Starting phenix.real_space_refine (version: dev) on Mon Dec 12 03:23:38 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyb_0541/12_2022/6nyb_0541_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyb_0541/12_2022/6nyb_0541.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyb_0541/12_2022/6nyb_0541_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyb_0541/12_2022/6nyb_0541_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyb_0541/12_2022/6nyb_0541_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyb_0541/12_2022/6nyb_0541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyb_0541/12_2022/6nyb_0541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyb_0541/12_2022/6nyb_0541_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyb_0541/12_2022/6nyb_0541_updated.pdb" } resolution = 4.1 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= 0.001 sd= 0.007 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 506": "NH1" <-> "NH2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A ARG 682": "NH1" <-> "NH2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "C ARG 55": "NH1" <-> "NH2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 55": "NH1" <-> "NH2" Residue "D GLU 73": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 8842 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2819 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 15, 'TRANS': 334} Chain breaks: 2 Chain: "B" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2258 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 16, 'TRANS': 272} Chain breaks: 1 Chain: "C" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1846 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 5, 'TRANS': 223} Chain: "D" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1833 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 223} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' ZN': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {' MG': 1, 'ADP': 1, 'LCJ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 136 SG CYS A 248 61.072 29.426 55.042 1.00 69.52 S ATOM 161 SG CYS A 251 62.989 27.854 57.470 1.00 79.60 S ATOM 343 SG CYS A 272 60.523 25.561 55.470 1.00113.58 S ATOM 249 SG CYS A 261 53.756 37.009 46.317 1.00107.92 S ATOM 271 SG CYS A 264 53.994 38.015 49.372 1.00114.35 S ATOM 401 SG CYS A 280 50.374 39.002 48.986 1.00149.39 S Time building chain proxies: 5.38, per 1000 atoms: 0.61 Number of scatterers: 8842 At special positions: 0 Unit cell: (111.3, 93.28, 125.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) I 1 52.95 Zn 2 29.99 S 52 16.00 P 7 15.00 Mg 1 11.99 F 1 9.00 O 1668 8.00 N 1527 7.00 C 5583 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=0, symmetry=0 Time building additional restraints: 3.86 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 272 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 248 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 251 " pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 280 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 235 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 264 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 261 " Number of angles added : 3 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 5 sheets defined 53.1% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 492 through 507 removed outlier: 3.651A pdb=" N GLN A 496 " --> pdb=" O PRO A 492 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 504 " --> pdb=" O ASN A 500 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 507 " --> pdb=" O GLY A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 550 through 569 Processing helix chain 'A' and resid 579 through 581 No H-bonds generated for 'chain 'A' and resid 579 through 581' Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 622 through 626 Processing helix chain 'A' and resid 635 through 651 Processing helix chain 'A' and resid 663 through 670 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.548A pdb=" N LEU A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET A 693 " --> pdb=" O MET A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 703 No H-bonds generated for 'chain 'A' and resid 701 through 703' Processing helix chain 'A' and resid 707 through 718 removed outlier: 3.601A pdb=" N ALA A 712 " --> pdb=" O PRO A 708 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 105 through 120 removed outlier: 3.537A pdb=" N GLN B 116 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL B 117 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU B 120 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 removed outlier: 3.529A pdb=" N LYS B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 183 removed outlier: 3.787A pdb=" N LYS B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 232 through 235 No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 243 through 258 Processing helix chain 'B' and resid 310 through 319 Processing helix chain 'B' and resid 332 through 341 Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.516A pdb=" N ALA B 366 " --> pdb=" O LYS B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'C' and resid 4 through 15 Processing helix chain 'C' and resid 21 through 32 removed outlier: 3.758A pdb=" N THR C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 69 removed outlier: 3.916A pdb=" N LEU C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 44 " --> pdb=" O GLU C 40 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL C 52 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 55 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 101 Processing helix chain 'C' and resid 112 through 130 Processing helix chain 'C' and resid 138 through 159 removed outlier: 3.578A pdb=" N GLU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 180 Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 212 through 228 Processing helix chain 'D' and resid 3 through 15 Processing helix chain 'D' and resid 20 through 30 removed outlier: 3.950A pdb=" N VAL D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 67 removed outlier: 3.814A pdb=" N LEU D 44 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL D 52 " --> pdb=" O TYR D 48 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG D 55 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D 67 " --> pdb=" O SER D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 89 removed outlier: 3.579A pdb=" N GLU D 81 " --> pdb=" O GLN D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 103 removed outlier: 3.932A pdb=" N LEU D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 132 removed outlier: 3.784A pdb=" N GLU D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 159 removed outlier: 3.984A pdb=" N ASP D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER D 145 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 180 Processing helix chain 'D' and resid 185 through 201 Processing helix chain 'D' and resid 213 through 229 Processing sheet with id= A, first strand: chain 'A' and resid 237 through 240 Processing sheet with id= B, first strand: chain 'A' and resid 527 through 530 removed outlier: 6.520A pdb=" N LYS A 473 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG A 462 " --> pdb=" O LYS A 473 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 582 through 585 Processing sheet with id= D, first strand: chain 'B' and resid 129 through 135 removed outlier: 6.853A pdb=" N CYS B 142 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA B 132 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER B 140 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR B 134 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU B 138 " --> pdb=" O TYR B 134 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 92 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N SER B 86 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS B 70 " --> pdb=" O SER B 86 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 196 through 198 407 hydrogen bonds defined for protein. 1212 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: 2.72 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 3024 1.37 - 1.55: 5889 1.55 - 1.74: 11 1.74 - 1.92: 84 1.92 - 2.11: 2 Bond restraints: 9010 Sorted by residual: bond pdb=" C4 AGS A 801 " pdb=" C5 AGS A 801 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.96e+01 bond pdb=" C5 AGS A 801 " pdb=" C6 AGS A 801 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.33e+01 bond pdb=" PG AGS A 801 " pdb=" S1G AGS A 801 " ideal model delta sigma weight residual 1.949 2.074 -0.125 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C8 AGS A 801 " pdb=" N7 AGS A 801 " ideal model delta sigma weight residual 1.311 1.358 -0.047 1.00e-02 1.00e+04 2.22e+01 ... (remaining 9005 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.64: 265 106.64 - 114.14: 5035 114.14 - 121.63: 4262 121.63 - 129.12: 2541 129.12 - 136.62: 54 Bond angle restraints: 12157 Sorted by residual: angle pdb=" C5 AGS A 801 " pdb=" C4 AGS A 801 " pdb=" N3 AGS A 801 " ideal model delta sigma weight residual 126.80 119.45 7.35 7.41e-01 1.82e+00 9.84e+01 angle pdb=" C4 AGS A 801 " pdb=" C5 AGS A 801 " pdb=" N7 AGS A 801 " ideal model delta sigma weight residual 110.73 106.42 4.31 4.52e-01 4.89e+00 9.11e+01 angle pdb=" C5 AGS A 801 " pdb=" N7 AGS A 801 " pdb=" C8 AGS A 801 " ideal model delta sigma weight residual 103.67 107.48 -3.81 4.26e-01 5.51e+00 7.99e+01 angle pdb=" N1 AGS A 801 " pdb=" C2 AGS A 801 " pdb=" N3 AGS A 801 " ideal model delta sigma weight residual 128.80 123.21 5.59 8.41e-01 1.41e+00 4.42e+01 angle pdb=" C4 AGS A 801 " pdb=" N9 AGS A 801 " pdb=" C8 AGS A 801 " ideal model delta sigma weight residual 105.70 108.67 -2.97 4.55e-01 4.83e+00 4.25e+01 ... (remaining 12152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.85: 5034 18.85 - 37.70: 335 37.70 - 56.56: 93 56.56 - 75.41: 21 75.41 - 94.26: 5 Dihedral angle restraints: 5488 sinusoidal: 2282 harmonic: 3206 Sorted by residual: dihedral pdb=" C ASP A 587 " pdb=" N ASP A 587 " pdb=" CA ASP A 587 " pdb=" CB ASP A 587 " ideal model delta harmonic sigma weight residual -122.60 -139.54 16.94 0 2.50e+00 1.60e-01 4.59e+01 dihedral pdb=" N ASP A 587 " pdb=" C ASP A 587 " pdb=" CA ASP A 587 " pdb=" CB ASP A 587 " ideal model delta harmonic sigma weight residual 122.80 138.29 -15.49 0 2.50e+00 1.60e-01 3.84e+01 dihedral pdb=" C ASP B 190 " pdb=" N ASP B 190 " pdb=" CA ASP B 190 " pdb=" CB ASP B 190 " ideal model delta harmonic sigma weight residual -122.60 -135.64 13.04 0 2.50e+00 1.60e-01 2.72e+01 ... (remaining 5485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 1209 0.138 - 0.277: 121 0.277 - 0.415: 2 0.415 - 0.554: 1 0.554 - 0.692: 1 Chirality restraints: 1334 Sorted by residual: chirality pdb=" CA ASP A 587 " pdb=" N ASP A 587 " pdb=" C ASP A 587 " pdb=" CB ASP A 587 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA ASP B 190 " pdb=" N ASP B 190 " pdb=" C ASP B 190 " pdb=" CB ASP B 190 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" CA ASP A 576 " pdb=" N ASP A 576 " pdb=" C ASP A 576 " pdb=" CB ASP A 576 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 ... (remaining 1331 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 726 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.21e+00 pdb=" C ARG A 726 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG A 726 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 727 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 628 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C GLN A 628 " -0.042 2.00e-02 2.50e+03 pdb=" O GLN A 628 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A 629 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 104 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C HIS D 104 " 0.040 2.00e-02 2.50e+03 pdb=" O HIS D 104 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU D 105 " -0.014 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.65: 89 2.65 - 3.23: 7986 3.23 - 3.80: 13946 3.80 - 4.38: 19090 4.38 - 4.96: 31467 Nonbonded interactions: 72578 Sorted by model distance: nonbonded pdb=" O2B ADP B 601 " pdb="MG MG B 602 " model vdw 2.070 2.170 nonbonded pdb=" O3P SEP A 729 " pdb=" NH2 ARG D 56 " model vdw 2.247 2.520 nonbonded pdb=" O PHE A 468 " pdb=" N ASN A 486 " model vdw 2.256 2.520 nonbonded pdb=" NZ LYS D 88 " pdb=" OE2 GLU D 92 " model vdw 2.350 2.520 nonbonded pdb=" O SER A 520 " pdb=" O GLN A 524 " model vdw 2.367 3.040 ... (remaining 72573 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 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG )) or resid 6 through 59 or (resid 60 and (name N \ or name CA or name C or name O or name CB )) or resid 61 through 201 or (resid \ 202 and (name N or name CA or name C or name O or name CB )) or resid 203 throug \ h 230)) selection = chain 'D' } 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: 9 Type Number sf(0) Gaussians I 1 10.91 5 Zn 2 6.06 5 P 7 5.49 5 Mg 1 5.21 5 S 52 5.16 5 C 5583 2.51 5 N 1527 2.21 5 O 1668 1.98 5 F 1 1.80 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 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: 0.300 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: 0.000 Extract box with map and model: 2.640 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 29.050 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 : 0.014 0.125 9010 Z= 0.876 Angle : 1.755 12.235 12157 Z= 1.314 Chirality : 0.091 0.692 1334 Planarity : 0.003 0.029 1548 Dihedral : 14.333 94.262 3414 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.39 % Favored : 94.43 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.29 % 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: -3.02 (0.22), residues: 1077 helix: -1.43 (0.18), residues: 596 sheet: -2.52 (0.58), residues: 57 loop : -2.65 (0.27), residues: 424 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 406 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 8 residues processed: 426 average time/residue: 0.2377 time to fit residues: 132.1122 Evaluate side-chains 240 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 232 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1831 time to fit residues: 3.5829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 0.0060 chunk 62 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 GLN B 87 HIS B 243 GLN C 8 GLN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 9010 Z= 0.202 Angle : 0.657 7.182 12157 Z= 0.337 Chirality : 0.041 0.168 1334 Planarity : 0.005 0.064 1548 Dihedral : 6.446 89.494 1221 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 0.21 % 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: -0.79 (0.24), residues: 1077 helix: 0.53 (0.20), residues: 600 sheet: -1.71 (0.65), residues: 54 loop : -1.91 (0.28), residues: 423 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 283 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 285 average time/residue: 0.2203 time to fit residues: 83.9404 Evaluate side-chains 190 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0750 time to fit residues: 1.6262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 80 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS B 87 HIS B 119 HIS ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9010 Z= 0.253 Angle : 0.642 7.842 12157 Z= 0.327 Chirality : 0.042 0.176 1334 Planarity : 0.006 0.106 1548 Dihedral : 6.232 95.172 1221 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.10 % 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: -0.30 (0.25), residues: 1077 helix: 0.88 (0.21), residues: 604 sheet: -0.98 (0.62), residues: 60 loop : -1.71 (0.29), residues: 413 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.2072 time to fit residues: 72.4524 Evaluate side-chains 174 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.254 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN A 568 HIS A 661 ASN B 87 HIS B 195 ASN D 42 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 9010 Z= 0.422 Angle : 0.755 8.266 12157 Z= 0.389 Chirality : 0.046 0.216 1334 Planarity : 0.006 0.091 1548 Dihedral : 6.498 97.707 1221 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.31 % 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 (0.25), residues: 1077 helix: 0.68 (0.21), residues: 603 sheet: -1.18 (0.62), residues: 59 loop : -1.64 (0.30), residues: 415 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 208 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 211 average time/residue: 0.1990 time to fit residues: 60.0528 Evaluate side-chains 155 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0930 time to fit residues: 1.8237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS A 542 HIS ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 ASN ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN D 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 9010 Z= 0.258 Angle : 0.638 7.882 12157 Z= 0.324 Chirality : 0.042 0.175 1334 Planarity : 0.004 0.061 1548 Dihedral : 6.347 101.708 1221 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 0.10 % 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: -0.11 (0.26), residues: 1077 helix: 1.02 (0.21), residues: 603 sheet: -0.90 (0.64), residues: 59 loop : -1.57 (0.30), residues: 415 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.1850 time to fit residues: 58.1893 Evaluate side-chains 163 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 ASN ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN D 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9010 Z= 0.190 Angle : 0.618 8.397 12157 Z= 0.310 Chirality : 0.042 0.174 1334 Planarity : 0.004 0.068 1548 Dihedral : 6.194 106.738 1221 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 0.10 % 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: 0.15 (0.26), residues: 1077 helix: 1.19 (0.22), residues: 603 sheet: -0.79 (0.64), residues: 60 loop : -1.41 (0.30), residues: 414 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 216 average time/residue: 0.1712 time to fit residues: 53.7634 Evaluate side-chains 165 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0828 time to fit residues: 1.7047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 0.0770 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 62 optimal weight: 40.0000 chunk 47 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 ASN ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.6010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9010 Z= 0.205 Angle : 0.610 7.776 12157 Z= 0.310 Chirality : 0.041 0.160 1334 Planarity : 0.004 0.044 1548 Dihedral : 6.154 109.010 1221 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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: 0.26 (0.26), residues: 1077 helix: 1.30 (0.22), residues: 605 sheet: -0.74 (0.62), residues: 60 loop : -1.40 (0.30), residues: 412 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1814 time to fit residues: 56.2000 Evaluate side-chains 163 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 ASN ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN D 146 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.6357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 9010 Z= 0.336 Angle : 0.719 9.009 12157 Z= 0.366 Chirality : 0.044 0.231 1334 Planarity : 0.005 0.075 1548 Dihedral : 6.414 111.444 1221 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % 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: 0.01 (0.26), residues: 1077 helix: 1.09 (0.22), residues: 602 sheet: -0.72 (0.62), residues: 59 loop : -1.51 (0.30), residues: 416 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1835 time to fit residues: 53.6158 Evaluate side-chains 153 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 ASN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN D 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.6423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9010 Z= 0.179 Angle : 0.647 11.862 12157 Z= 0.323 Chirality : 0.042 0.161 1334 Planarity : 0.004 0.049 1548 Dihedral : 6.219 112.825 1221 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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: 0.25 (0.26), residues: 1077 helix: 1.30 (0.22), residues: 600 sheet: -0.49 (0.63), residues: 63 loop : -1.45 (0.30), residues: 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1793 time to fit residues: 56.3031 Evaluate side-chains 161 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN D 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.6546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9010 Z= 0.202 Angle : 0.675 12.514 12157 Z= 0.338 Chirality : 0.043 0.158 1334 Planarity : 0.004 0.040 1548 Dihedral : 6.281 115.139 1221 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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: 0.28 (0.26), residues: 1077 helix: 1.33 (0.22), residues: 592 sheet: -0.42 (0.63), residues: 63 loop : -1.41 (0.30), residues: 422 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1893 time to fit residues: 58.0020 Evaluate side-chains 163 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.193 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 87 optimal weight: 0.2980 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 ASN ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN B 239 HIS D 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.102781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.076466 restraints weight = 20940.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.078751 restraints weight = 13234.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.080274 restraints weight = 9906.920| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.6668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9010 Z= 0.203 Angle : 0.688 11.016 12157 Z= 0.349 Chirality : 0.043 0.177 1334 Planarity : 0.004 0.049 1548 Dihedral : 6.225 116.001 1221 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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: 0.26 (0.26), residues: 1077 helix: 1.30 (0.22), residues: 593 sheet: -0.39 (0.64), residues: 63 loop : -1.39 (0.30), residues: 421 =============================================================================== Job complete usr+sys time: 1968.32 seconds wall clock time: 36 minutes 23.19 seconds (2183.19 seconds total)