) cc_final: 0.8440 (t80) REVERT: D 425 CYS cc_start: 0.7979 (m) cc_final: 0.7628 (m) REVERT: D 476 ILE cc_start: 0.8709 (mt) cc_final: 0.8472 (mt) REVERT: D 518 LEU cc_start: 0.8800 (mt) cc_final: 0.8438 (mt) REVERT: D 594 ARG cc_start: 0.8504 (ttp80) cc_final: 0.8192 (ttp80) REVERT: D 644 GLU cc_start: 0.7049 (mp0) cc_final: 0.6485 (tm-30) outliers start: 3 outliers final: 0 residues processed: 505 average time/residue: 0.1286 time to fit residues: 101.7428 Evaluate side-chains 381 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [220, 175, 80, 58, 238, 49, 86, 148, 15, 23, 5] chunk 220 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN B1204 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 = 0.3623 r_free = 0.3623 target = 0.123101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.096888 restraints weight = 40241.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.099269 restraints weight = 24573.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100890 restraints weight = 17960.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101713 restraints weight = 14828.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.102497 restraints weight = 13313.381| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 19239 Z= 0.293 Angle : 0.780 11.584 25999 Z= 0.409 Chirality : 0.048 0.303 2911 Planarity : 0.005 0.058 3188 Dihedral : 6.351 95.037 2601 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.10 % Allowed : 4.44 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.16), residues: 2362 helix: 0.78 (0.14), residues: 1304 sheet: -2.09 (0.42), residues: 144 loop : -1.90 (0.18), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 628 TYR 0.032 0.003 TYR C1031 PHE 0.031 0.003 PHE C 546 TRP 0.040 0.003 TRP D1032 HIS 0.008 0.002 HIS D1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.29 (19227) covalent geometry : angle 0.77312 / 0.41 (25975) SS BOND : bond 0.01647 / 1.23 ( 12) SS BOND : angle 3.49215 / 2.32 ( 24) hydrogen bonds : bond 0.04591 / 3.00 ( 958) hydrogen bonds : angle 4.46051 / 3.08 ( 2811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 419 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7970 (mt) cc_final: 0.7518 (pt) REVERT: A 511 LYS cc_start: 0.7108 (mttp) cc_final: 0.6427 (tptt) REVERT: A 600 ILE cc_start: 0.9298 (mt) cc_final: 0.8981 (mm) REVERT: A 639 LEU cc_start: 0.8788 (tp) cc_final: 0.8519 (tt) REVERT: A 1008 GLN cc_start: 0.7908 (pt0) cc_final: 0.7651 (mt0) REVERT: A 1199 MET cc_start: 0.7757 (mmm) cc_final: 0.7514 (mmt) REVERT: B 445 VAL cc_start: 0.7139 (p) cc_final: 0.6926 (t) REVERT: B 500 ILE cc_start: 0.9010 (mt) cc_final: 0.8682 (mm) REVERT: B 620 LEU cc_start: 0.8253 (tp) cc_final: 0.8041 (tp) REVERT: B 708 MET cc_start: 0.7102 (mpp) cc_final: 0.6621 (mpp) REVERT: B 1008 GLN cc_start: 0.7477 (pt0) cc_final: 0.6927 (pt0) REVERT: B 1021 SER cc_start: 0.8365 (m) cc_final: 0.8034 (p) REVERT: B 1023 MET cc_start: 0.8725 (tpt) cc_final: 0.8186 (tpt) REVERT: B 1115 PHE cc_start: 0.7059 (t80) cc_final: 0.6455 (t80) REVERT: B 1131 HIS cc_start: 0.7763 (m-70) cc_final: 0.5914 (t-90) REVERT: C 438 PHE cc_start: 0.6224 (p90) cc_final: 0.5855 (p90) REVERT: C 527 MET cc_start: 0.8327 (ttm) cc_final: 0.7938 (ttm) REVERT: C 629 MET cc_start: 0.4205 (tmm) cc_final: 0.3936 (tmm) REVERT: C 758 VAL cc_start: 0.8757 (t) cc_final: 0.8399 (t) REVERT: C 817 LYS cc_start: 0.7989 (mmpt) cc_final: 0.7683 (mmmt) REVERT: C 1020 PHE cc_start: 0.8210 (t80) cc_final: 0.7876 (t80) REVERT: C 1075 LEU cc_start: 0.6371 (mm) cc_final: 0.5380 (tp) REVERT: C 1130 ARG cc_start: 0.7419 (tpm170) cc_final: 0.5772 (tpt-90) REVERT: D 518 LEU cc_start: 0.8807 (mt) cc_final: 0.8489 (mt) REVERT: D 524 GLU cc_start: 0.8460 (mp0) cc_final: 0.8258 (mp0) REVERT: D 533 TYR cc_start: 0.8960 (t80) cc_final: 0.8731 (t80) REVERT: D 580 SER cc_start: 0.9389 (m) cc_final: 0.8863 (p) REVERT: D 647 TYR cc_start: 0.7766 (p90) cc_final: 0.7547 (p90) REVERT: D 768 TYR cc_start: 0.7160 (m-80) cc_final: 0.6811 (m-80) REVERT: D 772 GLU cc_start: 0.5454 (mp0) cc_final: 0.5096 (mp0) outliers start: 2 outliers final: 0 residues processed: 420 average time/residue: 0.1218 time to fit residues: 80.1767 Evaluate side-chains 318 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [57, 118, 6, 40, 35, 36, 122, 147, 173, 231, 16] chunk 57 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 231 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS A 619 ASN B1204 HIS C1059 HIS D 435 HIS D 747 ASN ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN D1204 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.127757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101706 restraints weight = 39252.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.104189 restraints weight = 23928.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.105852 restraints weight = 17474.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.106596 restraints weight = 14403.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107457 restraints weight = 13007.612| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19239 Z= 0.137 Angle : 0.630 14.773 25999 Z= 0.324 Chirality : 0.042 0.269 2911 Planarity : 0.004 0.073 3188 Dihedral : 5.889 85.381 2601 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.17), residues: 2362 helix: 1.36 (0.14), residues: 1297 sheet: -1.81 (0.45), residues: 139 loop : -1.68 (0.18), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 594 TYR 0.018 0.001 TYR C 424 PHE 0.020 0.001 PHE D 541 TRP 0.034 0.002 TRP C 460 HIS 0.006 0.001 HIS D1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (19227) covalent geometry : angle 0.62174 / 0.32 (25975) SS BOND : bond 0.01447 / 1.17 ( 12) SS BOND : angle 3.46044 / 2.17 ( 24) hydrogen bonds : bond 0.03611 / 2.34 ( 958) hydrogen bonds : angle 3.95892 / 2.74 ( 2811) *********************** 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 457 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7869 (mt) cc_final: 0.7345 (pt) REVERT: A 476 ILE cc_start: 0.9076 (mt) cc_final: 0.8711 (pt) REVERT: A 511 LYS cc_start: 0.6987 (mttp) cc_final: 0.6360 (tptt) REVERT: A 732 TYR cc_start: 0.7898 (m-10) cc_final: 0.7328 (m-80) REVERT: A 1008 GLN cc_start: 0.7756 (pt0) cc_final: 0.7549 (mt0) REVERT: A 1063 TRP cc_start: 0.7723 (m100) cc_final: 0.7465 (m-10) REVERT: A 1130 ARG cc_start: 0.7944 (mmt-90) cc_final: 0.7590 (mmp80) REVERT: A 1199 MET cc_start: 0.7683 (mmm) cc_final: 0.7466 (mmt) REVERT: B 431 GLU cc_start: 0.7861 (tp30) cc_final: 0.7264 (tp30) REVERT: B 460 TRP cc_start: 0.6690 (m100) cc_final: 0.6445 (m100) REVERT: B 500 ILE cc_start: 0.9067 (mt) cc_final: 0.8668 (mm) REVERT: B 592 SER cc_start: 0.8304 (t) cc_final: 0.8070 (p) REVERT: B 1021 SER cc_start: 0.8296 (m) cc_final: 0.7951 (p) REVERT: B 1023 MET cc_start: 0.8683 (tpt) cc_final: 0.8102 (tpt) REVERT: B 1065 THR cc_start: 0.6966 (t) cc_final: 0.6070 (m) REVERT: B 1115 PHE cc_start: 0.7119 (t80) cc_final: 0.6332 (t80) REVERT: B 1131 HIS cc_start: 0.7591 (m-70) cc_final: 0.5916 (t-170) REVERT: C 438 PHE cc_start: 0.6134 (p90) cc_final: 0.5662 (p90) REVERT: C 501 SER cc_start: 0.8133 (p) cc_final: 0.7793 (t) REVERT: C 527 MET cc_start: 0.8151 (ttm) cc_final: 0.7789 (ttm) REVERT: C 671 TRP cc_start: 0.7034 (t-100) cc_final: 0.6687 (t-100) REVERT: C 711 TYR cc_start: 0.7812 (t80) cc_final: 0.7576 (t80) REVERT: C 817 LYS cc_start: 0.8049 (mmpt) cc_final: 0.7719 (mmmt) REVERT: C 1020 PHE cc_start: 0.8090 (t80) cc_final: 0.7832 (t80) REVERT: C 1031 TYR cc_start: 0.3883 (p90) cc_final: 0.3134 (p90) REVERT: C 1130 ARG cc_start: 0.7245 (tpm170) cc_final: 0.5802 (tpt-90) REVERT: D 518 LEU cc_start: 0.8674 (mt) cc_final: 0.8407 (mt) REVERT: D 580 SER cc_start: 0.9335 (m) cc_final: 0.8732 (p) REVERT: D 594 ARG cc_start: 0.8531 (ttp80) cc_final: 0.8037 (ttp80) REVERT: D 629 MET cc_start: 0.7613 (ppp) cc_final: 0.6346 (mtp) REVERT: D 644 GLU cc_start: 0.7156 (mp0) cc_final: 0.6738 (tt0) REVERT: D 772 GLU cc_start: 0.5357 (mp0) cc_final: 0.4923 (mp0) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.1260 time to fit residues: 90.8673 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 : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [200, 73, 162, 131, 46, 130, 65, 222, 51, 196, 163] chunk 200 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 131 optimal weight: 0.0570 chunk 46 optimal weight: 10.0000 chunk 130 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 222 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 196 optimal weight: 0.6980 chunk 163 optimal weight: 9.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1159 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1078 GLN ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.128578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.102532 restraints weight = 39258.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105026 restraints weight = 23972.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.106706 restraints weight = 17527.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.107722 restraints weight = 14479.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108176 restraints weight = 12902.444| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5035 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= 0.126 Angle : 0.611 14.264 25999 Z= 0.311 Chirality : 0.041 0.237 2911 Planarity : 0.004 0.072 3188 Dihedral : 5.762 86.511 2601 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.17), residues: 2362 helix: 1.56 (0.14), residues: 1300 sheet: -1.65 (0.45), residues: 139 loop : -1.62 (0.18), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1036 TYR 0.020 0.001 TYR A 673 PHE 0.020 0.001 PHE B1200 TRP 0.026 0.002 TRP D1177 HIS 0.014 0.001 HIS D1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (19227) covalent geometry : angle 0.60539 / 0.31 (25975) SS BOND : bond 0.01016 / 0.73 ( 12) SS BOND : angle 2.77749 / 1.60 ( 24) hydrogen bonds : bond 0.03484 / 2.25 ( 958) hydrogen bonds : angle 3.84383 / 2.65 ( 2811) *********************** 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 450 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 0.746 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: 0.7832 (mt) cc_final: 0.7306 (pt) REVERT: A 476 ILE cc_start: 0.9075 (mt) cc_final: 0.8680 (pt) REVERT: A 511 LYS cc_start: 0.6970 (mttp) cc_final: 0.6345 (tptt) REVERT: A 629 MET cc_start: 0.3689 (mpp) cc_final: 0.3070 (tpt) REVERT: A 732 TYR cc_start: 0.7913 (m-10) cc_final: 0.7336 (m-80) REVERT: A 1008 GLN cc_start: 0.7760 (pt0) cc_final: 0.7476 (mt0) REVERT: A 1063 TRP cc_start: 0.7697 (m100) cc_final: 0.7441 (m-10) REVERT: B 431 GLU cc_start: 0.7851 (tp30) cc_final: 0.7329 (tp30) REVERT: B 500 ILE cc_start: 0.9082 (mt) cc_final: 0.8704 (mm) REVERT: B 519 ASP cc_start: 0.8442 (m-30) cc_final: 0.8108 (t70) REVERT: B 592 SER cc_start: 0.8211 (t) cc_final: 0.7939 (p) REVERT: B 1023 MET cc_start: 0.8751 (tpt) cc_final: 0.8159 (tpt) REVERT: B 1115 PHE cc_start: 0.7129 (t80) cc_final: 0.6408 (t80) REVERT: B 1119 LEU cc_start: 0.8911 (mt) cc_final: 0.8637 (mt) REVERT: B 1131 HIS cc_start: 0.7637 (m-70) cc_final: 0.5810 (t-170) REVERT: B 1156 ILE cc_start: 0.8549 (mm) cc_final: 0.8168 (mt) REVERT: C 414 MET cc_start: 0.5412 (ptt) cc_final: 0.4800 (tmm) REVERT: C 438 PHE cc_start: 0.5929 (p90) cc_final: 0.5490 (p90) REVERT: C 501 SER cc_start: 0.8181 (p) cc_final: 0.7845 (t) REVERT: C 817 LYS cc_start: 0.8082 (mmpt) cc_final: 0.7745 (mmmt) REVERT: C 1020 PHE cc_start: 0.8090 (t80) cc_final: 0.7814 (t80) REVERT: C 1031 TYR cc_start: 0.3705 (p90) cc_final: 0.2998 (p90) REVERT: C 1130 ARG cc_start: 0.7303 (tpm170) cc_final: 0.5793 (tpt-90) REVERT: C 1156 ILE cc_start: 0.8663 (mt) cc_final: 0.8382 (mp) REVERT: C 1179 PHE cc_start: 0.8651 (t80) cc_final: 0.8353 (t80) REVERT: D 425 CYS cc_start: 0.8012 (m) cc_final: 0.7764 (m) REVERT: D 518 LEU cc_start: 0.8604 (mt) cc_final: 0.8342 (mt) REVERT: D 580 SER cc_start: 0.9278 (m) cc_final: 0.8682 (p) REVERT: D 644 GLU cc_start: 0.7290 (mp0) cc_final: 0.6833 (tt0) REVERT: D 1199 MET cc_start: 0.7890 (mtp) cc_final: 0.7631 (mmm) outliers start: 0 outliers final: 0 residues processed: 450 average time/residue: 0.1198 time to fit residues: 85.3954 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 : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [162, 141, 108, 82, 131, 237, 77, 76, 154, 12, 98] chunk 162 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1159 ASN D1081 HIS D1159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102103 restraints weight = 39177.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.104564 restraints weight = 23750.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106199 restraints weight = 17321.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.107037 restraints weight = 14330.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.107310 restraints weight = 12852.606| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19239 Z= 0.145 Angle : 0.625 13.937 25999 Z= 0.322 Chirality : 0.041 0.225 2911 Planarity : 0.004 0.061 3188 Dihedral : 5.829 87.323 2601 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.17), residues: 2362 helix: 1.63 (0.14), residues: 1299 sheet: -1.54 (0.47), residues: 134 loop : -1.62 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 594 TYR 0.024 0.001 TYR B1031 PHE 0.024 0.001 PHE A1020 TRP 0.028 0.002 TRP D1177 HIS 0.005 0.001 HIS D1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (19227) covalent geometry : angle 0.62152 / 0.32 (25975) SS BOND : bond 0.01115 / 0.67 ( 12) SS BOND : angle 2.35886 / 1.40 ( 24) hydrogen bonds : bond 0.03585 / 2.31 ( 958) hydrogen bonds : angle 3.91640 / 2.71 ( 2811) *********************** 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 445 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7833 (mt) cc_final: 0.7306 (pt) REVERT: A 425 CYS cc_start: 0.8224 (p) cc_final: 0.7981 (p) REVERT: A 476 ILE cc_start: 0.9152 (mt) cc_final: 0.8690 (pt) REVERT: A 511 LYS cc_start: 0.6998 (mttp) cc_final: 0.6366 (tptt) REVERT: A 600 ILE cc_start: 0.9194 (mt) cc_final: 0.8798 (mm) REVERT: A 629 MET cc_start: 0.3756 (mpp) cc_final: 0.3178 (tpt) REVERT: A 732 TYR cc_start: 0.7939 (m-10) cc_final: 0.7456 (m-80) REVERT: A 770 LYS cc_start: 0.6254 (mmpt) cc_final: 0.6041 (mmmt) REVERT: A 1063 TRP cc_start: 0.7725 (m100) cc_final: 0.7488 (m-10) REVERT: B 431 GLU cc_start: 0.7845 (tp30) cc_final: 0.7377 (tp30) REVERT: B 500 ILE cc_start: 0.9087 (mt) cc_final: 0.8710 (mm) REVERT: B 592 SER cc_start: 0.8231 (t) cc_final: 0.7977 (p) REVERT: B 1023 MET cc_start: 0.8747 (tpt) cc_final: 0.8162 (tpt) REVERT: B 1115 PHE cc_start: 0.7100 (t80) cc_final: 0.6476 (t80) REVERT: B 1119 LEU cc_start: 0.8880 (mt) cc_final: 0.8664 (mt) REVERT: C 438 PHE cc_start: 0.5969 (p90) cc_final: 0.5541 (p90) REVERT: C 501 SER cc_start: 0.8186 (p) cc_final: 0.7868 (t) REVERT: C 629 MET cc_start: 0.3953 (tmm) cc_final: 0.3711 (tmm) REVERT: C 654 SER cc_start: 0.7789 (p) cc_final: 0.7296 (p) REVERT: C 674 MET cc_start: 0.7110 (mtt) cc_final: 0.6801 (mpp) REVERT: C 817 LYS cc_start: 0.8077 (mmpt) cc_final: 0.7753 (mmmt) REVERT: C 1020 PHE cc_start: 0.8101 (t80) cc_final: 0.7817 (t80) REVERT: C 1031 TYR cc_start: 0.3984 (p90) cc_final: 0.3348 (p90) REVERT: C 1156 ILE cc_start: 0.8664 (mt) cc_final: 0.8368 (mp) REVERT: D 407 MET cc_start: 0.7272 (mpp) cc_final: 0.6970 (mpp) REVERT: D 425 CYS cc_start: 0.8080 (m) cc_final: 0.7784 (m) REVERT: D 463 MET cc_start: 0.6484 (mtm) cc_final: 0.6256 (mtm) REVERT: D 518 LEU cc_start: 0.8613 (mt) cc_final: 0.8314 (mt) REVERT: D 580 SER cc_start: 0.9346 (m) cc_final: 0.8752 (p) REVERT: D 629 MET cc_start: 0.7648 (ppp) cc_final: 0.6391 (mtp) REVERT: D 644 GLU cc_start: 0.7270 (mp0) cc_final: 0.6837 (tt0) REVERT: D 772 GLU cc_start: 0.5666 (mp0) cc_final: 0.4979 (mp0) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.1229 time to fit residues: 86.7796 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 : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [192, 167, 60, 205, 35, 135, 100, 43, 9, 131, 183] chunk 192 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN B 412 HIS B1008 GLN B1159 ASN D 587 GLN D1159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.124568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100071 restraints weight = 39680.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101123 restraints weight = 25502.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.101650 restraints weight = 18468.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102238 restraints weight = 17850.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102363 restraints weight = 15880.050| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 19239 Z= 0.236 Angle : 0.728 15.080 25999 Z= 0.378 Chirality : 0.046 0.236 2911 Planarity : 0.005 0.064 3188 Dihedral : 6.261 92.002 2601 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.05 % Allowed : 1.35 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2362 helix: 1.10 (0.14), residues: 1304 sheet: -1.80 (0.46), residues: 134 loop : -1.77 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 628 TYR 0.032 0.002 TYR B1031 PHE 0.027 0.002 PHE A 623 TRP 0.038 0.002 TRP D 767 HIS 0.008 0.002 HIS D1081 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.24 (19227) covalent geometry : angle 0.72467 / 0.38 (25975) SS BOND : bond 0.00783 / 0.51 ( 12) SS BOND : angle 2.40993 / 1.37 ( 24) hydrogen bonds : bond 0.04249 / 2.76 ( 958) hydrogen bonds : angle 4.35862 / 3.02 ( 2811) *********************** 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 422 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 421 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7770 (mt) cc_final: 0.7385 (pt) REVERT: A 425 CYS cc_start: 0.8227 (p) cc_final: 0.7913 (p) REVERT: A 511 LYS cc_start: 0.7128 (mttp) cc_final: 0.6418 (tptt) REVERT: A 600 ILE cc_start: 0.9262 (mt) cc_final: 0.8977 (mm) REVERT: A 629 MET cc_start: 0.3799 (mpp) cc_final: 0.3258 (tpt) REVERT: A 732 TYR cc_start: 0.8136 (m-10) cc_final: 0.7842 (m-80) REVERT: A 770 LYS cc_start: 0.6287 (mmpt) cc_final: 0.6026 (mmmt) REVERT: B 412 HIS cc_start: 0.7019 (t70) cc_final: 0.6817 (t70) REVERT: B 431 GLU cc_start: 0.7817 (tp30) cc_final: 0.7466 (tp30) REVERT: B 500 ILE cc_start: 0.9062 (mt) cc_final: 0.8658 (mm) REVERT: B 592 SER cc_start: 0.8322 (t) cc_final: 0.8083 (p) REVERT: B 692 ARG cc_start: 0.6759 (ttt180) cc_final: 0.6362 (ptm160) REVERT: B 1008 GLN cc_start: 0.7398 (pt0) cc_final: 0.6937 (pt0) REVERT: B 1023 MET cc_start: 0.8647 (tpt) cc_final: 0.7962 (tpt) REVERT: B 1115 PHE cc_start: 0.7086 (t80) cc_final: 0.6416 (t80) REVERT: B 1131 HIS cc_start: 0.7717 (m-70) cc_final: 0.5877 (t-170) REVERT: C 414 MET cc_start: 0.7018 (ptp) cc_final: 0.4760 (ttt) REVERT: C 438 PHE cc_start: 0.6443 (p90) cc_final: 0.6136 (p90) REVERT: C 501 SER cc_start: 0.8313 (p) cc_final: 0.7927 (t) REVERT: C 629 MET cc_start: 0.4136 (tmm) cc_final: 0.3894 (tmm) REVERT: C 674 MET cc_start: 0.7050 (mtt) cc_final: 0.6831 (mpp) REVERT: C 715 ARG cc_start: 0.6816 (ttt180) cc_final: 0.6596 (ttm-80) REVERT: C 817 LYS cc_start: 0.8105 (mmpt) cc_final: 0.7749 (mmmt) REVERT: C 1009 MET cc_start: 0.8736 (tpt) cc_final: 0.8480 (tpp) REVERT: C 1020 PHE cc_start: 0.8087 (t80) cc_final: 0.7758 (t80) REVERT: C 1023 MET cc_start: 0.7515 (tpt) cc_final: 0.7298 (tpt) REVERT: C 1060 SER cc_start: 0.7830 (t) cc_final: 0.7514 (p) REVERT: D 407 MET cc_start: 0.7214 (mpp) cc_final: 0.6952 (mpp) REVERT: D 425 CYS cc_start: 0.7989 (m) cc_final: 0.7715 (m) REVERT: D 518 LEU cc_start: 0.8713 (mt) cc_final: 0.8349 (mt) REVERT: D 524 GLU cc_start: 0.8544 (mp0) cc_final: 0.8206 (mp0) REVERT: D 580 SER cc_start: 0.9407 (m) cc_final: 0.8897 (p) REVERT: D 587 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.7152 (mp-120) REVERT: D 629 MET cc_start: 0.7062 (ppp) cc_final: 0.6293 (mtp) REVERT: D 644 GLU cc_start: 0.7332 (mp0) cc_final: 0.6962 (tt0) outliers start: 1 outliers final: 0 residues processed: 422 average time/residue: 0.1224 time to fit residues: 81.9829 Evaluate side-chains 332 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 331 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [217, 196, 20, 205, 30, 93, 71, 102, 41, 92, 208] chunk 217 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 205 optimal weight: 5.9990 chunk 30 optimal weight: 0.0970 chunk 93 optimal weight: 0.0670 chunk 71 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 chunk 208 optimal weight: 6.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1198 HIS B1159 ASN C 435 HIS D 435 HIS D1159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.129956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.104033 restraints weight = 38734.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.106578 restraints weight = 23561.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108278 restraints weight = 17306.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.109065 restraints weight = 14261.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109921 restraints weight = 12851.903| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19239 Z= 0.120 Angle : 0.624 14.548 25999 Z= 0.318 Chirality : 0.041 0.209 2911 Planarity : 0.004 0.083 3188 Dihedral : 5.753 83.521 2601 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.17), residues: 2362 helix: 1.65 (0.15), residues: 1290 sheet: -1.64 (0.46), residues: 132 loop : -1.54 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 594 TYR 0.019 0.001 TYR A 533 PHE 0.025 0.001 PHE A1020 TRP 0.026 0.001 TRP D1177 HIS 0.007 0.002 HIS D 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (19227) covalent geometry : angle 0.62053 / 0.32 (25975) SS BOND : bond 0.00696 / 0.41 ( 12) SS BOND : angle 2.24097 / 1.27 ( 24) hydrogen bonds : bond 0.03490 / 2.24 ( 958) hydrogen bonds : angle 3.93032 / 2.72 ( 2811) ********************** 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 464 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 0.710 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: 0.7831 (mt) cc_final: 0.7368 (pt) REVERT: A 425 CYS cc_start: 0.8225 (p) cc_final: 0.7876 (p) REVERT: A 476 ILE cc_start: 0.9093 (mt) cc_final: 0.8717 (pt) REVERT: A 511 LYS cc_start: 0.6991 (mttp) cc_final: 0.6389 (tptt) REVERT: A 541 PHE cc_start: 0.8588 (t80) cc_final: 0.8326 (t80) REVERT: A 629 MET cc_start: 0.3658 (mpp) cc_final: 0.3143 (tpt) REVERT: A 732 TYR cc_start: 0.7738 (m-10) cc_final: 0.7395 (m-80) REVERT: A 760 ASP cc_start: 0.6594 (p0) cc_final: 0.6114 (t0) REVERT: A 1063 TRP cc_start: 0.7666 (m100) cc_final: 0.7418 (m-10) REVERT: A 1078 GLN cc_start: 0.7263 (tt0) cc_final: 0.6224 (mm-40) REVERT: B 431 GLU cc_start: 0.7766 (tp30) cc_final: 0.7332 (tp30) REVERT: B 500 ILE cc_start: 0.9066 (mt) cc_final: 0.8696 (mm) REVERT: B 519 ASP cc_start: 0.8302 (m-30) cc_final: 0.8097 (t70) REVERT: B 635 SER cc_start: 0.8612 (t) cc_final: 0.7988 (p) REVERT: B 1023 MET cc_start: 0.8699 (tpt) cc_final: 0.8091 (tpt) REVERT: B 1115 PHE cc_start: 0.6944 (t80) cc_final: 0.6272 (t80) REVERT: B 1131 HIS cc_start: 0.7511 (m-70) cc_final: 0.5948 (t-170) REVERT: C 438 PHE cc_start: 0.6024 (p90) cc_final: 0.5593 (p90) REVERT: C 501 SER cc_start: 0.8360 (p) cc_final: 0.7976 (t) REVERT: C 674 MET cc_start: 0.6997 (mtt) cc_final: 0.6767 (mpp) REVERT: C 715 ARG cc_start: 0.6850 (ttt180) cc_final: 0.6635 (ttm-80) REVERT: C 817 LYS cc_start: 0.8066 (mmpt) cc_final: 0.7740 (mmmt) REVERT: C 1156 ILE cc_start: 0.8620 (mt) cc_final: 0.8364 (mp) REVERT: D 422 GLU cc_start: 0.6898 (pp20) cc_final: 0.6596 (pm20) REVERT: D 425 CYS cc_start: 0.8128 (m) cc_final: 0.7789 (m) REVERT: D 518 LEU cc_start: 0.8534 (mt) cc_final: 0.8279 (mt) REVERT: D 580 SER cc_start: 0.9259 (m) cc_final: 0.8630 (p) REVERT: D 629 MET cc_start: 0.7576 (ppp) cc_final: 0.6464 (mtp) REVERT: D 644 GLU cc_start: 0.7172 (mp0) cc_final: 0.6859 (tt0) REVERT: D 649 THR cc_start: 0.8861 (p) cc_final: 0.8471 (t) REVERT: D 772 GLU cc_start: 0.5713 (mp0) cc_final: 0.5110 (mp0) outliers start: 0 outliers final: 0 residues processed: 464 average time/residue: 0.1185 time to fit residues: 87.6300 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 : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [28, 231, 75, 0, 236, 224, 1, 82, 194, 219, 16] chunk 28 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 236 optimal weight: 0.0270 chunk 224 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN A1198 HIS B1159 ASN D1159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.129679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103462 restraints weight = 39317.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.106086 restraints weight = 24009.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.107792 restraints weight = 17572.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108851 restraints weight = 14485.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.109352 restraints weight = 12888.819| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19239 Z= 0.124 Angle : 0.621 14.426 25999 Z= 0.318 Chirality : 0.041 0.205 2911 Planarity : 0.004 0.082 3188 Dihedral : 5.658 84.855 2601 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.17), residues: 2362 helix: 1.67 (0.14), residues: 1295 sheet: -1.53 (0.46), residues: 134 loop : -1.48 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 594 TYR 0.020 0.001 TYR B1031 PHE 0.022 0.001 PHE B1020 TRP 0.024 0.002 TRP C1063 HIS 0.008 0.001 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (19227) covalent geometry : angle 0.61776 / 0.32 (25975) SS BOND : bond 0.00712 / 0.42 ( 12) SS BOND : angle 2.16708 / 1.19 ( 24) hydrogen bonds : bond 0.03492 / 2.26 ( 958) hydrogen bonds : angle 3.94707 / 2.74 ( 2811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3350.93 seconds wall clock time: 58 minutes 35.27 seconds (3515.27 seconds total)