Starting phenix.real_space_refine on Sat Jun 29 10:19:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8usw_42520/06_2024/8usw_42520_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8usw_42520/06_2024/8usw_42520.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8usw_42520/06_2024/8usw_42520_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8usw_42520/06_2024/8usw_42520_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8usw_42520/06_2024/8usw_42520_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8usw_42520/06_2024/8usw_42520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8usw_42520/06_2024/8usw_42520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8usw_42520/06_2024/8usw_42520_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8usw_42520/06_2024/8usw_42520_updated.pdb" } resolution = 4.23 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= 0.001 sd= 0.013 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 63 5.16 5 C 11070 2.51 5 N 3337 2.21 5 O 3505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 707": "OE1" <-> "OE2" Residue "A GLU 786": "OE1" <-> "OE2" Residue "B GLU 522": "OE1" <-> "OE2" Residue "B TYR 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 830": "OE1" <-> "OE2" Residue "C GLU 781": "OE1" <-> "OE2" Residue "D GLU 585": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 17975 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 4434 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 388} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 693} Chain breaks: 1 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1397 Unresolved non-hydrogen angles: 1799 Unresolved non-hydrogen dihedrals: 1170 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 19, 'TYR:plan': 15, 'ASN:plan1': 23, 'TRP:plan': 8, 'HIS:plan': 14, 'PHE:plan': 13, 'GLU:plan': 28, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 743 Chain: "B" Number of atoms: 4528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 4528 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 708} Chain breaks: 4 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1405 Unresolved non-hydrogen angles: 1822 Unresolved non-hydrogen dihedrals: 1164 Unresolved non-hydrogen chiralities: 158 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 12, 'TYR:plan': 7, 'ASN:plan1': 23, 'TRP:plan': 9, 'ASP:plan': 16, 'PHE:plan': 24, 'GLU:plan': 25, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 715 Chain: "C" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 4447 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 385} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 693} Chain breaks: 1 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1384 Unresolved non-hydrogen angles: 1783 Unresolved non-hydrogen dihedrals: 1159 Unresolved non-hydrogen chiralities: 133 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 18, 'TYR:plan': 15, 'ASN:plan1': 22, 'TRP:plan': 8, 'HIS:plan': 13, 'PHE:plan': 13, 'GLU:plan': 27, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 737 Chain: "D" Number of atoms: 4532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 4532 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 408} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 708} Chain breaks: 4 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1400 Unresolved non-hydrogen angles: 1814 Unresolved non-hydrogen dihedrals: 1159 Unresolved non-hydrogen chiralities: 157 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 12, 'TYR:plan': 6, 'ASN:plan1': 23, 'TRP:plan': 9, 'ASP:plan': 16, 'PHE:plan': 24, 'GLU:plan': 25, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 713 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'DQC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'DQC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.75, per 1000 atoms: 0.60 Number of scatterers: 17975 At special positions: 0 Unit cell: (118.128, 169.488, 194.312, 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 63 16.00 O 3505 8.00 N 3337 7.00 C 11070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 575 " distance=2.04 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 576 " distance=2.04 Simple disulfide: pdb=" SG CYS B 859 " - pdb=" SG CYS B 913 " 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=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 537 " - pdb=" SG CYS D 575 " distance=2.02 Simple disulfide: pdb=" SG CYS D 543 " - pdb=" SG CYS D 576 " distance=2.04 Simple disulfide: pdb=" SG CYS D 859 " - pdb=" SG CYS D 913 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.16 Conformation dependent library (CDL) restraints added in 3.4 seconds 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5508 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 26 sheets defined 36.2% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.92 Creating SS restraints... Processing helix chain 'A' and resid 35 through 51 removed outlier: 3.646A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 3.920A pdb=" N ALA A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 110 removed outlier: 4.257A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 146 through 157 removed outlier: 3.775A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 187 removed outlier: 3.601A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.846A pdb=" N GLU A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 237 removed outlier: 4.050A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 257 through 260 removed outlier: 4.060A pdb=" N ARG A 260 " --> pdb=" O ASN A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 277 through 295 removed outlier: 3.538A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'A' and resid 458 through 470 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 561 through 577 Processing helix chain 'A' and resid 629 through 657 Processing helix chain 'A' and resid 671 through 673 No H-bonds generated for 'chain 'A' and resid 671 through 673' Processing helix chain 'A' and resid 689 through 695 removed outlier: 3.894A pdb=" N ARG A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 699 No H-bonds generated for 'chain 'A' and resid 697 through 699' Processing helix chain 'A' and resid 704 through 708 Processing helix chain 'A' and resid 714 through 718 Processing helix chain 'A' and resid 721 through 723 No H-bonds generated for 'chain 'A' and resid 721 through 723' Processing helix chain 'A' and resid 733 through 742 Processing helix chain 'A' and resid 769 through 781 Processing helix chain 'A' and resid 784 through 792 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 125 through 137 Processing helix chain 'B' and resid 177 through 191 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 246 through 259 removed outlier: 4.065A pdb=" N VAL B 254 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 304 through 319 Processing helix chain 'B' and resid 332 through 344 Processing helix chain 'B' and resid 385 through 412 removed outlier: 3.851A pdb=" N ILE B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 429 through 438 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 570 through 572 No H-bonds generated for 'chain 'B' and resid 570 through 572' Processing helix chain 'B' and resid 579 through 591 Processing helix chain 'B' and resid 615 through 620 Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 741 through 768 Processing helix chain 'B' and resid 803 through 807 Processing helix chain 'B' and resid 814 through 817 No H-bonds generated for 'chain 'B' and resid 814 through 817' Processing helix chain 'B' and resid 826 through 833 removed outlier: 3.609A pdb=" N LYS B 833 " --> pdb=" O VAL B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 852 Processing helix chain 'B' and resid 882 through 884 No H-bonds generated for 'chain 'B' and resid 882 through 884' Processing helix chain 'B' and resid 886 through 897 Processing helix chain 'B' and resid 900 through 907 Processing helix chain 'B' and resid 928 through 954 Processing helix chain 'C' and resid 35 through 52 Processing helix chain 'C' and resid 71 through 81 Processing helix chain 'C' and resid 103 through 113 removed outlier: 3.808A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 156 removed outlier: 3.662A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 187 removed outlier: 4.187A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 212 removed outlier: 3.785A pdb=" N LYS C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 237 removed outlier: 3.971A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 260 Processing helix chain 'C' and resid 277 through 297 removed outlier: 3.630A pdb=" N GLN C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 removed outlier: 3.650A pdb=" N SER C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 471 removed outlier: 4.586A pdb=" N MET C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 507 removed outlier: 3.750A pdb=" N SER C 507 " --> pdb=" O GLY C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 578 Processing helix chain 'C' and resid 629 through 656 Processing helix chain 'C' and resid 670 through 673 Processing helix chain 'C' and resid 688 through 693 Processing helix chain 'C' and resid 697 through 707 removed outlier: 4.440A pdb=" N THR C 701 " --> pdb=" O GLU C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 723 Processing helix chain 'C' and resid 733 through 742 Processing helix chain 'C' and resid 771 through 781 Processing helix chain 'C' and resid 784 through 792 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 125 through 137 removed outlier: 3.661A pdb=" N ARG D 137 " --> pdb=" O ASP D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 191 Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 246 through 259 removed outlier: 4.075A pdb=" N VAL D 254 " --> pdb=" O ASP D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 285 Processing helix chain 'D' and resid 304 through 319 Processing helix chain 'D' and resid 332 through 345 removed outlier: 3.578A pdb=" N PHE D 345 " --> pdb=" O ILE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 385 through 412 Proline residue: D 408 - end of helix Processing helix chain 'D' and resid 429 through 438 removed outlier: 3.657A pdb=" N ARG D 435 " --> pdb=" O GLN D 431 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE D 436 " --> pdb=" O TYR D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 561 Processing helix chain 'D' and resid 570 through 572 No H-bonds generated for 'chain 'D' and resid 570 through 572' Processing helix chain 'D' and resid 579 through 591 Processing helix chain 'D' and resid 616 through 621 Processing helix chain 'D' and resid 636 through 641 removed outlier: 3.917A pdb=" N VAL D 641 " --> pdb=" O ALA D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 768 Processing helix chain 'D' and resid 783 through 786 No H-bonds generated for 'chain 'D' and resid 783 through 786' Processing helix chain 'D' and resid 801 through 809 Processing helix chain 'D' and resid 813 through 819 removed outlier: 3.569A pdb=" N ARG D 818 " --> pdb=" O HIS D 814 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ARG D 819 " --> pdb=" O GLU D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 833 Processing helix chain 'D' and resid 882 through 896 removed outlier: 4.228A pdb=" N ALA D 885 " --> pdb=" O PRO D 882 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN D 886 " --> pdb=" O LEU D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 899 through 907 Processing helix chain 'D' and resid 927 through 953 Processing sheet with id= A, first strand: chain 'A' and resid 26 through 32 removed outlier: 5.548A pdb=" N GLN A 59 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 29 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN A 61 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ALA A 31 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR A 63 " --> pdb=" O ALA A 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'A' and resid 194 through 197 removed outlier: 6.676A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 246 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU A 221 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU A 248 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 397 through 401 removed outlier: 7.385A pdb=" N THR A 473 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE A 400 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU A 475 " --> pdb=" O ILE A 400 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 409 through 412 removed outlier: 4.172A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 729 through 732 removed outlier: 3.777A pdb=" N PHE A 729 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 541 " --> pdb=" O PHE A 729 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP A 731 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 539 " --> pdb=" O TRP A 731 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 351 through 357 removed outlier: 5.337A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN A 357 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 147 through 152 removed outlier: 7.124A pdb=" N GLY B 51 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU B 196 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 53 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA B 198 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER B 459 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 266 through 269 Processing sheet with id= J, first strand: chain 'B' and resid 375 through 379 removed outlier: 5.995A pdb=" N ASN B 467 " --> pdb=" O ARG B 480 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ARG B 480 " --> pdb=" O ASN B 467 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLN B 469 " --> pdb=" O TRP B 478 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TRP B 478 " --> pdb=" O GLN B 469 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 541 through 544 Processing sheet with id= L, first strand: chain 'B' and resid 653 through 655 removed outlier: 3.954A pdb=" N GLY B 654 " --> pdb=" O MET B 844 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET B 844 " --> pdb=" O GLY B 654 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 26 through 32 removed outlier: 5.607A pdb=" N GLN C 59 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE C 29 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASN C 61 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA C 31 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR C 63 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 90 through 92 Processing sheet with id= O, first strand: chain 'C' and resid 194 through 196 removed outlier: 8.795A pdb=" N LEU C 195 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL C 218 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU C 166 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE C 220 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL C 246 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU C 221 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU C 248 " --> pdb=" O LEU C 221 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 372 through 374 removed outlier: 6.494A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 398 through 402 removed outlier: 3.798A pdb=" N GLU C 475 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE C 400 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR C 402 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 434 through 437 Processing sheet with id= S, first strand: chain 'D' and resid 148 through 152 removed outlier: 6.311A pdb=" N VAL D 48 " --> pdb=" O GLU D 149 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL D 151 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL D 50 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY D 51 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU D 196 " --> pdb=" O GLY D 51 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 266 through 269 removed outlier: 5.528A pdb=" N ARG D 353 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N MET D 327 " --> pdb=" O ARG D 353 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL D 355 " --> pdb=" O MET D 327 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 374 through 379 removed outlier: 3.502A pdb=" N LEU D 374 " --> pdb=" O LEU D 468 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ASN D 467 " --> pdb=" O ARG D 480 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ARG D 480 " --> pdb=" O ASN D 467 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN D 469 " --> pdb=" O TRP D 478 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TRP D 478 " --> pdb=" O GLN D 469 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 441 through 443 Processing sheet with id= W, first strand: chain 'D' and resid 514 through 519 removed outlier: 6.824A pdb=" N ASP D 594 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL D 517 " --> pdb=" O ASP D 594 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP D 596 " --> pdb=" O VAL D 517 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N THR D 519 " --> pdb=" O ASP D 596 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR D 598 " --> pdb=" O THR D 519 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'D' and resid 527 through 529 Processing sheet with id= Y, first strand: chain 'D' and resid 606 through 609 removed outlier: 3.789A pdb=" N ALA D 607 " --> pdb=" O THR D 614 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR D 614 " --> pdb=" O ALA D 607 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 861 through 863 removed outlier: 3.583A pdb=" N VAL D 657 " --> pdb=" O LEU D 862 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY D 654 " --> pdb=" O MET D 844 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N MET D 844 " --> pdb=" O GLY D 654 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY D 795 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 843 " --> pdb=" O GLY D 795 " (cutoff:3.500A) 776 hydrogen bonds defined for protein. 2151 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.70 Time building geometry restraints manager: 6.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3319 1.29 - 1.43: 4266 1.43 - 1.56: 10505 1.56 - 1.69: 0 1.69 - 1.83: 98 Bond restraints: 18188 Sorted by residual: bond pdb=" C7 DQC C 901 " pdb=" C9 DQC C 901 " ideal model delta sigma weight residual 1.527 1.281 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C7 DQC A 901 " pdb=" C9 DQC A 901 " ideal model delta sigma weight residual 1.527 1.281 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" N4 DQC C 901 " pdb=" O6 DQC C 901 " ideal model delta sigma weight residual 1.402 1.223 0.179 2.00e-02 2.50e+03 8.01e+01 bond pdb=" N4 DQC A 901 " pdb=" O6 DQC A 901 " ideal model delta sigma weight residual 1.402 1.224 0.178 2.00e-02 2.50e+03 7.91e+01 bond pdb=" C4 DQC C 901 " pdb=" N2 DQC C 901 " ideal model delta sigma weight residual 1.495 1.350 0.145 2.00e-02 2.50e+03 5.28e+01 ... (remaining 18183 not shown) Histogram of bond angle deviations from ideal: 97.29 - 112.81: 10131 112.81 - 128.33: 14741 128.33 - 143.85: 83 143.85 - 159.37: 0 159.37 - 174.89: 2 Bond angle restraints: 24957 Sorted by residual: angle pdb=" C PHE C 484 " pdb=" CA PHE C 484 " pdb=" CB PHE C 484 " ideal model delta sigma weight residual 110.31 121.79 -11.48 2.09e+00 2.29e-01 3.02e+01 angle pdb=" N GLU B 830 " pdb=" CA GLU B 830 " pdb=" C GLU B 830 " ideal model delta sigma weight residual 112.90 106.88 6.02 1.31e+00 5.83e-01 2.11e+01 angle pdb=" N LYS D 846 " pdb=" CA LYS D 846 " pdb=" C LYS D 846 " ideal model delta sigma weight residual 112.97 108.45 4.52 1.06e+00 8.90e-01 1.82e+01 angle pdb=" N ARG B 622 " pdb=" CA ARG B 622 " pdb=" C ARG B 622 " ideal model delta sigma weight residual 113.15 108.36 4.79 1.19e+00 7.06e-01 1.62e+01 angle pdb=" CA LEU A 505 " pdb=" CB LEU A 505 " pdb=" CG LEU A 505 " ideal model delta sigma weight residual 116.30 103.01 13.29 3.50e+00 8.16e-02 1.44e+01 ... (remaining 24952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 10114 17.92 - 35.85: 522 35.85 - 53.77: 81 53.77 - 71.69: 14 71.69 - 89.61: 8 Dihedral angle restraints: 10739 sinusoidal: 2258 harmonic: 8481 Sorted by residual: dihedral pdb=" CA SER D 778 " pdb=" C SER D 778 " pdb=" N GLY D 779 " pdb=" CA GLY D 779 " ideal model delta harmonic sigma weight residual 180.00 -144.41 -35.59 0 5.00e+00 4.00e-02 5.07e+01 dihedral pdb=" CB CYS B 537 " pdb=" SG CYS B 537 " pdb=" SG CYS B 575 " pdb=" CB CYS B 575 " ideal model delta sinusoidal sigma weight residual 93.00 154.34 -61.34 1 1.00e+01 1.00e-02 5.00e+01 dihedral pdb=" CA MET B 817 " pdb=" C MET B 817 " pdb=" N ARG B 818 " pdb=" CA ARG B 818 " ideal model delta harmonic sigma weight residual 180.00 -149.14 -30.86 0 5.00e+00 4.00e-02 3.81e+01 ... (remaining 10736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2666 0.074 - 0.149: 373 0.149 - 0.223: 14 0.223 - 0.297: 1 0.297 - 0.372: 2 Chirality restraints: 3056 Sorted by residual: chirality pdb=" CA PHE C 484 " pdb=" N PHE C 484 " pdb=" C PHE C 484 " pdb=" CB PHE C 484 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CB ILE A 760 " pdb=" CA ILE A 760 " pdb=" CG1 ILE A 760 " pdb=" CG2 ILE A 760 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA MET B 902 " pdb=" N MET B 902 " pdb=" C MET B 902 " pdb=" CB MET B 902 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3053 not shown) Planarity restraints: 3417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DQC A 901 " 0.001 2.00e-02 2.50e+03 1.68e-02 1.06e+01 pdb=" C2 DQC A 901 " 0.007 2.00e-02 2.50e+03 pdb=" C3 DQC A 901 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DQC A 901 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DQC A 901 " -0.016 2.00e-02 2.50e+03 pdb=" C6 DQC A 901 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DQC A 901 " -0.014 2.00e-02 2.50e+03 pdb=" C8 DQC A 901 " -0.003 2.00e-02 2.50e+03 pdb=" C9 DQC A 901 " -0.022 2.00e-02 2.50e+03 pdb=" N1 DQC A 901 " -0.004 2.00e-02 2.50e+03 pdb=" N2 DQC A 901 " 0.004 2.00e-02 2.50e+03 pdb=" N4 DQC A 901 " -0.013 2.00e-02 2.50e+03 pdb=" N8 DQC A 901 " 0.052 2.00e-02 2.50e+03 pdb=" O1 DQC A 901 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DQC A 901 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 DQC C 901 " -0.001 2.00e-02 2.50e+03 1.67e-02 1.04e+01 pdb=" C2 DQC C 901 " -0.007 2.00e-02 2.50e+03 pdb=" C3 DQC C 901 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DQC C 901 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DQC C 901 " 0.016 2.00e-02 2.50e+03 pdb=" C6 DQC C 901 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DQC C 901 " 0.014 2.00e-02 2.50e+03 pdb=" C8 DQC C 901 " 0.004 2.00e-02 2.50e+03 pdb=" C9 DQC C 901 " 0.021 2.00e-02 2.50e+03 pdb=" N1 DQC C 901 " 0.004 2.00e-02 2.50e+03 pdb=" N2 DQC C 901 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DQC C 901 " 0.012 2.00e-02 2.50e+03 pdb=" N8 DQC C 901 " -0.052 2.00e-02 2.50e+03 pdb=" O1 DQC C 901 " 0.007 2.00e-02 2.50e+03 pdb=" O2 DQC C 901 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 527 " 0.025 2.00e-02 2.50e+03 2.43e-02 1.03e+01 pdb=" CG PHE D 527 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE D 527 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE D 527 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 527 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 527 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE D 527 " 0.003 2.00e-02 2.50e+03 ... (remaining 3414 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 99 2.44 - 3.06: 12958 3.06 - 3.67: 26253 3.67 - 4.29: 32476 4.29 - 4.90: 52596 Nonbonded interactions: 124382 Sorted by model distance: nonbonded pdb=" OD2 ASP C 732 " pdb=" O6 DQC C 901 " model vdw 1.827 3.040 nonbonded pdb=" OE1 GLN C 405 " pdb=" CZ PHE C 484 " model vdw 1.861 3.340 nonbonded pdb=" NZ LYS B 586 " pdb=" CE2 TYR B 894 " model vdw 1.913 3.420 nonbonded pdb=" O THR B 553 " pdb=" OG SER B 556 " model vdw 1.936 2.440 nonbonded pdb=" OD1 ASP A 732 " pdb=" O6 DQC A 901 " model vdw 2.039 3.040 ... (remaining 124377 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 486 or (resid 487 and (name N or name CA or nam \ e C or name O or name CB )) or resid 488 through 561 or (resid 562 through 566 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 567 through 66 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 663 through \ 705 or (resid 706 and (name N or name CA or name C or name O or name CB )) or re \ sid 707 through 765 or (resid 766 and (name N or name CA or name C or name O or \ name CB )) or resid 767 through 798 or resid 901)) selection = (chain 'C' and (resid 25 through 395 or (resid 396 and (name N or name CA or nam \ e C or name O or name CB )) or resid 397 through 405 or (resid 406 and (name N o \ r name CA or name C or name O or name CB )) or resid 407 through 439 or (resid 4 \ 40 through 444 and (name N or name CA or name C or name O or name CB )) or (resi \ d 445 through 449 and (name N or name CA or name C or name O or name CB )) or re \ sid 450 through 495 or (resid 496 and (name N or name CA or name C or name O or \ name CB )) or resid 497 through 510 or (resid 511 and (name N or name CA or name \ C or name O or name CB )) or resid 512 through 542 or (resid 543 through 546 an \ d (name N or name CA or name C or name O or name CB )) or resid 547 through 677 \ or (resid 678 and (name N or name CA or name C or name O or name CB )) or resid \ 679 through 697 or (resid 698 and (name N or name CA or name C or name O or name \ CB )) or resid 699 through 798 or resid 901)) } ncs_group { reference = (chain 'B' and (resid 38 through 659 or (resid 660 through 741 and (name N or na \ me CA or name C or name O or name CB )) or resid 742 through 955)) selection = (chain 'D' and (resid 38 through 773 or (resid 774 through 775 and (name N or na \ me CA or name C or name O or name CB )) or resid 776 through 869 or (resid 870 a \ nd (name N or name CA or name C or name O or name CB )) or resid 871 through 955 \ )) } 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: 4.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.180 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 48.190 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.100 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 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 : 0.008 0.246 18188 Z= 0.552 Angle : 0.770 13.285 24957 Z= 0.428 Chirality : 0.049 0.372 3056 Planarity : 0.005 0.064 3417 Dihedral : 12.064 89.613 5195 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.33 % Favored : 90.29 % Rotamer: Outliers : 1.10 % Allowed : 0.70 % Favored : 98.19 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2914 helix: 1.89 (0.17), residues: 1082 sheet: -1.00 (0.26), residues: 400 loop : -1.85 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 731 HIS 0.007 0.002 HIS C 705 PHE 0.056 0.003 PHE D 527 TYR 0.020 0.002 TYR B 579 ARG 0.005 0.001 ARG A 673 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 1.924 Fit side-chains revert: symmetry clash REVERT: A 484 PHE cc_start: 0.8525 (m-80) cc_final: 0.7983 (m-10) REVERT: B 544 LEU cc_start: 0.9105 (tp) cc_final: 0.8844 (tt) REVERT: B 813 MET cc_start: 0.8488 (ppp) cc_final: 0.8156 (ppp) REVERT: B 909 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7209 (ttm110) REVERT: D 514 HIS cc_start: 0.7757 (OUTLIER) cc_final: 0.7522 (m-70) REVERT: D 845 ASP cc_start: 0.8201 (m-30) cc_final: 0.7997 (m-30) outliers start: 11 outliers final: 2 residues processed: 175 average time/residue: 0.2290 time to fit residues: 66.8078 Evaluate side-chains 149 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 145 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 50.0000 chunk 221 optimal weight: 30.0000 chunk 122 optimal weight: 0.7980 chunk 75 optimal weight: 30.0000 chunk 149 optimal weight: 30.0000 chunk 118 optimal weight: 0.5980 chunk 228 optimal weight: 10.0000 chunk 88 optimal weight: 50.0000 chunk 139 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 chunk 265 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 HIS ** C 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 626 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18188 Z= 0.177 Angle : 0.522 6.379 24957 Z= 0.284 Chirality : 0.043 0.221 3056 Planarity : 0.004 0.055 3417 Dihedral : 4.471 30.862 3025 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.28 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2914 helix: 2.14 (0.17), residues: 1099 sheet: -0.63 (0.27), residues: 376 loop : -1.82 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 731 HIS 0.004 0.001 HIS C 705 PHE 0.020 0.002 PHE D 527 TYR 0.031 0.002 TYR B 894 ARG 0.006 0.001 ARG B 909 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 813 MET cc_start: 0.8378 (ppp) cc_final: 0.7480 (ppp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2128 time to fit residues: 66.3738 Evaluate side-chains 152 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 147 optimal weight: 40.0000 chunk 82 optimal weight: 50.0000 chunk 220 optimal weight: 8.9990 chunk 180 optimal weight: 50.0000 chunk 73 optimal weight: 50.0000 chunk 265 optimal weight: 2.9990 chunk 286 optimal weight: 0.0170 chunk 236 optimal weight: 50.0000 chunk 263 optimal weight: 0.8980 chunk 90 optimal weight: 40.0000 chunk 213 optimal weight: 7.9990 overall best weight: 4.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 HIS A 719 GLN ** C 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 514 HIS ** D 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 18188 Z= 0.479 Angle : 0.690 10.865 24957 Z= 0.367 Chirality : 0.047 0.201 3056 Planarity : 0.004 0.059 3417 Dihedral : 4.903 33.429 3025 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.36 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.17), residues: 2914 helix: 2.05 (0.17), residues: 1096 sheet: -0.91 (0.27), residues: 386 loop : -1.83 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 792 HIS 0.011 0.002 HIS C 780 PHE 0.045 0.003 PHE D 527 TYR 0.019 0.002 TYR A 692 ARG 0.004 0.001 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 544 LEU cc_start: 0.9146 (tp) cc_final: 0.8810 (tt) REVERT: B 813 MET cc_start: 0.8824 (ppp) cc_final: 0.7770 (ppp) REVERT: C 732 ASP cc_start: 0.7590 (p0) cc_final: 0.7365 (p0) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2141 time to fit residues: 61.6209 Evaluate side-chains 136 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 262 optimal weight: 0.0870 chunk 199 optimal weight: 50.0000 chunk 137 optimal weight: 0.0770 chunk 29 optimal weight: 30.0000 chunk 126 optimal weight: 50.0000 chunk 178 optimal weight: 8.9990 chunk 266 optimal weight: 3.9990 chunk 282 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 252 optimal weight: 50.0000 chunk 76 optimal weight: 30.0000 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 514 HIS ** D 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18188 Z= 0.220 Angle : 0.529 6.777 24957 Z= 0.285 Chirality : 0.044 0.255 3056 Planarity : 0.004 0.057 3417 Dihedral : 4.443 30.909 3025 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.52 % Favored : 92.14 % Rotamer: Outliers : 0.10 % Allowed : 5.22 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.17), residues: 2914 helix: 2.24 (0.17), residues: 1101 sheet: -0.89 (0.26), residues: 400 loop : -1.73 (0.17), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 907 HIS 0.005 0.001 HIS C 780 PHE 0.018 0.002 PHE D 527 TYR 0.047 0.002 TYR B 816 ARG 0.004 0.000 ARG D 798 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 PHE cc_start: 0.8501 (m-80) cc_final: 0.8187 (m-80) REVERT: A 732 ASP cc_start: 0.8276 (p0) cc_final: 0.8020 (p0) REVERT: B 544 LEU cc_start: 0.9111 (tp) cc_final: 0.8807 (tt) REVERT: B 813 MET cc_start: 0.8718 (ppp) cc_final: 0.7525 (ppp) REVERT: D 514 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.7482 (m-70) REVERT: D 900 MET cc_start: 0.8923 (mmp) cc_final: 0.8290 (tpp) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.2056 time to fit residues: 65.7188 Evaluate side-chains 151 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 235 optimal weight: 40.0000 chunk 160 optimal weight: 30.0000 chunk 4 optimal weight: 50.0000 chunk 210 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 240 optimal weight: 40.0000 chunk 195 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 144 optimal weight: 50.0000 chunk 253 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 overall best weight: 7.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 HIS ** C 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 514 HIS ** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.147 18188 Z= 0.814 Angle : 0.938 17.582 24957 Z= 0.492 Chirality : 0.053 0.296 3056 Planarity : 0.006 0.119 3417 Dihedral : 5.676 37.297 3025 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.01 % Favored : 87.58 % Rotamer: Outliers : 0.10 % Allowed : 10.04 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.17), residues: 2914 helix: 1.67 (0.17), residues: 1104 sheet: -1.36 (0.26), residues: 398 loop : -2.02 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 792 HIS 0.016 0.003 HIS A 780 PHE 0.042 0.004 PHE B 632 TYR 0.031 0.004 TYR A 456 ARG 0.009 0.001 ARG D 798 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 813 MET cc_start: 0.9108 (ppp) cc_final: 0.8066 (ppp) REVERT: C 732 ASP cc_start: 0.7584 (p0) cc_final: 0.7329 (p0) REVERT: D 570 ILE cc_start: 0.8258 (mm) cc_final: 0.7980 (mm) REVERT: D 845 ASP cc_start: 0.8453 (m-30) cc_final: 0.8221 (m-30) outliers start: 1 outliers final: 1 residues processed: 160 average time/residue: 0.1963 time to fit residues: 55.7900 Evaluate side-chains 141 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 50.0000 chunk 254 optimal weight: 50.0000 chunk 55 optimal weight: 6.9990 chunk 165 optimal weight: 40.0000 chunk 69 optimal weight: 2.9990 chunk 282 optimal weight: 0.7980 chunk 234 optimal weight: 50.0000 chunk 130 optimal weight: 3.9990 chunk 23 optimal weight: 40.0000 chunk 93 optimal weight: 50.0000 chunk 148 optimal weight: 50.0000 overall best weight: 10.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 HIS B 640 GLN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 790 GLN ** D 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.187 18188 Z= 1.143 Angle : 1.188 18.253 24957 Z= 0.623 Chirality : 0.061 0.367 3056 Planarity : 0.008 0.153 3417 Dihedral : 6.758 43.133 3025 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 23.86 Ramachandran Plot: Outliers : 0.38 % Allowed : 14.14 % Favored : 85.48 % Rotamer: Outliers : 0.30 % Allowed : 7.33 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.50 (0.16), residues: 2914 helix: 0.94 (0.16), residues: 1106 sheet: -1.70 (0.27), residues: 375 loop : -2.47 (0.16), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP A 792 HIS 0.023 0.004 HIS A 780 PHE 0.090 0.006 PHE B 632 TYR 0.042 0.005 TYR D 908 ARG 0.015 0.001 ARG A 673 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 754 PHE cc_start: 0.8727 (t80) cc_final: 0.8521 (t80) outliers start: 3 outliers final: 3 residues processed: 147 average time/residue: 0.2069 time to fit residues: 53.4024 Evaluate side-chains 132 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 272 optimal weight: 50.0000 chunk 31 optimal weight: 50.0000 chunk 160 optimal weight: 20.0000 chunk 206 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 237 optimal weight: 5.9990 chunk 157 optimal weight: 30.0000 chunk 281 optimal weight: 1.9990 chunk 176 optimal weight: 30.0000 chunk 171 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 HIS ** C 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 18188 Z= 0.441 Angle : 0.721 9.572 24957 Z= 0.385 Chirality : 0.048 0.272 3056 Planarity : 0.005 0.068 3417 Dihedral : 5.665 40.799 3025 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.64 % Favored : 89.05 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.06 (0.16), residues: 2914 helix: 1.36 (0.16), residues: 1102 sheet: -1.45 (0.27), residues: 381 loop : -2.27 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 907 HIS 0.008 0.002 HIS A 780 PHE 0.038 0.003 PHE B 527 TYR 0.019 0.002 TYR B 579 ARG 0.005 0.001 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.209 Fit side-chains revert: symmetry clash REVERT: B 544 LEU cc_start: 0.9125 (tp) cc_final: 0.8822 (tt) REVERT: B 813 MET cc_start: 0.8753 (ppp) cc_final: 0.8012 (ppp) REVERT: C 732 ASP cc_start: 0.7963 (p0) cc_final: 0.7628 (p0) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1988 time to fit residues: 58.5061 Evaluate side-chains 137 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 174 optimal weight: 50.0000 chunk 112 optimal weight: 0.8980 chunk 168 optimal weight: 50.0000 chunk 84 optimal weight: 40.0000 chunk 55 optimal weight: 9.9990 chunk 54 optimal weight: 50.0000 chunk 178 optimal weight: 0.0570 chunk 191 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 221 optimal weight: 20.0000 overall best weight: 3.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 HIS ** C 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 18188 Z= 0.387 Angle : 0.675 11.263 24957 Z= 0.358 Chirality : 0.047 0.224 3056 Planarity : 0.004 0.063 3417 Dihedral : 5.289 38.873 3025 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.47 % Favored : 89.22 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.17), residues: 2914 helix: 1.65 (0.17), residues: 1098 sheet: -1.37 (0.27), residues: 374 loop : -2.14 (0.17), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 792 HIS 0.007 0.001 HIS C 780 PHE 0.026 0.003 PHE B 527 TYR 0.040 0.002 TYR B 816 ARG 0.004 0.001 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.822 Fit side-chains revert: symmetry clash REVERT: B 544 LEU cc_start: 0.9109 (tp) cc_final: 0.8802 (tt) REVERT: B 813 MET cc_start: 0.8747 (ppp) cc_final: 0.7806 (ppp) REVERT: C 709 HIS cc_start: 0.6002 (t70) cc_final: 0.5714 (t70) REVERT: C 732 ASP cc_start: 0.7890 (p0) cc_final: 0.7606 (p0) REVERT: D 845 ASP cc_start: 0.8263 (m-30) cc_final: 0.8013 (m-30) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1948 time to fit residues: 55.8279 Evaluate side-chains 137 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 256 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 245 optimal weight: 50.0000 chunk 262 optimal weight: 7.9990 chunk 157 optimal weight: 50.0000 chunk 114 optimal weight: 4.9990 chunk 205 optimal weight: 0.4980 chunk 80 optimal weight: 9.9990 chunk 236 optimal weight: 40.0000 chunk 248 optimal weight: 50.0000 chunk 261 optimal weight: 0.8980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18188 Z= 0.311 Angle : 0.615 9.567 24957 Z= 0.327 Chirality : 0.045 0.214 3056 Planarity : 0.004 0.060 3417 Dihedral : 4.950 37.465 3025 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.06 % Favored : 90.63 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2914 helix: 1.88 (0.17), residues: 1095 sheet: -1.32 (0.27), residues: 379 loop : -2.02 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 792 HIS 0.007 0.001 HIS A 404 PHE 0.031 0.002 PHE B 794 TYR 0.015 0.002 TYR B 816 ARG 0.003 0.000 ARG B 793 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.792 Fit side-chains revert: symmetry clash REVERT: B 544 LEU cc_start: 0.9106 (tp) cc_final: 0.8804 (tt) REVERT: B 813 MET cc_start: 0.8750 (ppp) cc_final: 0.7876 (ppp) REVERT: C 709 HIS cc_start: 0.6124 (t70) cc_final: 0.5832 (t70) REVERT: C 732 ASP cc_start: 0.7863 (p0) cc_final: 0.7589 (p0) REVERT: D 845 ASP cc_start: 0.8244 (m-30) cc_final: 0.7994 (m-30) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1949 time to fit residues: 54.3619 Evaluate side-chains 139 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 172 optimal weight: 9.9990 chunk 277 optimal weight: 0.7980 chunk 169 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 192 optimal weight: 0.0030 chunk 290 optimal weight: 8.9990 chunk 267 optimal weight: 0.9990 chunk 231 optimal weight: 30.0000 chunk 24 optimal weight: 50.0000 chunk 178 optimal weight: 50.0000 chunk 142 optimal weight: 0.0980 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18188 Z= 0.203 Angle : 0.561 9.451 24957 Z= 0.297 Chirality : 0.044 0.313 3056 Planarity : 0.004 0.061 3417 Dihedral : 4.536 34.258 3025 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.24 % Favored : 91.49 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.17), residues: 2914 helix: 2.06 (0.17), residues: 1101 sheet: -1.25 (0.26), residues: 400 loop : -1.90 (0.17), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 907 HIS 0.006 0.001 HIS A 780 PHE 0.027 0.002 PHE A 693 TYR 0.022 0.002 TYR B 816 ARG 0.003 0.000 ARG A 794 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5828 Ramachandran restraints generated. 2914 Oldfield, 0 Emsley, 2914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 469 THR cc_start: 0.6469 (m) cc_final: 0.6229 (m) REVERT: A 470 MET cc_start: 0.8357 (mmm) cc_final: 0.7116 (mtm) REVERT: B 544 LEU cc_start: 0.9076 (tp) cc_final: 0.8753 (tt) REVERT: B 813 MET cc_start: 0.8615 (ppp) cc_final: 0.7642 (ppp) REVERT: C 512 MET cc_start: 0.8351 (mmp) cc_final: 0.8118 (mmp) REVERT: C 732 ASP cc_start: 0.7870 (p0) cc_final: 0.7648 (p0) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1967 time to fit residues: 57.8703 Evaluate side-chains 144 residues out of total 2586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 184 optimal weight: 0.5980 chunk 246 optimal weight: 50.0000 chunk 70 optimal weight: 0.8980 chunk 213 optimal weight: 0.9990 chunk 34 optimal weight: 50.0000 chunk 64 optimal weight: 0.4980 chunk 232 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 238 optimal weight: 40.0000 chunk 29 optimal weight: 50.0000 chunk 42 optimal weight: 0.0670 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN ** C 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 514 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.150559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.125364 restraints weight = 57930.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.116755 restraints weight = 71227.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.115756 restraints weight = 53427.154| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18188 Z= 0.148 Angle : 0.525 9.440 24957 Z= 0.278 Chirality : 0.043 0.318 3056 Planarity : 0.004 0.061 3417 Dihedral : 4.178 30.373 3025 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.69 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2914 helix: 2.23 (0.17), residues: 1105 sheet: -1.07 (0.27), residues: 393 loop : -1.82 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 907 HIS 0.007 0.001 HIS D 514 PHE 0.022 0.001 PHE A 693 TYR 0.027 0.001 TYR B 816 ARG 0.002 0.000 ARG A 794 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3206.93 seconds wall clock time: 57 minutes 44.37 seconds (3464.37 seconds total)