Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 19:49:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stx_25438/08_2023/7stx_25438_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stx_25438/08_2023/7stx_25438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stx_25438/08_2023/7stx_25438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stx_25438/08_2023/7stx_25438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stx_25438/08_2023/7stx_25438_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stx_25438/08_2023/7stx_25438_updated.pdb" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 44 5.16 5 C 5508 2.51 5 N 1438 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B GLU 349": "OE1" <-> "OE2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B GLU 451": "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 643": "OE1" <-> "OE2" Residue "B ARG 656": "NH1" <-> "NH2" Residue "B ASP 668": "OD1" <-> "OD2" Residue "B ASP 670": "OD1" <-> "OD2" Residue "B GLU 673": "OE1" <-> "OE2" 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 746": "OE1" <-> "OE2" Residue "B GLU 792": "OE1" <-> "OE2" Residue "B GLU 802": "OE1" <-> "OE2" Residue "B GLU 933": "OE1" <-> "OE2" Residue "B GLU 965": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 8611 Number of models: 1 Model: "" Number of chains: 5 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: 7246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7246 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 31, 'TRANS': 882} Chain breaks: 4 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TYR:plan': 1, 'UNK:plan-1': 28, 'ASP:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.58, per 1000 atoms: 0.53 Number of scatterers: 8611 At special positions: 0 Unit cell: (94.62, 101.26, 114.54, 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 5508 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.3 seconds 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 2 sheets defined 57.1% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 88 through 102 Processing helix chain 'A' and resid 117 through 126 removed outlier: 3.913A pdb=" N GLN A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 23 removed outlier: 3.573A pdb=" N UNK B 22 " --> pdb=" O UNK B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 34 removed outlier: 3.567A pdb=" N UNK B 32 " --> pdb=" O UNK B 28 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N UNK B 33 " --> pdb=" O UNK B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 62 through 71 removed outlier: 4.558A pdb=" N LEU B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.804A pdb=" N ILE B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.952A pdb=" N THR B 99 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS B 100 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR B 102 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 126 Processing helix chain 'B' and resid 129 through 142 removed outlier: 3.870A pdb=" N GLN B 133 " --> pdb=" O TYR B 129 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLN B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 161 removed outlier: 3.884A pdb=" N SER B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 153 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 removed outlier: 4.202A pdb=" N MET B 184 " --> pdb=" O MET B 180 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 209 through 217 removed outlier: 3.770A pdb=" N ASP B 214 " --> pdb=" O GLN B 210 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 241 removed outlier: 3.959A pdb=" N MET B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 259 removed outlier: 3.956A pdb=" N LEU B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 removed outlier: 3.911A pdb=" N THR B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.537A pdb=" N VAL B 303 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LYS B 304 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE B 305 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B 307 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE B 310 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 312 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 315 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 335 removed outlier: 3.839A pdb=" N LEU B 328 " --> pdb=" O HIS B 324 " (cutoff:3.500A) removed outlier: 3.592A 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: 3.822A pdb=" N GLY B 390 " --> pdb=" O ASN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 423 removed outlier: 3.676A pdb=" N GLN B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS B 414 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 448 removed outlier: 4.174A pdb=" N VAL B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 471 removed outlier: 4.140A pdb=" N LEU B 469 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 482 removed outlier: 3.704A pdb=" N GLU B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) 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 543 through 550 removed outlier: 4.629A pdb=" N ARG B 548 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B 550 " --> pdb=" O THR B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 584 removed outlier: 3.977A 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 623 Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 673 through 699 removed outlier: 3.543A pdb=" N GLY B 699 " --> pdb=" O ARG B 695 " (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: 3.648A pdb=" N GLU B 739 " --> pdb=" O GLU B 735 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 746 " --> pdb=" O LYS B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 766 removed outlier: 3.750A pdb=" N ASN B 766 " --> pdb=" O GLY B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 789 removed outlier: 4.172A pdb=" N SER B 776 " --> pdb=" O CYS B 772 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 779 " --> pdb=" O SER B 775 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 781 " --> pdb=" O PHE B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 819 removed outlier: 3.790A pdb=" N GLU B 799 " --> pdb=" O MET B 795 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 800 " --> pdb=" O GLU B 796 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 810 " --> pdb=" O LYS B 806 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 811 " --> pdb=" O SER B 807 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP B 814 " --> pdb=" O ASP B 810 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 816 " --> pdb=" O LEU B 812 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 817 " --> pdb=" O LYS B 813 " (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 867 removed outlier: 3.965A pdb=" N LEU B 841 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 844 " --> pdb=" O ASN B 840 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 847 " --> pdb=" O PHE B 843 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL B 850 " --> pdb=" O GLU B 846 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 860 " --> pdb=" O SER B 856 " (cutoff:3.500A) Proline residue: B 864 - end of helix Processing helix chain 'B' and resid 884 through 904 removed outlier: 3.921A pdb=" N SER B 889 " --> pdb=" O PRO B 885 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 895 " --> pdb=" O GLN B 891 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY B 896 " --> pdb=" O ASP B 892 " (cutoff:3.500A) removed outlier: 3.854A 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: 3.540A pdb=" N SER B 938 " --> pdb=" O GLU B 934 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS B 939 " --> pdb=" O ARG B 935 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 947 " --> pdb=" O GLY B 943 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS B 951 " --> pdb=" O SER B 947 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU B 965 " --> pdb=" O LYS B 961 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR B 966 " --> pdb=" O LYS B 962 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR B 967 " --> pdb=" O ARG B 963 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS B 968 " --> pdb=" O LEU B 964 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 4 through 6 Processing sheet with id= B, first strand: chain 'A' and resid 111 through 113 333 hydrogen bonds defined for protein. 957 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: 2.17 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.80: 8771 1.80 - 2.42: 13 2.42 - 3.03: 0 3.03 - 3.65: 0 3.65 - 4.27: 2 Bond restraints: 8786 Sorted by residual: bond pdb=" AP1 COA A 201 " pdb="AO5* COA A 201 " ideal model delta sigma weight residual 1.610 4.271 -2.661 2.00e-02 2.50e+03 1.77e+04 bond pdb=" AO6 COA A 201 " pdb=" AP2 COA A 201 " ideal model delta sigma weight residual 1.610 4.182 -2.572 2.00e-02 2.50e+03 1.65e+04 bond pdb="AC1* COA A 201 " pdb="AO4* COA A 201 " ideal model delta sigma weight residual 1.410 1.641 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" PC9 COA A 201 " pdb=" PO9 COA A 201 " ideal model delta sigma weight residual 1.410 1.202 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb="AC1* COA A 201 " pdb="AC2* COA A 201 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 8781 not shown) Histogram of bond angle deviations from ideal: 14.37 - 38.35: 2 38.35 - 62.33: 0 62.33 - 86.31: 3 86.31 - 110.29: 2161 110.29 - 134.26: 9723 Bond angle restraints: 11889 Sorted by residual: angle pdb=" AO3 COA A 201 " pdb=" AP1 COA A 201 " pdb="AO5* COA A 201 " ideal model delta sigma weight residual 102.60 14.37 88.23 3.00e+00 1.11e-01 8.65e+02 angle pdb=" AO3 COA A 201 " pdb=" AP2 COA A 201 " pdb=" AO6 COA A 201 " ideal model delta sigma weight residual 102.60 18.36 84.24 3.00e+00 1.11e-01 7.88e+02 angle pdb=" N GLN B 462 " pdb=" CA GLN B 462 " pdb=" C GLN B 462 " ideal model delta sigma weight residual 110.41 79.86 30.55 1.23e+00 6.61e-01 6.17e+02 angle pdb=" N PRO B 701 " pdb=" CA PRO B 701 " pdb=" C PRO B 701 " ideal model delta sigma weight residual 111.77 80.65 31.12 1.67e+00 3.59e-01 3.47e+02 angle pdb=" N LEU B 640 " pdb=" CA LEU B 640 " pdb=" C LEU B 640 " ideal model delta sigma weight residual 109.07 81.03 28.04 1.61e+00 3.86e-01 3.03e+02 ... (remaining 11884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 4933 25.94 - 51.87: 319 51.87 - 77.81: 36 77.81 - 103.74: 11 103.74 - 129.68: 2 Dihedral angle restraints: 5301 sinusoidal: 2128 harmonic: 3173 Sorted by residual: dihedral pdb=" C LYS B 145 " pdb=" N LYS B 145 " pdb=" CA LYS B 145 " pdb=" CB LYS B 145 " ideal model delta harmonic sigma weight residual -122.60 -93.42 -29.18 0 2.50e+00 1.60e-01 1.36e+02 dihedral pdb=" C GLN B 462 " pdb=" N GLN B 462 " pdb=" CA GLN B 462 " pdb=" CB GLN B 462 " ideal model delta harmonic sigma weight residual -122.60 -95.16 -27.44 0 2.50e+00 1.60e-01 1.21e+02 dihedral pdb=" C LYS B 667 " pdb=" N LYS B 667 " pdb=" CA LYS B 667 " pdb=" CB LYS B 667 " ideal model delta harmonic sigma weight residual -122.60 -98.27 -24.33 0 2.50e+00 1.60e-01 9.47e+01 ... (remaining 5298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 1283 0.145 - 0.291: 36 0.291 - 0.436: 10 0.436 - 0.581: 3 0.581 - 0.727: 2 Chirality restraints: 1334 Sorted by residual: chirality pdb=" CA LYS B 145 " pdb=" N LYS B 145 " pdb=" C LYS B 145 " pdb=" CB LYS B 145 " both_signs ideal model delta sigma weight residual False 2.51 3.24 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CA GLN B 462 " pdb=" N GLN B 462 " pdb=" C GLN B 462 " pdb=" CB GLN B 462 " both_signs ideal model delta sigma weight residual False 2.51 3.21 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CA LEU B 640 " pdb=" N LEU B 640 " pdb=" C LEU B 640 " pdb=" CB LEU B 640 " both_signs ideal model delta sigma weight residual False 2.51 3.04 -0.53 2.00e-01 2.50e+01 6.95e+00 ... (remaining 1331 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 43 " -0.032 2.00e-02 2.50e+03 3.72e-02 2.42e+01 pdb=" CG PHE A 43 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 PHE A 43 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE A 43 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 43 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 PHE A 43 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 43 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 666 " -0.023 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C PRO B 666 " 0.082 2.00e-02 2.50e+03 pdb=" O PRO B 666 " -0.031 2.00e-02 2.50e+03 pdb=" N LYS B 667 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 757 " -0.060 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO B 758 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 758 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 758 " -0.048 5.00e-02 4.00e+02 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 7 2.07 - 2.78: 2076 2.78 - 3.48: 10781 3.48 - 4.19: 20066 4.19 - 4.90: 36013 Nonbonded interactions: 68943 Sorted by model distance: nonbonded pdb=" CG2 ILE B 277 " pdb=" OG SER B 298 " model vdw 1.362 3.460 nonbonded pdb=" AO6 COA A 201 " pdb=" AP1 COA A 201 " model vdw 1.635 2.720 nonbonded pdb=" AP2 COA A 201 " pdb="AO5* COA A 201 " model vdw 1.641 2.720 nonbonded pdb=" OD1 ASN A 16 " pdb=" NE2 GLN B 538 " model vdw 1.673 2.520 nonbonded pdb=" N GLN B 462 " pdb=" O GLN B 462 " model vdw 1.881 2.496 ... (remaining 68938 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 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: 1.290 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: 5.520 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.530 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 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 : 0.041 2.661 8786 Z= 2.567 Angle : 1.857 88.232 11889 Z= 0.933 Chirality : 0.079 0.727 1334 Planarity : 0.009 0.092 1508 Dihedral : 17.272 129.678 3243 Min Nonbonded Distance : 1.362 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.66 % Favored : 89.95 % Rotamer Outliers : 2.09 % Cbeta Deviations : 1.07 % 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: -5.56 (0.18), residues: 1035 helix: -3.42 (0.12), residues: 673 sheet: -4.64 (0.68), residues: 35 loop : -3.70 (0.27), residues: 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 229 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 210 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 5 residues processed: 225 average time/residue: 0.2577 time to fit residues: 75.4402 Evaluate side-chains 113 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0939 time to fit residues: 2.2008 ------------------------------------------------------------------------------- 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: 0.6980 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.0870 chunk 61 optimal weight: 0.2980 chunk 96 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 ASN B 387 GLN B 428 HIS ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B 501 HIS B 573 ASN B 605 ASN B 766 ASN B 868 ASN B 898 GLN B 914 HIS B 951 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8786 Z= 0.198 Angle : 0.682 10.637 11889 Z= 0.339 Chirality : 0.040 0.225 1334 Planarity : 0.006 0.071 1508 Dihedral : 9.293 134.846 1190 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.70 % Favored : 91.21 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -3.54 (0.23), residues: 1035 helix: -1.72 (0.18), residues: 660 sheet: -3.83 (0.80), residues: 36 loop : -3.21 (0.29), residues: 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 156 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.053 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 152 average time/residue: 0.2779 time to fit residues: 55.1448 Evaluate side-chains 119 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 0.877 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0868 time to fit residues: 3.1581 ------------------------------------------------------------------------------- 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: 0.6980 chunk 29 optimal weight: 0.1980 chunk 80 optimal weight: 0.0170 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 ASN B 898 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8786 Z= 0.172 Angle : 0.610 11.567 11889 Z= 0.305 Chirality : 0.040 0.179 1334 Planarity : 0.005 0.065 1508 Dihedral : 8.091 105.108 1190 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.60 % Favored : 91.30 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -2.63 (0.25), residues: 1035 helix: -0.94 (0.19), residues: 664 sheet: -4.07 (0.77), residues: 30 loop : -2.99 (0.31), residues: 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 149 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 145 average time/residue: 0.2527 time to fit residues: 49.1635 Evaluate side-chains 119 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 0.886 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0882 time to fit residues: 2.0728 ------------------------------------------------------------------------------- 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: 0.9990 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 0.0570 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 102 optimal weight: 0.0470 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN B 914 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 8786 Z= 0.171 Angle : 0.592 8.807 11889 Z= 0.299 Chirality : 0.040 0.216 1334 Planarity : 0.005 0.063 1508 Dihedral : 7.634 109.410 1190 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.34 % Favored : 92.46 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -2.05 (0.26), residues: 1035 helix: -0.42 (0.20), residues: 662 sheet: -3.83 (0.83), residues: 30 loop : -2.91 (0.32), residues: 343 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 146 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.056 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 140 average time/residue: 0.2331 time to fit residues: 44.5825 Evaluate side-chains 128 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0881 time to fit residues: 2.8213 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 ASN B 413 GLN B 473 HIS B 771 GLN B 798 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.5649 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= 0.295 Angle : 0.701 9.286 11889 Z= 0.350 Chirality : 0.044 0.196 1334 Planarity : 0.005 0.067 1508 Dihedral : 8.180 102.702 1190 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.89 % Favored : 91.01 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -2.19 (0.25), residues: 1035 helix: -0.56 (0.20), residues: 669 sheet: -3.69 (0.67), residues: 44 loop : -2.86 (0.33), residues: 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 158 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 1.000 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 153 average time/residue: 0.2176 time to fit residues: 46.8055 Evaluate side-chains 132 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1103 time to fit residues: 3.6203 ------------------------------------------------------------------------------- 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: 3.9990 chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 0.0270 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 354 GLN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8786 Z= 0.186 Angle : 0.607 10.756 11889 Z= 0.304 Chirality : 0.040 0.219 1334 Planarity : 0.005 0.063 1508 Dihedral : 7.531 96.035 1190 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.21 % Favored : 91.69 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.26), residues: 1035 helix: -0.07 (0.20), residues: 664 sheet: -3.62 (0.79), residues: 37 loop : -2.83 (0.32), residues: 334 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 134 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.009 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 131 average time/residue: 0.2061 time to fit residues: 37.7819 Evaluate side-chains 119 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 0.877 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0935 time to fit residues: 1.7948 ------------------------------------------------------------------------------- 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: 0.7980 chunk 58 optimal weight: 0.0980 chunk 74 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 0.0060 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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** B 798 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.6105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8786 Z= 0.168 Angle : 0.586 9.094 11889 Z= 0.294 Chirality : 0.040 0.213 1334 Planarity : 0.004 0.063 1508 Dihedral : 7.285 94.704 1190 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.12 % Favored : 91.79 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.32 (0.26), residues: 1035 helix: 0.22 (0.20), residues: 667 sheet: -3.40 (0.91), residues: 30 loop : -2.86 (0.31), residues: 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 132 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.082 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 128 average time/residue: 0.2127 time to fit residues: 38.3574 Evaluate side-chains 112 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 1.027 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0913 time to fit residues: 2.1924 ------------------------------------------------------------------------------- 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: 0.2980 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 0.0970 chunk 64 optimal weight: 0.4980 chunk 69 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 92 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 289 HIS ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8786 Z= 0.163 Angle : 0.582 7.970 11889 Z= 0.290 Chirality : 0.039 0.197 1334 Planarity : 0.004 0.061 1508 Dihedral : 7.085 94.937 1190 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.54 % Favored : 92.37 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1035 helix: 0.57 (0.21), residues: 659 sheet: -3.28 (0.92), residues: 30 loop : -2.80 (0.31), residues: 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 123 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 0.975 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 121 average time/residue: 0.2059 time to fit residues: 35.3935 Evaluate side-chains 116 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0915 time to fit residues: 2.1949 ------------------------------------------------------------------------------- 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: 0.3980 chunk 97 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 0.0670 chunk 90 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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: 0.6930 moved from start: 0.6369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8786 Z= 0.174 Angle : 0.597 9.264 11889 Z= 0.296 Chirality : 0.040 0.178 1334 Planarity : 0.004 0.062 1508 Dihedral : 7.084 99.302 1190 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.21 % Favored : 91.69 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1035 helix: 0.73 (0.21), residues: 653 sheet: -3.11 (0.96), residues: 30 loop : -2.73 (0.31), residues: 352 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 120 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 0.998 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 118 average time/residue: 0.2166 time to fit residues: 36.0088 Evaluate side-chains 110 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4263 ------------------------------------------------------------------------------- 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: 2.9990 chunk 47 optimal weight: 0.0570 chunk 69 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8786 Z= 0.194 Angle : 0.635 15.099 11889 Z= 0.310 Chirality : 0.040 0.173 1334 Planarity : 0.004 0.062 1508 Dihedral : 7.258 112.647 1190 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.60 % Favored : 91.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1035 helix: 0.75 (0.21), residues: 652 sheet: -3.18 (0.93), residues: 30 loop : -2.76 (0.31), residues: 353 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 115 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.046 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2077 time to fit residues: 33.8450 Evaluate side-chains 109 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3460 ------------------------------------------------------------------------------- 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: 0.8980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 0.0470 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 30.0000 chunk 73 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.186448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.150485 restraints weight = 8780.418| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.78 r_work: 0.3802 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.6666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8786 Z= 0.209 Angle : 0.644 14.748 11889 Z= 0.315 Chirality : 0.041 0.182 1334 Planarity : 0.004 0.063 1508 Dihedral : 7.613 133.157 1190 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.89 % Favored : 91.01 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -0.82 (0.26), residues: 1035 helix: 0.75 (0.21), residues: 650 sheet: -3.35 (0.90), residues: 30 loop : -2.81 (0.31), residues: 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2452.22 seconds wall clock time: 44 minutes 44.72 seconds (2684.72 seconds total)