Starting phenix.real_space_refine on Mon Sep 30 11:17:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuh_43530/09_2024/8vuh_43530_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuh_43530/09_2024/8vuh_43530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuh_43530/09_2024/8vuh_43530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuh_43530/09_2024/8vuh_43530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuh_43530/09_2024/8vuh_43530_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuh_43530/09_2024/8vuh_43530_neut.cif" } resolution = 4.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 16046 2.51 5 N 4408 2.21 5 O 4601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 25161 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 5691 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 33, 'TRANS': 753} Chain breaks: 2 Unresolved non-hydrogen bonds: 555 Unresolved non-hydrogen angles: 705 Unresolved non-hydrogen dihedrals: 463 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 9, 'TRP:plan': 4, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 24, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 346 Chain: "B" Number of atoms: 5498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 5498 Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 198} Link IDs: {'PTRANS': 30, 'TRANS': 750} Chain breaks: 2 Unresolved non-hydrogen bonds: 711 Unresolved non-hydrogen angles: 910 Unresolved non-hydrogen dihedrals: 593 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 11, 'TRP:plan': 5, 'ASP:plan': 22, 'PHE:plan': 13, 'GLU:plan': 26, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 436 Chain: "C" Number of atoms: 5457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 5457 Classifications: {'peptide': 788} Incomplete info: {'truncation_to_alanine': 215} Link IDs: {'PTRANS': 33, 'TRANS': 754} Chain breaks: 2 Unresolved non-hydrogen bonds: 804 Unresolved non-hydrogen angles: 1007 Unresolved non-hydrogen dihedrals: 671 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 5, 'ASP:plan': 17, 'PHE:plan': 9, 'GLU:plan': 35, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 491 Chain: "D" Number of atoms: 5359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5359 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 248} Link IDs: {'PTRANS': 30, 'TRANS': 748} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 838 Unresolved non-hydrogen angles: 1068 Unresolved non-hydrogen dihedrals: 690 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 19, 'TRP:plan': 4, 'ASP:plan': 29, 'PHE:plan': 13, 'GLU:plan': 25, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 490 Chain: "H" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 867 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 110} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 773 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "L" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 792 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 102} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "M" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 724 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 102} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 53 Time building chain proxies: 15.77, per 1000 atoms: 0.63 Number of scatterers: 25161 At special positions: 0 Unit cell: (136.96, 203.728, 190.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 106 16.00 O 4601 8.00 N 4408 7.00 C 16046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 779 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.02 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " distance=2.04 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 780 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.04 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 779 " distance=2.03 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 455 " distance=2.02 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 725 " - pdb=" SG CYS D 780 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 251 " - pdb=" SG CYS I 325 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS M 251 " - pdb=" SG CYS M 320 " 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: 6.94 Conformation dependent library (CDL) restraints added in 3.8 seconds 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6678 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 46 sheets defined 37.1% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 103 through 114 removed outlier: 4.079A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.698A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 156 removed outlier: 3.735A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 183 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.645A pdb=" N LEU A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 237 removed outlier: 4.049A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 4.000A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.958A pdb=" N ALA A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 582 removed outlier: 8.654A pdb=" N THR A 561 " --> pdb=" O PRO A 557 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 582 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 591 removed outlier: 3.854A pdb=" N PHE A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 598 Processing helix chain 'A' and resid 607 through 639 Processing helix chain 'A' and resid 650 through 655 removed outlier: 3.637A pdb=" N ARG A 654 " --> pdb=" O ASP A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 677 Processing helix chain 'A' and resid 680 through 689 removed outlier: 3.559A pdb=" N TYR A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 689 " --> pdb=" O ARG A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 704 Processing helix chain 'A' and resid 714 through 724 Processing helix chain 'A' and resid 750 through 763 removed outlier: 4.634A pdb=" N SER A 756 " --> pdb=" O ASN A 752 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN A 763 " --> pdb=" O LYS A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 774 Processing helix chain 'A' and resid 781 through 783 No H-bonds generated for 'chain 'A' and resid 781 through 783' Processing helix chain 'A' and resid 784 through 798 removed outlier: 4.188A pdb=" N VAL A 788 " --> pdb=" O ASN A 784 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 798 " --> pdb=" O GLY A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 813 Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.737A pdb=" N LEU B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 90 Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.553A pdb=" N HIS B 119 " --> pdb=" O PHE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 166 removed outlier: 3.691A pdb=" N TYR B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B 166 " --> pdb=" O MET B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 194 removed outlier: 4.280A pdb=" N ASP B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 220 Processing helix chain 'B' and resid 233 through 246 Processing helix chain 'B' and resid 287 through 311 Processing helix chain 'B' and resid 458 through 472 Processing helix chain 'B' and resid 496 through 502 removed outlier: 3.597A pdb=" N VAL B 500 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 520 removed outlier: 3.855A pdb=" N GLU B 520 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 578 removed outlier: 4.120A pdb=" N MET B 561 " --> pdb=" O VAL B 557 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 removed outlier: 4.066A pdb=" N VAL B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE B 593 " --> pdb=" O TRP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 635 Processing helix chain 'B' and resid 652 through 657 Processing helix chain 'B' and resid 669 through 678 removed outlier: 3.998A pdb=" N ASN B 673 " --> pdb=" O SER B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 686 removed outlier: 3.671A pdb=" N THR B 686 " --> pdb=" O HIS B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 703 removed outlier: 4.014A pdb=" N THR B 702 " --> pdb=" O VAL B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 721 Processing helix chain 'B' and resid 722 through 726 removed outlier: 4.125A pdb=" N LYS B 726 " --> pdb=" O GLU B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 766 Processing helix chain 'B' and resid 767 through 776 Processing helix chain 'B' and resid 790 through 814 removed outlier: 3.826A pdb=" N PHE B 794 " --> pdb=" O MET B 790 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B 795 " --> pdb=" O ALA B 791 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP B 810 " --> pdb=" O ILE B 806 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 814 " --> pdb=" O TRP B 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 Processing helix chain 'C' and resid 70 through 83 Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.727A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 159 removed outlier: 3.607A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER C 159 " --> pdb=" O MET C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 188 removed outlier: 4.059A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 225 through 236 removed outlier: 3.562A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.582A pdb=" N ILE C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER C 255 " --> pdb=" O ARG C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 255' Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 277 through 297 removed outlier: 3.946A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 327 removed outlier: 3.812A pdb=" N PHE C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 499 through 504 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.932A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 580 Processing helix chain 'C' and resid 584 through 595 Processing helix chain 'C' and resid 607 through 638 Processing helix chain 'C' and resid 650 through 655 Processing helix chain 'C' and resid 669 through 676 removed outlier: 3.855A pdb=" N TYR C 673 " --> pdb=" O SER C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 689 removed outlier: 3.641A pdb=" N LYS C 689 " --> pdb=" O ARG C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 703 removed outlier: 3.840A pdb=" N ARG C 703 " --> pdb=" O ILE C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 724 removed outlier: 3.609A pdb=" N LYS C 724 " --> pdb=" O GLU C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 764 removed outlier: 4.557A pdb=" N ASN C 752 " --> pdb=" O PRO C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 764 through 774 removed outlier: 4.159A pdb=" N ASP C 768 " --> pdb=" O GLY C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 812 Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.571A pdb=" N SER D 91 " --> pdb=" O CYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 119 removed outlier: 3.688A pdb=" N MET D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 133 removed outlier: 3.711A pdb=" N MET D 133 " --> pdb=" O GLY D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 164 Processing helix chain 'D' and resid 179 through 193 Processing helix chain 'D' and resid 213 through 220 Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.851A pdb=" N SER D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 4.404A pdb=" N SER D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 310 removed outlier: 3.722A pdb=" N LYS D 309 " --> pdb=" O SER D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 338 removed outlier: 3.929A pdb=" N PHE D 337 " --> pdb=" O THR D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 448 removed outlier: 4.314A pdb=" N GLU D 448 " --> pdb=" O SER D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 471 Processing helix chain 'D' and resid 497 through 502 Processing helix chain 'D' and resid 556 through 578 Processing helix chain 'D' and resid 580 through 594 Processing helix chain 'D' and resid 603 through 633 removed outlier: 4.105A pdb=" N SER D 607 " --> pdb=" O LYS D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 652 removed outlier: 4.046A pdb=" N ARG D 652 " --> pdb=" O LYS D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 678 Processing helix chain 'D' and resid 680 through 685 removed outlier: 4.137A pdb=" N TYR D 684 " --> pdb=" O TYR D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 689 removed outlier: 4.152A pdb=" N ASN D 689 " --> pdb=" O THR D 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 686 through 689' Processing helix chain 'D' and resid 692 through 702 removed outlier: 3.663A pdb=" N THR D 702 " --> pdb=" O VAL D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 722 removed outlier: 3.810A pdb=" N TYR D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 765 Processing helix chain 'D' and resid 766 through 776 removed outlier: 3.747A pdb=" N GLU D 770 " --> pdb=" O GLY D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 782 removed outlier: 3.778A pdb=" N HIS D 781 " --> pdb=" O GLY D 778 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASN D 782 " --> pdb=" O ILE D 779 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 778 through 782' Processing helix chain 'D' and resid 786 through 814 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'M' and resid 311 through 315 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 66 removed outlier: 7.197A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168 removed outlier: 6.590A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 271 removed outlier: 4.982A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 340 removed outlier: 4.065A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 412 removed outlier: 3.855A pdb=" N CYS A 455 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 434 " --> pdb=" O CYS A 455 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA7, first strand: chain 'A' and resid 709 through 713 removed outlier: 3.781A pdb=" N ILE A 540 " --> pdb=" O THR A 730 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 40 removed outlier: 3.745A pdb=" N LEU B 40 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 124 through 125 removed outlier: 6.355A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 173 removed outlier: 7.617A pdb=" N PHE B 170 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL B 203 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 172 " --> pdb=" O VAL B 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 256 through 257 removed outlier: 6.606A pdb=" N VAL B 257 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N TYR B 281 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY B 376 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL B 365 " --> pdb=" O LYS B 374 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LYS B 374 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB4, first strand: chain 'B' and resid 409 through 410 removed outlier: 3.569A pdb=" N THR B 410 " --> pdb=" O TYR B 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 418 through 419 Processing sheet with id=AB6, first strand: chain 'B' and resid 440 through 441 Processing sheet with id=AB7, first strand: chain 'B' and resid 530 through 531 removed outlier: 3.678A pdb=" N THR B 739 " --> pdb=" O THR B 531 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 533 through 535 Processing sheet with id=AB9, first strand: chain 'C' and resid 27 through 28 removed outlier: 6.844A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 64 through 65 removed outlier: 6.961A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 91 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 194 through 196 removed outlier: 6.280A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 248 through 249 removed outlier: 4.103A pdb=" N VAL C 249 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C 269 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C 362 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 397 through 398 Processing sheet with id=AC5, first strand: chain 'C' and resid 401 through 402 Processing sheet with id=AC6, first strand: chain 'C' and resid 409 through 411 Processing sheet with id=AC7, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AC8, first strand: chain 'C' and resid 534 through 535 removed outlier: 4.232A pdb=" N LYS C 534 " --> pdb=" O PHE C 739 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 662 through 664 removed outlier: 6.913A pdb=" N ALA C 663 " --> pdb=" O ILE C 711 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N ASP C 713 " --> pdb=" O ALA C 663 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU C 538 " --> pdb=" O GLU C 732 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLU C 732 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE C 540 " --> pdb=" O THR C 730 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 542 " --> pdb=" O VAL C 728 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL C 728 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 227 through 228 removed outlier: 6.799A pdb=" N ILE D 227 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP D 255 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N VAL D 279 " --> pdb=" O TRP D 255 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 342 through 343 Processing sheet with id=AD3, first strand: chain 'D' and resid 406 through 410 removed outlier: 7.687A pdb=" N LEU D 406 " --> pdb=" O ASP D 476 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N TYR D 478 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE D 408 " --> pdb=" O TYR D 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 418 through 419 Processing sheet with id=AD5, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AD6, first strand: chain 'D' and resid 522 through 523 Processing sheet with id=AD7, first strand: chain 'D' and resid 534 through 537 removed outlier: 3.716A pdb=" N ILE D 709 " --> pdb=" O GLY D 663 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD9, first strand: chain 'H' and resid 58 through 60 removed outlier: 4.847A pdb=" N TRP H 34 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP H 99 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP H 106 " --> pdb=" O VAL H 100 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 39 through 40 Processing sheet with id=AE2, first strand: chain 'I' and resid 232 through 236 Processing sheet with id=AE3, first strand: chain 'I' and resid 276 through 281 removed outlier: 5.417A pdb=" N TRP I 277 " --> pdb=" O ARG I 268 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG I 268 " --> pdb=" O TRP I 277 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY I 279 " --> pdb=" O TRP I 266 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 297 through 302 Processing sheet with id=AE5, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.990A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'L' and resid 21 through 23 Processing sheet with id=AE7, first strand: chain 'L' and resid 46 through 50 removed outlier: 6.713A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 233 through 234 Processing sheet with id=AE9, first strand: chain 'M' and resid 239 through 240 removed outlier: 6.622A pdb=" N TRP M 265 " --> pdb=" O VAL M 277 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 239 through 240 1013 hydrogen bonds defined for protein. 2892 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: 9.34 Time building geometry restraints manager: 8.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.50: 15488 1.50 - 1.79: 10116 1.79 - 2.08: 102 2.08 - 2.38: 0 2.38 - 2.67: 1 Bond restraints: 25707 Sorted by residual: bond pdb=" C ILE C 272 " pdb=" N ASN C 273 " ideal model delta sigma weight residual 1.333 2.668 -1.335 1.45e-02 4.76e+03 8.47e+03 bond pdb=" C PRO C 142 " pdb=" N PRO C 143 " ideal model delta sigma weight residual 1.334 2.029 -0.695 2.34e-02 1.83e+03 8.83e+02 bond pdb=" C PHE C 348 " pdb=" N ALA C 349 " ideal model delta sigma weight residual 1.332 1.255 0.077 1.40e-02 5.10e+03 3.05e+01 bond pdb=" CB PRO D 57 " pdb=" CG PRO D 57 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.88e+00 bond pdb=" C SER B 278 " pdb=" N VAL B 279 " ideal model delta sigma weight residual 1.329 1.294 0.035 2.31e-02 1.87e+03 2.32e+00 ... (remaining 25702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.66: 35138 6.66 - 13.33: 26 13.33 - 19.99: 2 19.99 - 26.66: 1 26.66 - 33.32: 1 Bond angle restraints: 35168 Sorted by residual: angle pdb=" O PHE C 348 " pdb=" C PHE C 348 " pdb=" N ALA C 349 " ideal model delta sigma weight residual 122.09 88.77 33.32 1.83e+00 2.99e-01 3.32e+02 angle pdb=" CA PHE C 348 " pdb=" C PHE C 348 " pdb=" N ALA C 349 " ideal model delta sigma weight residual 117.49 139.46 -21.97 1.62e+00 3.81e-01 1.84e+02 angle pdb=" CA ILE C 272 " pdb=" C ILE C 272 " pdb=" N ASN C 273 " ideal model delta sigma weight residual 116.19 100.77 15.42 1.32e+00 5.74e-01 1.37e+02 angle pdb=" O ILE C 272 " pdb=" C ILE C 272 " pdb=" N ASN C 273 " ideal model delta sigma weight residual 122.93 134.92 -11.99 1.06e+00 8.90e-01 1.28e+02 angle pdb=" C PHE C 348 " pdb=" N ALA C 349 " pdb=" CA ALA C 349 " ideal model delta sigma weight residual 121.54 141.02 -19.48 1.91e+00 2.74e-01 1.04e+02 ... (remaining 35163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13816 17.93 - 35.86: 1079 35.86 - 53.79: 178 53.79 - 71.72: 24 71.72 - 89.64: 13 Dihedral angle restraints: 15110 sinusoidal: 4758 harmonic: 10352 Sorted by residual: dihedral pdb=" CB CYS C 436 " pdb=" SG CYS C 436 " pdb=" SG CYS C 455 " pdb=" CB CYS C 455 " ideal model delta sinusoidal sigma weight residual 93.00 -178.52 -88.48 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS D 725 " pdb=" SG CYS D 725 " pdb=" SG CYS D 780 " pdb=" CB CYS D 780 " ideal model delta sinusoidal sigma weight residual -86.00 -167.33 81.33 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS D 436 " pdb=" SG CYS D 436 " pdb=" SG CYS D 456 " pdb=" CB CYS D 456 " ideal model delta sinusoidal sigma weight residual 93.00 169.27 -76.27 1 1.00e+01 1.00e-02 7.32e+01 ... (remaining 15107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2855 0.040 - 0.080: 948 0.080 - 0.121: 311 0.121 - 0.161: 37 0.161 - 0.201: 3 Chirality restraints: 4154 Sorted by residual: chirality pdb=" CA THR C 105 " pdb=" N THR C 105 " pdb=" C THR C 105 " pdb=" CB THR C 105 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE B 313 " pdb=" CA ILE B 313 " pdb=" CG1 ILE B 313 " pdb=" CG2 ILE B 313 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CB ILE A 220 " pdb=" CA ILE A 220 " pdb=" CG1 ILE A 220 " pdb=" CG2 ILE A 220 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.15e-01 ... (remaining 4151 not shown) Planarity restraints: 4539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO C 142 " -0.062 2.00e-02 2.50e+03 1.02e-01 1.05e+02 pdb=" C PRO C 142 " 0.177 2.00e-02 2.50e+03 pdb=" O PRO C 142 " -0.072 2.00e-02 2.50e+03 pdb=" N PRO C 143 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 348 " -0.063 2.00e-02 2.50e+03 9.94e-02 9.88e+01 pdb=" C PHE C 348 " 0.172 2.00e-02 2.50e+03 pdb=" O PHE C 348 " -0.046 2.00e-02 2.50e+03 pdb=" N ALA C 349 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 272 " -0.035 2.00e-02 2.50e+03 7.18e-02 5.16e+01 pdb=" C ILE C 272 " 0.122 2.00e-02 2.50e+03 pdb=" O ILE C 272 " -0.062 2.00e-02 2.50e+03 pdb=" N ASN C 273 " -0.024 2.00e-02 2.50e+03 ... (remaining 4536 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 341 2.60 - 3.17: 23121 3.17 - 3.75: 39884 3.75 - 4.32: 49145 4.32 - 4.90: 79534 Nonbonded interactions: 192025 Sorted by model distance: nonbonded pdb=" CD1 LEU C 76 " pdb=" N MET D 324 " model vdw 2.020 3.540 nonbonded pdb=" N GLY B 275 " pdb=" O LEU B 366 " model vdw 2.108 3.120 nonbonded pdb=" O PHE B 115 " pdb=" OG SER B 118 " model vdw 2.110 3.040 nonbonded pdb=" CD1 LEU C 76 " pdb=" CB MET D 324 " model vdw 2.110 3.860 nonbonded pdb=" O VAL B 535 " pdb=" OG1 THR B 729 " model vdw 2.148 3.040 ... (remaining 192020 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 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 46 or (resid 47 through 49 and (na \ me N or name CA or name C or name O or name CB )) or resid 50 through 54 or (res \ id 55 through 60 and (name N or name CA or name C or name O or name CB )) or res \ id 61 through 62 or (resid 63 through 66 and (name N or name CA or name C or nam \ e O or name CB )) or resid 67 through 80 or (resid 81 and (name N or name CA or \ name C or name O or name CB )) or resid 82 or (resid 83 and (name N or name CA o \ r name C or name O or name CB )) or resid 84 through 85 or (resid 86 and (name N \ or name CA or name C or name O or name CB )) or resid 87 through 152 or (resid \ 153 and (name N or name CA or name C or name O or name CB )) or resid 154 throug \ h 182 or (resid 183 and (name N or name CA or name C or name O or name CB )) or \ resid 184 or (resid 185 through 188 and (name N or name CA or name C or name O o \ r name CB )) or resid 189 or (resid 190 through 193 and (name N or name CA or na \ me C or name O or name CB )) or resid 194 through 208 or (resid 209 and (name N \ or name CA or name C or name O or name CB )) or resid 210 through 214 or (resid \ 215 through 216 and (name N or name CA or name C or name O or name CB )) or resi \ d 217 through 251 or (resid 252 through 253 and (name N or name CA or name C or \ name O or name CB )) or resid 254 through 259 or (resid 260 and (name N or name \ CA or name C or name O or name CB )) or resid 261 through 274 or (resid 275 and \ (name N or name CA or name C or name O or name CB )) or resid 276 through 293 or \ (resid 294 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 5 through 305 or (resid 306 and (name N or name CA or name C or name O or name C \ B )) or resid 307 through 308 or (resid 309 and (name N or name CA or name C or \ name O or name CB )) or resid 310 through 315 or (resid 316 and (name N or name \ CA or name C or name O or name CB )) or resid 317 through 328 or (resid 329 and \ (name N or name CA or name C or name O or name CB )) or resid 330 through 336 or \ (resid 337 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 8 through 353 or (resid 354 and (name N or name CA or name C or name O or name C \ B )) or resid 355 through 357 or resid 359 or (resid 360 and (name N or name CA \ or name C or name O or name CB )) or resid 361 through 362 or (resid 363 and (na \ me N or name CA or name C or name O or name CB )) or resid 364 through 370 or (r \ esid 371 and (name N or name CA or name C or name O or name CB )) or resid 372 t \ hrough 375 or (resid 376 and (name N or name CA or name C or name O or name CB ) \ ) or resid 377 through 384 or (resid 385 and (name N or name CA or name C or nam \ e O or name CB )) or resid 386 or (resid 387 through 388 and (name N or name CA \ or name C or name O or name CB )) or resid 389 or (resid 390 and (name N or name \ CA or name C or name O or name CB )) or resid 391 through 393 or (resid 394 and \ (name N or name CA or name C or name O or name CB )) or resid 395 through 411 o \ r (resid 412 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 13 through 414 or (resid 415 through 417 and (name N or name CA or name C or nam \ e O or name CB )) or resid 418 through 420 or (resid 421 through 423 and (name N \ or name CA or name C or name O or name CB )) or resid 424 through 425 or (resid \ 426 through 427 and (name N or name CA or name C or name O or name CB )) or res \ id 428 through 440 or (resid 441 through 443 and (name N or name CA or name C or \ name O or name CB )) or resid 444 through 445 or (resid 446 and (name N or name \ CA or name C or name O or name CB )) or resid 447 through 449 or (resid 450 and \ (name N or name CA or name C or name O or name CB )) or resid 451 through 464 o \ r (resid 465 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 66 through 487 or (resid 488 through 489 and (name N or name CA or name C or nam \ e O or name CB )) or resid 490 or (resid 491 through 492 and (name N or name CA \ or name C or name O or name CB )) or resid 493 through 510 or (resid 511 and (na \ me N or name CA or name C or name O or name CB )) or resid 512 through 535 or (r \ esid 536 and (name N or name CA or name C or name O or name CB )) or resid 537 t \ hrough 542 or (resid 543 and (name N or name CA or name C or name O or name CB ) \ ) or resid 544 through 550 or (resid 551 through 556 and (name N or name CA or n \ ame C or name O or name CB )) or resid 557 through 572 or (resid 573 through 582 \ and (name N or name CA or name C or name O or name CB )) or resid 583 or (resid \ 584 through 592 and (name N or name CA or name C or name O or name CB )) or res \ id 593 through 606 or (resid 607 through 613 and (name N or name CA or name C or \ name O or name CB )) or (resid 614 through 628 and (name N or name CA or name C \ or name O or name CB )) or resid 629 through 630 or (resid 631 through 640 and \ (name N or name CA or name C or name O or name CB )) or resid 641 through 644 or \ (resid 645 through 646 and (name N or name CA or name C or name O or name CB )) \ or resid 647 through 656 or (resid 657 through 659 and (name N or name CA or na \ me C or name O or name CB )) or resid 660 through 663 or (resid 664 through 667 \ and (name N or name CA or name C or name O or name CB )) or resid 668 through 67 \ 4 or (resid 675 and (name N or name CA or name C or name O or name CB )) or resi \ d 676 through 686 or (resid 687 through 688 and (name N or name CA or name C or \ name O or name CB )) or resid 689 through 704 or (resid 705 and (name N or name \ CA or name C or name O or name CB )) or resid 706 through 712 or (resid 713 and \ (name N or name CA or name C or name O or name CB )) or resid 714 through 722 or \ (resid 723 through 724 and (name N or name CA or name C or name O or name CB )) \ or resid 725 through 731 or (resid 732 and (name N or name CA or name C or name \ O or name CB )) or resid 733 through 744 or (resid 745 through 746 and (name N \ or name CA or name C or name O or name CB )) or resid 747 through 750 or (resid \ 751 and (name N or name CA or name C or name O or name CB )) or resid 752 throug \ h 761 or (resid 762 and (name N or name CA or name C or name O or name CB )) or \ resid 763 through 767 or (resid 768 and (name N or name CA or name C or name O o \ r name CB )) or resid 769 through 802 or (resid 803 through 813 and (name N or n \ ame CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 27 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 169 or (resid 170 and (name N or n \ ame CA or name C or name O or name CB )) or resid 171 through 197 or (resid 198 \ and (name N or name CA or name C or name O or name CB )) or resid 199 through 21 \ 2 or (resid 213 and (name N or name CA or name C or name O or name CB )) or resi \ d 214 through 258 or (resid 259 through 260 and (name N or name CA or name C or \ name O or name CB )) or resid 261 through 298 or (resid 299 through 300 and (nam \ e N or name CA or name C or name O or name CB )) or resid 301 through 322 or (re \ sid 323 and (name N or name CA or name C or name O or name CB )) or resid 324 th \ rough 357 or resid 359 through 447 or (resid 448 through 450 and (name N or name \ CA or name C or name O or name CB )) or resid 451 through 494 or (resid 495 and \ (name N or name CA or name C or name O or name CB )) or resid 496 through 560 o \ r (resid 561 through 566 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 567 through 582 and (name N or name CA or name C or name O or name C \ B )) or resid 583 through 584 or (resid 585 through 592 and (name N or name CA o \ r name C or name O or name CB )) or (resid 593 through 598 and (name N or name C \ A or name C or name O or name CB )) or resid 599 through 611 or (resid 612 throu \ gh 613 and (name N or name CA or name C or name O or name CB )) or (resid 614 th \ rough 628 and (name N or name CA or name C or name O or name CB )) or resid 629 \ through 631 or (resid 632 through 640 and (name N or name CA or name C or name O \ or name CB )) or resid 641 through 643 or (resid 644 through 646 and (name N or \ name CA or name C or name O or name CB )) or resid 647 through 723 or (resid 72 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 725 through \ 729 or (resid 730 and (name N or name CA or name C or name O or name CB )) or re \ sid 731 through 813)) } ncs_group { reference = (chain 'B' and (resid 35 through 42 or (resid 43 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 75 or (resid 76 through \ 78 and (name N or name CA or name C or name O or name CB )) or resid 79 through \ 90 or (resid 91 and (name N or name CA or name C or name O or name CB )) or (re \ sid 92 through 96 and (name N or name CA or name C or name O or name CB )) or re \ sid 97 through 104 or (resid 105 through 108 and (name N or name CA or name C or \ name O or name CB )) or resid 109 through 113 or (resid 114 and (name N or name \ CA or name C or name O or name CB )) or resid 115 through 132 or (resid 133 and \ (name N or name CA or name C or name O or name CB )) or resid 134 through 136 o \ r (resid 137 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 38 or (resid 139 and (name N or name CA or name C or name O or name CB )) or res \ id 140 through 149 or resid 151 through 192 or (resid 193 and (name N or name CA \ or name C or name O or name CB )) or resid 194 through 198 or (resid 199 and (n \ ame N or name CA or name C or name O or name CB )) or resid 200 through 201 or ( \ resid 202 and (name N or name CA or name C or name O or name CB )) or resid 203 \ through 206 or (resid 207 through 209 and (name N or name CA or name C or name O \ or name CB )) or resid 210 through 213 or (resid 214 and (name N or name CA or \ name C or name O or name CB )) or resid 215 through 263 or (resid 264 and (name \ N or name CA or name C or name O or name CB )) or resid 265 through 270 or (resi \ d 271 and (name N or name CA or name C or name O or name CB )) or resid 272 thro \ ugh 284 or (resid 285 and (name N or name CA or name C or name O or name CB )) o \ r resid 286 or (resid 287 and (name N or name CA or name C or name O or name CB \ )) or resid 288 through 303 or (resid 304 through 309 and (name N or name CA or \ name C or name O or name CB )) or resid 310 or (resid 311 and (name N or name CA \ or name C or name O or name CB )) or resid 312 through 316 or (resid 317 throug \ h 319 and (name N or name CA or name C or name O or name CB )) or resid 320 or ( \ resid 321 and (name N or name CA or name C or name O or name CB )) or resid 322 \ through 330 or (resid 331 through 333 and (name N or name CA or name C or name O \ or name CB )) or resid 334 through 338 or (resid 339 and (name N or name CA or \ name C or name O or name CB )) or resid 340 through 367 or (resid 368 through 36 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 370 or (resi \ d 371 and (name N or name CA or name C or name O or name CB )) or resid 372 thro \ ugh 381 or (resid 382 and (name N or name CA or name C or name O or name CB )) o \ r resid 383 through 388 or (resid 389 and (name N or name CA or name C or name O \ or name CB )) or resid 390 through 394 or (resid 395 and (name N or name CA or \ name C or name O or name CB )) or resid 396 through 398 or (resid 399 through 40 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 408 through \ 411 or (resid 412 through 414 and (name N or name CA or name C or name O or name \ CB )) or resid 415 through 424 or (resid 425 through 428 and (name N or name CA \ or name C or name O or name CB )) or resid 429 through 430 or (resid 431 and (n \ ame N or name CA or name C or name O or name CB )) or resid 432 through 437 or ( \ resid 438 and (name N or name CA or name C or name O or name CB )) or resid 439 \ or (resid 440 through 448 and (name N or name CA or name C or name O or name CB \ )) or resid 449 or (resid 450 and (name N or name CA or name C or name O or name \ CB )) or resid 451 through 469 or (resid 470 and (name N or name CA or name C o \ r name O or name CB )) or resid 471 through 480 or (resid 481 through 482 and (n \ ame N or name CA or name C or name O or name CB )) or resid 483 or (resid 484 an \ d (name N or name CA or name C or name O or name CB )) or resid 485 through 510 \ or (resid 511 and (name N or name CA or name C or name O or name CB )) or resid \ 512 through 515 or (resid 516 and (name N or name CA or name C or name O or name \ CB )) or resid 517 through 519 or (resid 520 and (name N or name CA or name C o \ r name O or name CB )) or resid 521 through 522 or (resid 523 and (name N or nam \ e CA or name C or name O or name CB )) or resid 524 or (resid 525 and (name N or \ name CA or name C or name O or name CB )) or resid 526 through 537 or (resid 53 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 539 through \ 540 or (resid 541 and (name N or name CA or name C or name O or name CB )) or re \ sid 542 through 579 or (resid 580 through 581 and (name N or name CA or name C o \ r name O or name CB )) or (resid 582 through 587 and (name N or name CA or name \ C or name O or name CB )) or resid 588 through 590 or (resid 591 through 597 and \ (name N or name CA or name C or name O or name CB )) or resid 598 through 606 o \ r (resid 607 through 609 and (name N or name CA or name C or name O or name CB ) \ ) or resid 610 through 618 or (resid 619 through 621 and (name N or name CA or n \ ame C or name O or name CB )) or resid 622 through 624 or (resid 625 and (name N \ or name CA or name C or name O or name CB )) or resid 626 through 627 or (resid \ 628 through 633 and (name N or name CA or name C or name O or name CB )) or res \ id 634 through 640 or (resid 641 through 643 and (name N or name CA or name C or \ name O or name CB )) or resid 644 or (resid 645 through 649 and (name N or name \ CA or name C or name O or name CB )) or resid 650 through 663 or (resid 664 thr \ ough 665 and (name N or name CA or name C or name O or name CB )) or resid 666 t \ hrough 669 or (resid 670 through 671 and (name N or name CA or name C or name O \ or name CB )) or resid 672 through 674 or (resid 675 through 677 and (name N or \ name CA or name C or name O or name CB )) or resid 678 through 682 or (resid 683 \ and (name N or name CA or name C or name O or name CB )) or resid 684 through 6 \ 85 or (resid 686 through 687 and (name N or name CA or name C or name O or name \ CB )) or resid 688 through 710 or (resid 711 through 713 and (name N or name CA \ or name C or name O or name CB )) or resid 714 through 733 or (resid 734 and (na \ me N or name CA or name C or name O or name CB )) or resid 735 through 766 or (r \ esid 767 and (name N or name CA or name C or name O or name CB )) or resid 768 t \ hrough 771 or (resid 772 through 774 and (name N or name CA or name C or name O \ or name CB )) or resid 775 through 780 or (resid 781 through 791 and (name N or \ name CA or name C or name O or name CB )) or resid 792 through 793 or (resid 794 \ through 814 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 35 through 44 or (resid 45 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 103 or (resid 104 throu \ gh 108 and (name N or name CA or name C or name O or name CB )) or resid 109 thr \ ough 181 or (resid 182 and (name N or name CA or name C or name O or name CB )) \ or resid 183 through 210 or (resid 211 and (name N or name CA or name C or name \ O or name CB )) or resid 212 through 223 or (resid 224 and (name N or name CA or \ name C or name O or name CB )) or resid 225 through 233 or (resid 234 through 2 \ 36 and (name N or name CA or name C or name O or name CB )) or resid 237 through \ 241 or (resid 242 through 243 and (name N or name CA or name C or name O or nam \ e CB )) or resid 244 through 282 or (resid 283 and (name N or name CA or name C \ or name O or name CB )) or resid 284 through 325 or (resid 326 and (name N or na \ me CA or name C or name O or name CB )) or resid 327 through 343 or (resid 344 a \ nd (name N or name CA or name C or name O or name CB )) or resid 345 through 351 \ or (resid 352 through 353 and (name N or name CA or name C or name O or name CB \ )) or resid 354 through 412 or (resid 413 through 414 and (name N or name CA or \ name C or name O or name CB )) or resid 415 through 427 or (resid 428 and (name \ N or name CA or name C or name O or name CB )) or resid 429 through 471 or (res \ id 472 and (name N or name CA or name C or name O or name CB )) or resid 473 or \ (resid 474 and (name N or name CA or name C or name O or name CB )) or resid 475 \ through 535 or (resid 536 and (name N or name CA or name C or name O or name CB \ )) or resid 537 through 553 or (resid 554 through 581 and (name N or name CA or \ name C or name O or name CB )) or resid 582 through 616 or (resid 617 through 6 \ 21 and (name N or name CA or name C or name O or name CB )) or resid 622 through \ 651 or (resid 652 and (name N or name CA or name C or name O or name CB )) or r \ esid 653 through 655 or (resid 656 through 657 and (name N or name CA or name C \ or name O or name CB )) or resid 658 through 670 or (resid 671 and (name N or na \ me CA or name C or name O or name CB )) or resid 672 through 689 or (resid 690 t \ hrough 691 and (name N or name CA or name C or name O or name CB )) or (resid 69 \ 2 through 696 and (name N or name CA or name C or name O or name CB )) or resid \ 697 through 700 or (resid 701 through 702 and (name N or name CA or name C or na \ me O or name CB )) or resid 703 through 704 or (resid 705 through 707 and (name \ N or name CA or name C or name O or name CB )) or resid 708 through 752 or (resi \ d 753 and (name N or name CA or name C or name O or name CB )) or resid 754 thro \ ugh 773 or (resid 774 and (name N or name CA or name C or name O or name CB )) o \ r resid 775 through 776 or (resid 777 and (name N or name CA or name C or name O \ or name CB )) or resid 778 or (resid 779 and (name N or name CA or name C or na \ me O or name CB )) or resid 780 through 781 or (resid 782 through 791 and (name \ N or name CA or name C or name O or name CB )) or resid 792 through 794 or (resi \ d 795 through 814 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'H' and ((resid 2 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 10 or (resid 11 through 13 and (name N or name CA \ or name C or name O or name CB )) or resid 14 or (resid 15 through 16 and (name \ N or name CA or name C or name O or name CB )) or resid 17 or (resid 18 through \ 21 and (name N or name CA or name C or name O or name CB )) or resid 22 or (res \ id 23 through 25 and (name N or name CA or name C or name O or name CB )) or res \ id 26 through 27 or (resid 28 through 32 and (name N or name CA or name C or nam \ e O or name CB )) or resid 33 through 35 or (resid 36 and (name N or name CA or \ name C or name O or name CB )) or resid 37 or (resid 38 and (name N or name CA o \ r name C or name O or name CB )) or resid 39 or (resid 40 and (name N or name CA \ or name C or name O or name CB )) or resid 41 through 43 or (resid 44 and (name \ N or name CA or name C or name O or name CB )) or resid 45 through 62 or (resid \ 63 through 65 and (name N or name CA or name C or name O or name CB )) or resid \ 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or res \ id 68 through 72 or (resid 73 and (name N or name CA or name C or name O or name \ CB )) or resid 74 through 75 or (resid 76 and (name N or name CA or name C or n \ ame O or name CB )) or resid 77 through 81 or (resid 82 through 93 and (name N o \ r name CA or name C or name O or name CB )) or resid 94 through 103 or (resid 10 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 105 through \ 113 or (resid 114 through 118 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'I' and (resid 231 through 241 or (resid 242 and (name N or name CA or na \ me C or name O or name CB )) or resid 243 through 275 or (resid 276 and (name N \ or name CA or name C or name O or name CB )) or resid 277 through 336 or (resid \ 337 and (name N or name CA or name C or name O or name CB )) or resid 338 throug \ h 347)) } ncs_group { reference = (chain 'L' and (resid 1 through 2 or (resid 3 and (name N or name CA or name C o \ r name O or name CB )) or resid 4 or (resid 5 through 6 and (name N or name CA o \ r name C or name O or name CB )) or resid 7 or (resid 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 28 or (resid 29 through 30 a \ nd (name N or name CA or name C or name O or name CB )) or resid 31 through 54 o \ r (resid 55 and (name N or name CA or name C or name O or name CB )) or resid 56 \ or (resid 57 and (name N or name CA or name C or name O or name CB )) or resid \ 58 or (resid 59 and (name N or name CA or name C or name O or name CB )) or resi \ d 60 through 61 or (resid 62 and (name N or name CA or name C or name O or name \ CB )) or resid 63 through 67 or (resid 68 and (name N or name CA or name C or na \ me O or name CB )) or resid 69 through 70 or (resid 71 and (name N or name CA or \ name C or name O or name CB )) or resid 72 through 75 or (resid 76 and (name N \ or name CA or name C or name O or name CB )) or resid 77 or (resid 78 and (name \ N or name CA or name C or name O or name CB )) or resid 79 through 80 or (resid \ 81 through 84 and (name N or name CA or name C or name O or name CB )) or resid \ 85 or (resid 86 through 88 and (name N or name CA or name C or name O or name CB \ )) or resid 89 through 91 or (resid 92 and (name N or name CA or name C or name \ O or name CB )) or resid 93 through 94 or (resid 95 and (name N or name CA or n \ ame C or name O or name CB )) or resid 96 through 98 or (resid 99 and (name N or \ name CA or name C or name O or name CB )) or resid 100 through 104 or (resid 10 \ 5 through 106 and (name N or name CA or name C or name O or name CB )) or resid \ 107 through 109)) selection = (chain 'M' and (resid 230 through 280 or (resid 281 through 284 and (name N or n \ ame CA or name C or name O or name CB )) or resid 285 through 289 or (resid 290 \ through 291 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 2 through 338)) } 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: 5.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.120 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 59.170 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4672 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 : 0.010 1.335 25707 Z= 0.711 Angle : 0.729 33.323 35168 Z= 0.393 Chirality : 0.044 0.201 4154 Planarity : 0.005 0.167 4539 Dihedral : 13.202 89.644 8372 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.98 % Favored : 86.71 % Rotamer: Outliers : 0.05 % Allowed : 4.86 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.14), residues: 3545 helix: 1.31 (0.16), residues: 1153 sheet: -2.02 (0.24), residues: 460 loop : -2.67 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 160 HIS 0.005 0.001 HIS A 53 PHE 0.020 0.002 PHE B 794 TYR 0.026 0.002 TYR B 478 ARG 0.006 0.001 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 233 time to evaluate : 2.877 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: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8110 (tpt) cc_final: 0.7819 (tpt) REVERT: A 128 TYR cc_start: 0.8561 (m-10) cc_final: 0.8209 (m-10) REVERT: A 209 MET cc_start: 0.7982 (pmm) cc_final: 0.7624 (pmm) REVERT: A 215 GLU cc_start: 0.6413 (pp20) cc_final: 0.5741 (pp20) REVERT: A 501 MET cc_start: 0.6664 (tpt) cc_final: 0.6363 (tpt) REVERT: B 133 MET cc_start: 0.8733 (mpp) cc_final: 0.8363 (mpp) REVERT: B 331 MET cc_start: 0.2420 (pmm) cc_final: 0.2055 (pmm) REVERT: B 420 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7212 (tm-30) REVERT: D 610 MET cc_start: 0.8640 (ppp) cc_final: 0.8355 (ppp) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.3185 time to fit residues: 123.5380 Evaluate side-chains 192 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 298 optimal weight: 10.0000 chunk 267 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 180 optimal weight: 30.0000 chunk 142 optimal weight: 9.9990 chunk 276 optimal weight: 7.9990 chunk 107 optimal weight: 0.0060 chunk 168 optimal weight: 10.0000 chunk 205 optimal weight: 0.7980 chunk 320 optimal weight: 6.9990 overall best weight: 3.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS B 111 GLN B 381 HIS B 673 ASN ** B 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 ASN C 171 HIS ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS D 146 GLN H 105 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4693 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25707 Z= 0.251 Angle : 0.650 10.555 35168 Z= 0.337 Chirality : 0.044 0.232 4154 Planarity : 0.004 0.050 4539 Dihedral : 5.087 29.173 3782 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.93 % Favored : 86.81 % Rotamer: Outliers : 0.05 % Allowed : 8.10 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 3549 helix: 1.40 (0.15), residues: 1173 sheet: -1.98 (0.24), residues: 463 loop : -2.69 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 315 HIS 0.011 0.001 HIS D 85 PHE 0.020 0.002 PHE B 416 TYR 0.018 0.002 TYR B 478 ARG 0.006 0.001 ARG B 437 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 2.740 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8044 (tpt) cc_final: 0.7696 (tpt) REVERT: A 128 TYR cc_start: 0.8580 (m-10) cc_final: 0.8191 (m-10) REVERT: A 192 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8348 (tm-30) REVERT: A 215 GLU cc_start: 0.6544 (pp20) cc_final: 0.5636 (tm-30) REVERT: A 321 PHE cc_start: 0.4505 (m-80) cc_final: 0.4244 (m-80) REVERT: A 501 MET cc_start: 0.6943 (tpt) cc_final: 0.6693 (tpt) REVERT: A 660 PHE cc_start: 0.7671 (m-80) cc_final: 0.6987 (m-80) REVERT: B 133 MET cc_start: 0.8625 (mpp) cc_final: 0.8256 (mpp) REVERT: B 194 SER cc_start: 0.8516 (m) cc_final: 0.8049 (p) REVERT: B 256 ILE cc_start: 0.6700 (OUTLIER) cc_final: 0.6436 (mt) REVERT: B 420 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7289 (tm-30) REVERT: D 112 MET cc_start: 0.0364 (ptt) cc_final: -0.2550 (mtt) REVERT: D 166 ASP cc_start: 0.7636 (t70) cc_final: 0.7385 (t0) REVERT: D 610 MET cc_start: 0.8664 (ppp) cc_final: 0.8390 (ppp) outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.3253 time to fit residues: 125.7756 Evaluate side-chains 195 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 178 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 266 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 321 optimal weight: 3.9990 chunk 346 optimal weight: 50.0000 chunk 286 optimal weight: 10.0000 chunk 318 optimal weight: 6.9990 chunk 109 optimal weight: 0.2980 chunk 257 optimal weight: 9.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 ASN B 673 ASN ** B 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN ** H 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4705 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25707 Z= 0.273 Angle : 0.673 10.253 35168 Z= 0.349 Chirality : 0.045 0.207 4154 Planarity : 0.005 0.062 4539 Dihedral : 5.207 28.508 3782 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.02 % Favored : 86.70 % Rotamer: Outliers : 0.14 % Allowed : 7.02 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.14), residues: 3549 helix: 1.28 (0.15), residues: 1180 sheet: -1.92 (0.24), residues: 460 loop : -2.80 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 198 HIS 0.009 0.001 HIS D 168 PHE 0.022 0.002 PHE B 310 TYR 0.019 0.002 TYR B 180 ARG 0.009 0.001 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 235 time to evaluate : 2.514 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8080 (tpt) cc_final: 0.7713 (tpt) REVERT: A 128 TYR cc_start: 0.8616 (m-10) cc_final: 0.8213 (m-10) REVERT: A 158 TYR cc_start: 0.7882 (m-80) cc_final: 0.7665 (m-80) REVERT: A 192 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8355 (tm-30) REVERT: A 215 GLU cc_start: 0.6701 (pp20) cc_final: 0.5834 (tm-30) REVERT: A 321 PHE cc_start: 0.4468 (m-80) cc_final: 0.3853 (m-80) REVERT: A 326 MET cc_start: 0.7955 (mpp) cc_final: 0.7723 (mpp) REVERT: A 394 MET cc_start: 0.9060 (mmp) cc_final: 0.7577 (ttt) REVERT: A 501 MET cc_start: 0.6908 (tpt) cc_final: 0.6623 (tpt) REVERT: A 743 MET cc_start: 0.2125 (mmm) cc_final: 0.1735 (mmm) REVERT: B 133 MET cc_start: 0.8664 (mpp) cc_final: 0.8337 (mpp) REVERT: B 194 SER cc_start: 0.8541 (m) cc_final: 0.8061 (p) REVERT: B 418 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.7736 (tp) REVERT: B 420 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7282 (tm-30) REVERT: D 112 MET cc_start: 0.0794 (ptt) cc_final: -0.2138 (mtt) REVERT: D 166 ASP cc_start: 0.7797 (t70) cc_final: 0.7548 (t0) REVERT: D 610 MET cc_start: 0.8756 (ppp) cc_final: 0.8501 (ppp) outliers start: 3 outliers final: 0 residues processed: 238 average time/residue: 0.3528 time to fit residues: 141.5897 Evaluate side-chains 198 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 317 optimal weight: 0.0030 chunk 241 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 153 optimal weight: 50.0000 chunk 215 optimal weight: 5.9990 chunk 322 optimal weight: 50.0000 chunk 341 optimal weight: 30.0000 chunk 168 optimal weight: 8.9990 chunk 305 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN ** B 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN H 105 ASN ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4648 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25707 Z= 0.200 Angle : 0.630 10.495 35168 Z= 0.322 Chirality : 0.044 0.206 4154 Planarity : 0.004 0.049 4539 Dihedral : 5.031 26.395 3782 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.78 % Favored : 87.94 % Rotamer: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.14), residues: 3549 helix: 1.43 (0.15), residues: 1189 sheet: -1.85 (0.24), residues: 473 loop : -2.77 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 381 HIS 0.004 0.001 HIS C 761 PHE 0.020 0.001 PHE B 195 TYR 0.018 0.001 TYR B 180 ARG 0.008 0.001 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 243 time to evaluate : 2.665 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8021 (tpt) cc_final: 0.7635 (tpt) REVERT: A 128 TYR cc_start: 0.8513 (m-10) cc_final: 0.8039 (m-10) REVERT: A 158 TYR cc_start: 0.7834 (m-80) cc_final: 0.7537 (m-80) REVERT: A 192 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8453 (tm-30) REVERT: A 209 MET cc_start: 0.7886 (pmm) cc_final: 0.7620 (pmm) REVERT: A 215 GLU cc_start: 0.6580 (pp20) cc_final: 0.5936 (pp20) REVERT: A 321 PHE cc_start: 0.4855 (m-80) cc_final: 0.4382 (m-80) REVERT: A 394 MET cc_start: 0.9042 (mmp) cc_final: 0.7551 (ttt) REVERT: A 501 MET cc_start: 0.6849 (tpt) cc_final: 0.6601 (tpt) REVERT: A 660 PHE cc_start: 0.7762 (m-10) cc_final: 0.7528 (m-80) REVERT: B 112 MET cc_start: 0.8083 (mmp) cc_final: 0.7598 (mmm) REVERT: B 133 MET cc_start: 0.8730 (mpp) cc_final: 0.8437 (mpp) REVERT: B 194 SER cc_start: 0.8521 (m) cc_final: 0.8106 (p) REVERT: B 420 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7292 (tm-30) REVERT: C 125 MET cc_start: -0.3272 (mmp) cc_final: -0.3697 (mmp) REVERT: D 112 MET cc_start: 0.1042 (ptt) cc_final: -0.1860 (mtt) REVERT: D 280 SER cc_start: 0.4166 (m) cc_final: 0.3916 (p) REVERT: D 610 MET cc_start: 0.8764 (ppp) cc_final: 0.8510 (ppp) outliers start: 1 outliers final: 0 residues processed: 244 average time/residue: 0.3236 time to fit residues: 130.8968 Evaluate side-chains 200 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 284 optimal weight: 30.0000 chunk 193 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 254 optimal weight: 0.0980 chunk 140 optimal weight: 0.0870 chunk 291 optimal weight: 8.9990 chunk 235 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 174 optimal weight: 0.0570 chunk 306 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN ** H 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4622 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25707 Z= 0.182 Angle : 0.623 10.308 35168 Z= 0.316 Chirality : 0.044 0.195 4154 Planarity : 0.004 0.061 4539 Dihedral : 4.929 26.919 3782 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.52 % Favored : 88.19 % Rotamer: Outliers : 0.05 % Allowed : 4.14 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.15), residues: 3549 helix: 1.56 (0.15), residues: 1183 sheet: -1.83 (0.24), residues: 463 loop : -2.69 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 315 HIS 0.005 0.001 HIS B 128 PHE 0.015 0.001 PHE B 794 TYR 0.016 0.001 TYR B 180 ARG 0.011 0.000 ARG A 736 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 2.675 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7988 (tpt) cc_final: 0.7598 (tpt) REVERT: A 128 TYR cc_start: 0.8519 (m-10) cc_final: 0.8081 (m-10) REVERT: A 192 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8477 (tm-30) REVERT: A 215 GLU cc_start: 0.7095 (pp20) cc_final: 0.6406 (tm-30) REVERT: A 237 MET cc_start: 0.9250 (mmm) cc_final: 0.8416 (ptm) REVERT: A 394 MET cc_start: 0.9040 (mmp) cc_final: 0.7511 (ttt) REVERT: A 501 MET cc_start: 0.6903 (tpt) cc_final: 0.6676 (mmm) REVERT: B 133 MET cc_start: 0.8789 (mpp) cc_final: 0.8528 (mpp) REVERT: B 194 SER cc_start: 0.8558 (m) cc_final: 0.8061 (p) REVERT: B 420 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7288 (tm-30) REVERT: C 125 MET cc_start: -0.3219 (mmp) cc_final: -0.3531 (mmp) REVERT: D 112 MET cc_start: 0.0983 (ptt) cc_final: -0.1936 (mtt) REVERT: D 280 SER cc_start: 0.4307 (m) cc_final: 0.4026 (p) REVERT: D 610 MET cc_start: 0.8753 (ppp) cc_final: 0.8494 (ppp) outliers start: 1 outliers final: 0 residues processed: 240 average time/residue: 0.3255 time to fit residues: 128.6564 Evaluate side-chains 204 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 114 optimal weight: 0.7980 chunk 307 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 200 optimal weight: 0.0050 chunk 84 optimal weight: 8.9990 chunk 341 optimal weight: 4.9990 chunk 283 optimal weight: 20.0000 chunk 158 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 179 optimal weight: 0.0370 overall best weight: 1.9676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS H 59 ASN H 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4621 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25707 Z= 0.186 Angle : 0.622 10.416 35168 Z= 0.315 Chirality : 0.044 0.189 4154 Planarity : 0.004 0.057 4539 Dihedral : 4.863 25.064 3782 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.72 % Favored : 88.00 % Rotamer: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.15), residues: 3549 helix: 1.62 (0.15), residues: 1189 sheet: -1.77 (0.24), residues: 473 loop : -2.73 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 381 HIS 0.006 0.001 HIS D 119 PHE 0.021 0.001 PHE B 195 TYR 0.028 0.001 TYR B 180 ARG 0.005 0.000 ARG C 654 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 2.525 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: symmetry clash REVERT: A 41 MET cc_start: 0.7978 (tpt) cc_final: 0.7585 (tpt) REVERT: A 128 TYR cc_start: 0.8534 (m-10) cc_final: 0.8092 (m-10) REVERT: A 192 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8499 (tm-30) REVERT: A 215 GLU cc_start: 0.7283 (pp20) cc_final: 0.6515 (tm-30) REVERT: A 237 MET cc_start: 0.9251 (mmm) cc_final: 0.8396 (ptm) REVERT: A 321 PHE cc_start: 0.4547 (m-80) cc_final: 0.4283 (m-80) REVERT: A 394 MET cc_start: 0.9025 (mmp) cc_final: 0.7502 (ttt) REVERT: B 133 MET cc_start: 0.8838 (mpp) cc_final: 0.8570 (mpp) REVERT: B 194 SER cc_start: 0.8468 (m) cc_final: 0.8048 (p) REVERT: B 420 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7219 (tm-30) REVERT: C 125 MET cc_start: -0.3191 (mmp) cc_final: -0.3492 (mmp) REVERT: D 112 MET cc_start: 0.1066 (ptt) cc_final: -0.1725 (mtt) REVERT: D 280 SER cc_start: 0.4186 (m) cc_final: 0.3908 (p) REVERT: D 561 MET cc_start: -0.0346 (mmp) cc_final: -0.1270 (ptt) REVERT: D 564 MET cc_start: -0.2528 (ttt) cc_final: -0.3252 (mtt) REVERT: D 610 MET cc_start: 0.8766 (ppp) cc_final: 0.8507 (ppp) outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.3590 time to fit residues: 144.2617 Evaluate side-chains 204 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 329 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 287 optimal weight: 1.9990 chunk 190 optimal weight: 30.0000 chunk 340 optimal weight: 30.0000 chunk 212 optimal weight: 20.0000 chunk 207 optimal weight: 0.9980 chunk 157 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS H 59 ASN ** H 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4659 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25707 Z= 0.213 Angle : 0.645 10.227 35168 Z= 0.327 Chirality : 0.044 0.184 4154 Planarity : 0.004 0.070 4539 Dihedral : 4.913 26.665 3782 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.06 % Favored : 87.66 % Rotamer: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.15), residues: 3549 helix: 1.58 (0.15), residues: 1183 sheet: -1.75 (0.24), residues: 485 loop : -2.71 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 315 HIS 0.005 0.001 HIS C 761 PHE 0.014 0.001 PHE C 458 TYR 0.022 0.001 TYR B 180 ARG 0.005 0.000 ARG D 244 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 2.864 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 41 MET cc_start: 0.8000 (tpt) cc_final: 0.7626 (tpt) REVERT: A 128 TYR cc_start: 0.8516 (m-10) cc_final: 0.8049 (m-10) REVERT: A 215 GLU cc_start: 0.7371 (pp20) cc_final: 0.6604 (tm-30) REVERT: A 237 MET cc_start: 0.9273 (mmm) cc_final: 0.8457 (ptm) REVERT: A 321 PHE cc_start: 0.4852 (m-80) cc_final: 0.4513 (m-80) REVERT: A 394 MET cc_start: 0.9021 (mmp) cc_final: 0.7455 (ttt) REVERT: A 501 MET cc_start: 0.7036 (mmm) cc_final: 0.6671 (tpt) REVERT: A 743 MET cc_start: 0.3174 (mmm) cc_final: 0.2954 (mmm) REVERT: B 133 MET cc_start: 0.8830 (mpp) cc_final: 0.8576 (mpp) REVERT: B 194 SER cc_start: 0.8610 (m) cc_final: 0.8012 (p) REVERT: B 420 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7204 (tm-30) REVERT: C 125 MET cc_start: -0.3176 (mmp) cc_final: -0.3407 (mmp) REVERT: D 112 MET cc_start: 0.1324 (ptt) cc_final: -0.1561 (mtt) REVERT: D 280 SER cc_start: 0.4343 (m) cc_final: 0.4042 (p) REVERT: D 338 MET cc_start: -0.2043 (mpp) cc_final: -0.2587 (mpp) REVERT: D 561 MET cc_start: -0.0313 (mmp) cc_final: -0.1222 (ptt) REVERT: D 564 MET cc_start: -0.2492 (ttt) cc_final: -0.3257 (mtt) REVERT: D 610 MET cc_start: 0.8850 (ppp) cc_final: 0.8580 (ppp) outliers start: 1 outliers final: 0 residues processed: 236 average time/residue: 0.3214 time to fit residues: 126.6744 Evaluate side-chains 198 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 210 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 216 optimal weight: 10.0000 chunk 231 optimal weight: 0.0670 chunk 168 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 267 optimal weight: 10.0000 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 ASN ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4586 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25707 Z= 0.169 Angle : 0.628 10.455 35168 Z= 0.314 Chirality : 0.044 0.183 4154 Planarity : 0.004 0.062 4539 Dihedral : 4.770 25.001 3782 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.02 % Favored : 88.70 % Rotamer: Outliers : 0.05 % Allowed : 1.94 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.15), residues: 3549 helix: 1.69 (0.15), residues: 1187 sheet: -1.85 (0.24), residues: 478 loop : -2.66 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 381 HIS 0.005 0.001 HIS D 387 PHE 0.034 0.001 PHE A 408 TYR 0.029 0.001 TYR B 710 ARG 0.007 0.000 ARG C 676 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 2.705 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 41 MET cc_start: 0.7950 (tpt) cc_final: 0.7546 (tpt) REVERT: A 128 TYR cc_start: 0.8481 (m-10) cc_final: 0.8040 (m-10) REVERT: A 215 GLU cc_start: 0.7285 (pp20) cc_final: 0.6482 (tm-30) REVERT: A 237 MET cc_start: 0.9236 (mmm) cc_final: 0.8392 (ptm) REVERT: A 321 PHE cc_start: 0.4769 (m-80) cc_final: 0.4488 (m-80) REVERT: A 326 MET cc_start: 0.7943 (mpp) cc_final: 0.7729 (mpp) REVERT: A 394 MET cc_start: 0.8979 (mmp) cc_final: 0.7486 (ttt) REVERT: A 743 MET cc_start: 0.2869 (mmm) cc_final: 0.2581 (mmm) REVERT: B 133 MET cc_start: 0.8888 (mpp) cc_final: 0.8687 (mpp) REVERT: B 194 SER cc_start: 0.8500 (m) cc_final: 0.8005 (p) REVERT: B 420 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7250 (tm-30) REVERT: C 125 MET cc_start: -0.3076 (mmp) cc_final: -0.3604 (mmp) REVERT: C 237 MET cc_start: 0.3344 (mtp) cc_final: 0.1926 (mmm) REVERT: D 112 MET cc_start: 0.1209 (ptt) cc_final: -0.1546 (mtt) REVERT: D 280 SER cc_start: 0.4543 (m) cc_final: 0.4139 (p) REVERT: D 338 MET cc_start: -0.2388 (mpp) cc_final: -0.2618 (mpp) REVERT: D 561 MET cc_start: -0.0408 (mmp) cc_final: -0.1255 (ptt) REVERT: D 564 MET cc_start: -0.2373 (ttt) cc_final: -0.3111 (mtt) REVERT: D 610 MET cc_start: 0.8860 (ppp) cc_final: 0.8591 (ppp) outliers start: 1 outliers final: 0 residues processed: 255 average time/residue: 0.3352 time to fit residues: 141.8478 Evaluate side-chains 200 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 309 optimal weight: 30.0000 chunk 325 optimal weight: 50.0000 chunk 297 optimal weight: 9.9990 chunk 317 optimal weight: 0.3980 chunk 190 optimal weight: 1.9990 chunk 138 optimal weight: 0.0570 chunk 248 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 286 optimal weight: 6.9990 chunk 299 optimal weight: 8.9990 chunk 315 optimal weight: 20.0000 overall best weight: 3.6904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 HIS ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4682 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25707 Z= 0.246 Angle : 0.674 10.348 35168 Z= 0.342 Chirality : 0.045 0.194 4154 Planarity : 0.004 0.063 4539 Dihedral : 4.996 26.708 3782 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.12 % Favored : 87.60 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 3549 helix: 1.52 (0.15), residues: 1185 sheet: -1.79 (0.24), residues: 468 loop : -2.68 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 255 HIS 0.011 0.001 HIS A 162 PHE 0.027 0.002 PHE A 533 TYR 0.020 0.002 TYR B 180 ARG 0.010 0.001 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.801 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: symmetry clash REVERT: A 41 MET cc_start: 0.8012 (tpt) cc_final: 0.7643 (tpt) REVERT: A 215 GLU cc_start: 0.7411 (pp20) cc_final: 0.6562 (tm-30) REVERT: A 237 MET cc_start: 0.9293 (mmm) cc_final: 0.8476 (ptm) REVERT: A 321 PHE cc_start: 0.4891 (m-80) cc_final: 0.4549 (m-80) REVERT: A 394 MET cc_start: 0.9012 (mmp) cc_final: 0.7431 (ttt) REVERT: B 133 MET cc_start: 0.8791 (mpp) cc_final: 0.8540 (mpp) REVERT: B 194 SER cc_start: 0.8487 (m) cc_final: 0.8020 (p) REVERT: B 420 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7177 (tm-30) REVERT: C 125 MET cc_start: -0.3091 (mmp) cc_final: -0.3572 (mmp) REVERT: C 237 MET cc_start: 0.3212 (mtp) cc_final: 0.1673 (mmm) REVERT: D 112 MET cc_start: 0.1269 (ptt) cc_final: -0.1530 (mtt) REVERT: D 280 SER cc_start: 0.4548 (m) cc_final: 0.4325 (p) REVERT: D 338 MET cc_start: -0.2557 (mpp) cc_final: -0.2778 (mpp) REVERT: D 561 MET cc_start: -0.0365 (mmp) cc_final: -0.1209 (ptt) REVERT: D 564 MET cc_start: -0.2150 (ttt) cc_final: -0.2914 (mtt) REVERT: D 610 MET cc_start: 0.8966 (ppp) cc_final: 0.8712 (ppp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.3041 time to fit residues: 117.2243 Evaluate side-chains 198 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 208 optimal weight: 20.0000 chunk 335 optimal weight: 8.9990 chunk 204 optimal weight: 9.9990 chunk 159 optimal weight: 40.0000 chunk 233 optimal weight: 7.9990 chunk 351 optimal weight: 50.0000 chunk 323 optimal weight: 0.0980 chunk 280 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 216 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN ** H 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4691 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25707 Z= 0.240 Angle : 0.681 10.375 35168 Z= 0.346 Chirality : 0.045 0.191 4154 Planarity : 0.004 0.089 4539 Dihedral : 5.112 28.800 3782 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.14 % Favored : 87.57 % Rotamer: Outliers : 0.05 % Allowed : 0.59 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3549 helix: 1.44 (0.15), residues: 1182 sheet: -1.89 (0.23), residues: 502 loop : -2.72 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 315 HIS 0.006 0.001 HIS B 682 PHE 0.030 0.002 PHE A 529 TYR 0.033 0.002 TYR A 109 ARG 0.014 0.001 ARG A 685 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7098 Ramachandran restraints generated. 3549 Oldfield, 0 Emsley, 3549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 2.825 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 41 MET cc_start: 0.8028 (tpt) cc_final: 0.7646 (tpt) REVERT: A 128 TYR cc_start: 0.8449 (m-10) cc_final: 0.7978 (m-10) REVERT: A 215 GLU cc_start: 0.7430 (pp20) cc_final: 0.6671 (tm-30) REVERT: A 321 PHE cc_start: 0.4920 (m-80) cc_final: 0.4675 (m-80) REVERT: A 394 MET cc_start: 0.9025 (mmp) cc_final: 0.7415 (ttt) REVERT: B 133 MET cc_start: 0.8760 (mpp) cc_final: 0.8517 (mpp) REVERT: B 194 SER cc_start: 0.8470 (m) cc_final: 0.8058 (p) REVERT: B 420 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7282 (tm-30) REVERT: C 125 MET cc_start: -0.3156 (mmp) cc_final: -0.3525 (mmp) REVERT: C 237 MET cc_start: 0.3099 (mtp) cc_final: 0.1495 (mmm) REVERT: D 112 MET cc_start: 0.1215 (ptt) cc_final: -0.1493 (mtt) REVERT: D 280 SER cc_start: 0.4514 (m) cc_final: 0.4289 (p) REVERT: D 561 MET cc_start: -0.0278 (mmp) cc_final: -0.1096 (ptt) REVERT: D 564 MET cc_start: -0.2090 (ttt) cc_final: -0.2880 (mtt) REVERT: D 610 MET cc_start: 0.8998 (ppp) cc_final: 0.8748 (ppp) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.3308 time to fit residues: 125.4723 Evaluate side-chains 192 residues out of total 3119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 222 optimal weight: 4.9990 chunk 298 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 258 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 280 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 288 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 HIS ** C 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.160086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.123362 restraints weight = 167326.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.121208 restraints weight = 144868.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.122930 restraints weight = 121693.881| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25707 Z= 0.230 Angle : 0.670 10.129 35168 Z= 0.340 Chirality : 0.044 0.188 4154 Planarity : 0.004 0.055 4539 Dihedral : 5.077 27.283 3782 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.98 % Favored : 87.74 % Rotamer: Outliers : 0.05 % Allowed : 0.45 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3549 helix: 1.50 (0.15), residues: 1178 sheet: -1.88 (0.23), residues: 501 loop : -2.72 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 381 HIS 0.006 0.001 HIS A 404 PHE 0.025 0.002 PHE A 533 TYR 0.021 0.001 TYR B 180 ARG 0.010 0.001 ARG A 675 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5338.69 seconds wall clock time: 96 minutes 11.23 seconds (5771.23 seconds total)