Starting phenix.real_space_refine (version: dev) on Sat Feb 18 18:20:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp9_21307/02_2023/6vp9_21307_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp9_21307/02_2023/6vp9_21307.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp9_21307/02_2023/6vp9_21307_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp9_21307/02_2023/6vp9_21307_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp9_21307/02_2023/6vp9_21307_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp9_21307/02_2023/6vp9_21307.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp9_21307/02_2023/6vp9_21307.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp9_21307/02_2023/6vp9_21307_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp9_21307/02_2023/6vp9_21307_neut_updated.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 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 Process input model Symmetric amino acids flipped Residue "A PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B GLU 286": "OE1" <-> "OE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "B GLU 441": "OE1" <-> "OE2" Residue "B GLU 451": "OE1" <-> "OE2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B GLU 551": "OE1" <-> "OE2" Residue "B GLU 579": "OE1" <-> "OE2" Residue "B ARG 613": "NH1" <-> "NH2" Residue "B GLU 615": "OE1" <-> "OE2" Residue "B GLU 633": "OE1" <-> "OE2" Residue "B ARG 656": "NH1" <-> "NH2" Residue "B GLU 681": "OE1" <-> "OE2" Residue "B GLU 683": "OE1" <-> "OE2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B GLU 739": "OE1" <-> "OE2" Residue "B GLU 802": "OE1" <-> "OE2" Residue "B GLU 933": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8610 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1272 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 7245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7245 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 32, 'TRANS': 881} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 113 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CMC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CMC:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.67, per 1000 atoms: 0.66 Number of scatterers: 8610 At special positions: 0 Unit cell: (107.07, 99.6, 100.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 3 15.00 O 1618 8.00 N 1438 7.00 C 5507 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.5 seconds 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2056 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 2 sheets defined 58.2% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 28 through 37 removed outlier: 3.603A pdb=" N TYR A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 102 Processing helix chain 'A' and resid 117 through 126 removed outlier: 3.671A pdb=" N GLN A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 23 Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 62 through 71 removed outlier: 4.329A pdb=" N LEU B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.537A pdb=" N ILE B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 106 removed outlier: 4.074A pdb=" N LYS B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 104 " --> pdb=" O LYS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 126 Processing helix chain 'B' and resid 129 through 142 removed outlier: 3.575A pdb=" N GLN B 133 " --> pdb=" O TYR B 129 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLN B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 161 removed outlier: 3.803A pdb=" N PHE B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP B 151 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 153 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 174 through 185 removed outlier: 4.139A pdb=" N MET B 184 " --> pdb=" O MET B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 209 through 217 removed outlier: 4.069A pdb=" N ASP B 214 " --> pdb=" O GLN B 210 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 234 through 241 removed outlier: 3.865A pdb=" N MET B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 259 removed outlier: 3.966A pdb=" N LEU B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 279 removed outlier: 3.733A pdb=" N THR B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.945A pdb=" N PHE B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 335 removed outlier: 3.804A pdb=" N LEU B 328 " --> pdb=" O HIS B 324 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 335 " --> pdb=" O ILE B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 358 Processing helix chain 'B' and resid 366 through 369 No H-bonds generated for 'chain 'B' and resid 366 through 369' Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 384 through 390 removed outlier: 3.685A pdb=" N GLY B 390 " --> pdb=" O ASN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 423 removed outlier: 3.745A pdb=" N HIS B 414 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 450 removed outlier: 4.294A pdb=" N VAL B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 450 " --> pdb=" O TYR B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 471 removed outlier: 4.244A pdb=" N LEU B 469 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 482 Processing helix chain 'B' and resid 488 through 501 Processing helix chain 'B' and resid 506 through 519 Processing helix chain 'B' and resid 523 through 529 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 543 through 550 removed outlier: 4.323A pdb=" N ARG B 548 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 550 " --> pdb=" O THR B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 584 removed outlier: 3.852A pdb=" N ALA B 584 " --> pdb=" O TYR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 604 Processing helix chain 'B' and resid 607 through 624 Processing helix chain 'B' and resid 631 through 638 removed outlier: 3.569A pdb=" N SER B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET B 638 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 700 removed outlier: 3.685A pdb=" N GLY B 699 " --> pdb=" O ARG B 695 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU B 700 " --> pdb=" O LEU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 727 No H-bonds generated for 'chain 'B' and resid 724 through 727' Processing helix chain 'B' and resid 729 through 746 removed outlier: 3.690A pdb=" N GLU B 739 " --> pdb=" O GLU B 735 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 746 " --> pdb=" O LYS B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 766 removed outlier: 4.203A pdb=" N PHE B 765 " --> pdb=" O GLY B 762 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN B 766 " --> pdb=" O GLY B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 789 removed outlier: 4.239A pdb=" N SER B 776 " --> pdb=" O CYS B 772 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 779 " --> pdb=" O SER B 775 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN B 781 " --> pdb=" O PHE B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 819 removed outlier: 3.764A pdb=" N GLU B 799 " --> pdb=" O MET B 795 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 800 " --> pdb=" O GLU B 796 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP B 810 " --> pdb=" O LYS B 806 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 811 " --> pdb=" O SER B 807 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 816 " --> pdb=" O LEU B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 829 No H-bonds generated for 'chain 'B' and resid 827 through 829' Processing helix chain 'B' and resid 836 through 868 removed outlier: 3.707A pdb=" N LEU B 841 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 844 " --> pdb=" O ASN B 840 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 850 " --> pdb=" O GLU B 846 " (cutoff:3.500A) Proline residue: B 864 - end of helix Processing helix chain 'B' and resid 884 through 903 removed outlier: 3.847A pdb=" N SER B 889 " --> pdb=" O PRO B 885 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 896 " --> pdb=" O ASP B 892 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 900 " --> pdb=" O GLY B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 911 No H-bonds generated for 'chain 'B' and resid 908 through 911' Processing helix chain 'B' and resid 934 through 968 removed outlier: 3.745A pdb=" N SER B 938 " --> pdb=" O GLU B 934 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS B 939 " --> pdb=" O ARG B 935 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 947 " --> pdb=" O GLY B 943 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS B 951 " --> pdb=" O SER B 947 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 965 " --> pdb=" O LYS B 961 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR B 966 " --> pdb=" O LYS B 962 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR B 967 " --> pdb=" O ARG B 963 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS B 968 " --> pdb=" O LEU B 964 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.542A pdb=" N ILE A 44 " --> pdb=" O ILE A 57 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 107 through 113 368 hydrogen bonds defined for protein. 1071 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: 2.68 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2775 1.34 - 1.46: 1589 1.46 - 1.58: 4344 1.58 - 1.70: 5 1.70 - 1.82: 73 Bond restraints: 8786 Sorted by residual: bond pdb=" C3B CMC A 201 " pdb=" C4B CMC A 201 " ideal model delta sigma weight residual 1.347 1.525 -0.178 2.00e-02 2.50e+03 7.93e+01 bond pdb=" C9P CMC A 201 " pdb=" N8P CMC A 201 " ideal model delta sigma weight residual 1.485 1.326 0.159 2.00e-02 2.50e+03 6.28e+01 bond pdb=" C5P CMC A 201 " pdb=" N4P CMC A 201 " ideal model delta sigma weight residual 1.493 1.336 0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" C4B CMC A 201 " pdb=" O4B CMC A 201 " ideal model delta sigma weight residual 1.596 1.452 0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" C6A CMC A 201 " pdb=" N6A CMC A 201 " ideal model delta sigma weight residual 1.468 1.330 0.138 2.00e-02 2.50e+03 4.74e+01 ... (remaining 8781 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.03: 164 106.03 - 113.03: 4767 113.03 - 120.03: 3319 120.03 - 127.03: 3550 127.03 - 134.03: 89 Bond angle restraints: 11889 Sorted by residual: angle pdb=" C1B CMC A 201 " pdb=" N9A CMC A 201 " pdb=" C4A CMC A 201 " ideal model delta sigma weight residual 90.87 125.78 -34.91 3.00e+00 1.11e-01 1.35e+02 angle pdb=" N1A CMC A 201 " pdb=" C6A CMC A 201 " pdb=" N6A CMC A 201 " ideal model delta sigma weight residual 94.05 118.82 -24.77 3.00e+00 1.11e-01 6.82e+01 angle pdb=" C5A CMC A 201 " pdb=" C6A CMC A 201 " pdb=" N6A CMC A 201 " ideal model delta sigma weight residual 145.98 123.82 22.16 3.00e+00 1.11e-01 5.46e+01 angle pdb=" N PRO B 17 " pdb=" CA PRO B 17 " pdb=" CB PRO B 17 " ideal model delta sigma weight residual 103.25 110.05 -6.80 1.05e+00 9.07e-01 4.19e+01 angle pdb=" C1B CMC A 201 " pdb=" N9A CMC A 201 " pdb=" C8A CMC A 201 " ideal model delta sigma weight residual 141.80 127.63 14.17 3.00e+00 1.11e-01 2.23e+01 ... (remaining 11884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4696 17.97 - 35.94: 467 35.94 - 53.91: 98 53.91 - 71.88: 16 71.88 - 89.86: 11 Dihedral angle restraints: 5288 sinusoidal: 2117 harmonic: 3171 Sorted by residual: dihedral pdb=" CA LYS B 535 " pdb=" C LYS B 535 " pdb=" N HIS B 536 " pdb=" CA HIS B 536 " ideal model delta harmonic sigma weight residual -180.00 -154.84 -25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LEU B 652 " pdb=" C LEU B 652 " pdb=" N ARG B 653 " pdb=" CA ARG B 653 " ideal model delta harmonic sigma weight residual -180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA THR A 26 " pdb=" C THR A 26 " pdb=" N TYR A 27 " pdb=" CA TYR A 27 " ideal model delta harmonic sigma weight residual 180.00 160.03 19.97 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 5285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1194 0.065 - 0.131: 135 0.131 - 0.196: 3 0.196 - 0.261: 1 0.261 - 0.326: 1 Chirality restraints: 1334 Sorted by residual: chirality pdb=" C3B CMC A 201 " pdb=" C2B CMC A 201 " pdb=" C4B CMC A 201 " pdb=" O3B CMC A 201 " both_signs ideal model delta sigma weight residual False -2.35 -2.68 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA PRO B 17 " pdb=" N PRO B 17 " pdb=" C PRO B 17 " pdb=" CB PRO B 17 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB THR B 225 " pdb=" CA THR B 225 " pdb=" OG1 THR B 225 " pdb=" CG2 THR B 225 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1331 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P CMC A 201 " 0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C9P CMC A 201 " -0.089 2.00e-02 2.50e+03 pdb=" CAP CMC A 201 " 0.113 2.00e-02 2.50e+03 pdb=" N8P CMC A 201 " -0.535 2.00e-02 2.50e+03 pdb=" O9P CMC A 201 " 0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P CMC A 201 " -0.338 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C5P CMC A 201 " 0.087 2.00e-02 2.50e+03 pdb=" C6P CMC A 201 " -0.163 2.00e-02 2.50e+03 pdb=" N4P CMC A 201 " 0.509 2.00e-02 2.50e+03 pdb=" O5P CMC A 201 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 755 " 0.039 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO B 756 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 756 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 756 " 0.033 5.00e-02 4.00e+02 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 77 2.61 - 3.18: 7793 3.18 - 3.75: 12615 3.75 - 4.33: 18688 4.33 - 4.90: 30428 Nonbonded interactions: 69601 Sorted by model distance: nonbonded pdb=" OD1 ASN A 16 " pdb=" NE2 GLN B 538 " model vdw 2.032 2.520 nonbonded pdb=" O ASN B 167 " pdb=" OG1 THR B 171 " model vdw 2.139 2.440 nonbonded pdb=" OE1 GLU B 735 " pdb=" OH TYR B 778 " model vdw 2.140 2.440 nonbonded pdb=" OH TYR B 149 " pdb=" O MET B 180 " model vdw 2.219 2.440 nonbonded pdb=" O ASN B 27 " pdb=" N ILE B 31 " model vdw 2.220 2.520 ... (remaining 69596 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 44 5.16 5 C 5507 2.51 5 N 1438 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.070 Check model and map are aligned: 0.130 Process input model: 26.850 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 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 : 0.007 0.178 8786 Z= 0.467 Angle : 0.832 34.914 11889 Z= 0.406 Chirality : 0.043 0.326 1334 Planarity : 0.012 0.302 1508 Dihedral : 15.370 89.856 3232 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.22), residues: 1061 helix: -1.76 (0.17), residues: 668 sheet: -3.84 (0.67), residues: 40 loop : -3.28 (0.29), residues: 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.199 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2501 time to fit residues: 42.5856 Evaluate side-chains 102 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.0470 chunk 96 optimal weight: 0.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 116 HIS B 159 GLN B 249 ASN B 387 GLN B 413 GLN B 447 GLN B 462 GLN B 490 GLN B 555 GLN B 605 ASN B 608 HIS B 659 ASN B 750 GLN B 766 ASN B 834 HIS B 868 ASN B 891 GLN B 898 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 8786 Z= 0.221 Angle : 0.587 9.311 11889 Z= 0.290 Chirality : 0.041 0.171 1334 Planarity : 0.004 0.050 1508 Dihedral : 6.278 98.445 1179 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.25), residues: 1061 helix: -0.74 (0.20), residues: 669 sheet: -3.79 (0.72), residues: 39 loop : -2.96 (0.29), residues: 353 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 1.043 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 124 average time/residue: 0.2180 time to fit residues: 37.5797 Evaluate side-chains 112 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0844 time to fit residues: 2.9037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.0970 chunk 29 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 555 GLN B 733 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 8786 Z= 0.156 Angle : 0.523 9.096 11889 Z= 0.260 Chirality : 0.039 0.140 1334 Planarity : 0.004 0.040 1508 Dihedral : 6.030 111.855 1179 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.26), residues: 1061 helix: -0.03 (0.21), residues: 661 sheet: -3.49 (0.77), residues: 39 loop : -2.55 (0.31), residues: 361 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 1.148 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 126 average time/residue: 0.2247 time to fit residues: 39.3860 Evaluate side-chains 114 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 1.234 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0781 time to fit residues: 2.4102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.0870 chunk 72 optimal weight: 0.0470 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 0.0070 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 8786 Z= 0.134 Angle : 0.504 8.654 11889 Z= 0.249 Chirality : 0.038 0.131 1334 Planarity : 0.003 0.035 1508 Dihedral : 5.871 117.834 1179 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.27), residues: 1061 helix: 0.44 (0.21), residues: 657 sheet: -3.18 (0.78), residues: 38 loop : -2.33 (0.32), residues: 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.013 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 123 average time/residue: 0.2364 time to fit residues: 40.1100 Evaluate side-chains 115 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0922 time to fit residues: 2.8916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 561 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 8786 Z= 0.303 Angle : 0.592 8.880 11889 Z= 0.290 Chirality : 0.042 0.153 1334 Planarity : 0.004 0.046 1508 Dihedral : 6.140 113.462 1179 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.26), residues: 1061 helix: 0.32 (0.21), residues: 661 sheet: -3.23 (0.79), residues: 39 loop : -2.51 (0.30), residues: 361 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 1.083 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 113 average time/residue: 0.2350 time to fit residues: 36.8941 Evaluate side-chains 109 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1065 time to fit residues: 2.7793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.8980 chunk 20 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 102 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8786 Z= 0.172 Angle : 0.517 8.798 11889 Z= 0.256 Chirality : 0.039 0.134 1334 Planarity : 0.003 0.038 1508 Dihedral : 6.197 121.579 1179 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.27), residues: 1061 helix: 0.58 (0.21), residues: 656 sheet: -2.88 (0.82), residues: 38 loop : -2.28 (0.32), residues: 367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 1.069 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 118 average time/residue: 0.2413 time to fit residues: 38.8585 Evaluate side-chains 108 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0859 time to fit residues: 2.1820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 0.0980 chunk 57 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 8786 Z= 0.147 Angle : 0.507 8.715 11889 Z= 0.250 Chirality : 0.038 0.132 1334 Planarity : 0.003 0.037 1508 Dihedral : 6.063 126.348 1179 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.27), residues: 1061 helix: 0.73 (0.21), residues: 661 sheet: -2.59 (0.84), residues: 37 loop : -2.24 (0.32), residues: 363 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 1.064 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 115 average time/residue: 0.2284 time to fit residues: 36.5928 Evaluate side-chains 104 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0924 time to fit residues: 2.1617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.1980 chunk 20 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8786 Z= 0.198 Angle : 0.531 9.061 11889 Z= 0.260 Chirality : 0.040 0.146 1334 Planarity : 0.003 0.038 1508 Dihedral : 6.007 126.186 1179 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.27), residues: 1061 helix: 0.67 (0.21), residues: 667 sheet: -2.34 (0.88), residues: 36 loop : -2.24 (0.32), residues: 358 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 1.110 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 102 average time/residue: 0.2505 time to fit residues: 35.1331 Evaluate side-chains 99 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0847 time to fit residues: 2.0972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 0.3980 chunk 74 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 8786 Z= 0.160 Angle : 0.517 9.462 11889 Z= 0.252 Chirality : 0.039 0.140 1334 Planarity : 0.003 0.036 1508 Dihedral : 5.938 128.927 1179 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.27), residues: 1061 helix: 0.80 (0.21), residues: 666 sheet: -2.41 (0.87), residues: 37 loop : -2.19 (0.32), residues: 358 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 1.150 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 108 average time/residue: 0.2452 time to fit residues: 36.2156 Evaluate side-chains 102 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1166 time to fit residues: 1.8773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.0970 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8786 Z= 0.163 Angle : 0.531 10.437 11889 Z= 0.258 Chirality : 0.039 0.188 1334 Planarity : 0.003 0.037 1508 Dihedral : 5.924 129.498 1179 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.27), residues: 1061 helix: 0.87 (0.21), residues: 667 sheet: -2.24 (0.87), residues: 36 loop : -2.20 (0.32), residues: 358 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 1.062 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 105 average time/residue: 0.2439 time to fit residues: 35.1472 Evaluate side-chains 101 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0862 time to fit residues: 1.9827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 86 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 30.0000 chunk 73 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.149256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125357 restraints weight = 9613.484| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 0.97 r_work: 0.3153 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 8786 Z= 0.149 Angle : 0.548 14.730 11889 Z= 0.258 Chirality : 0.039 0.227 1334 Planarity : 0.003 0.037 1508 Dihedral : 5.854 130.281 1179 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.27), residues: 1061 helix: 0.96 (0.21), residues: 667 sheet: -2.41 (0.84), residues: 37 loop : -2.17 (0.32), residues: 357 =============================================================================== Job complete usr+sys time: 1826.56 seconds wall clock time: 33 minutes 52.04 seconds (2032.04 seconds total)