Starting phenix.real_space_refine (version: dev) on Sat May 14 02:47:47 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqb_22288/05_2022/6xqb_22288.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqb_22288/05_2022/6xqb_22288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqb_22288/05_2022/6xqb_22288.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqb_22288/05_2022/6xqb_22288.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqb_22288/05_2022/6xqb_22288.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqb_22288/05_2022/6xqb_22288.pdb" } resolution = 3.4 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= 0.002 sd= 0.038 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 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 16323 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 12682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 12682 Classifications: {'peptide': 801} Link IDs: {'PTRANS': 25, 'TRANS': 775} Chain breaks: 5 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1713 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 993 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 444 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 229 Classifications: {'RNA': 7} Modifications used: {'rna3p_pyr': 3, 'rna3p_pur': 4, '3*END': 1} Link IDs: {'rna3p': 6} Chain: "F" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 259 Classifications: {'RNA': 8} Modifications used: {'rna3p_pyr': 4, 'rna3p_pur': 4} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3213 SG CYS A 301 37.207 66.986 36.975 1.00131.34 S ATOM 3290 SG CYS A 306 37.350 65.836 33.243 1.00128.23 S ATOM 3355 SG CYS A 310 40.424 66.248 34.854 1.00134.44 S ATOM 6095 SG CYS A 487 19.687 63.110 45.316 1.00126.47 S ATOM 8612 SG CYS A 645 17.972 62.844 42.341 1.00141.82 S ATOM 8622 SG CYS A 646 22.155 64.389 43.308 1.00142.48 S Time building chain proxies: 8.23, per 1000 atoms: 0.50 Number of scatterers: 16323 At special positions: 0 Unit cell: (84.55, 97.01, 108.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 61 16.00 P 15 15.00 Mg 1 11.99 O 1603 8.00 N 1392 7.00 C 5262 6.00 H 7987 1.00 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: 14.07 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " Number of angles added : 3 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 53.2% alpha, 11.5% beta 7 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 7.35 Creating SS restraints... Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.684A pdb=" N LYS A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.520A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 198 removed outlier: 3.867A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 242 Processing helix chain 'A' and resid 243 through 246 removed outlier: 4.018A pdb=" N THR A 246 " --> pdb=" O PRO A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.264A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 254 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 260 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 315 removed outlier: 3.614A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 319 removed outlier: 3.585A pdb=" N THR A 319 " --> pdb=" O LEU A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 316 through 319' Processing helix chain 'A' and resid 367 through 376 removed outlier: 4.455A pdb=" N ALA A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 removed outlier: 4.222A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 5.132A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.812A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.726A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.532A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 573 removed outlier: 3.682A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 573 " --> pdb=" O ARG A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 removed outlier: 3.912A pdb=" N ALA A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 638 removed outlier: 3.739A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 686 through 710 removed outlier: 3.893A pdb=" N SER A 709 " --> pdb=" O ASN A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 732 Processing helix chain 'A' and resid 738 through 752 removed outlier: 4.021A pdb=" N VAL A 742 " --> pdb=" O ASP A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 789 removed outlier: 4.050A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 843 removed outlier: 3.905A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 865 removed outlier: 3.834A pdb=" N ASP A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 872 Processing helix chain 'A' and resid 874 through 895 removed outlier: 3.505A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 894 " --> pdb=" O LYS A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 915 removed outlier: 3.703A pdb=" N SER A 913 " --> pdb=" O ASN A 909 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG A 914 " --> pdb=" O ASP A 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.533A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 removed outlier: 4.530A pdb=" N GLY B 113 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS B 114 " --> pdb=" O ARG B 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 114' Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 135 through 142 removed outlier: 3.559A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.751A pdb=" N ASN B 179 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.548A pdb=" N LEU C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 40 Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.634A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.515A pdb=" N THR D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 112 removed outlier: 3.610A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.416A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.416A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 115 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 390 removed outlier: 6.826A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 400 removed outlier: 7.200A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 822 369 hydrogen bonds defined for protein. 1011 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 14.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7963 1.03 - 1.22: 42 1.22 - 1.42: 3706 1.42 - 1.62: 4725 1.62 - 1.82: 93 Bond restraints: 16529 Sorted by residual: bond pdb=" C GLY A 203 " pdb=" N VAL A 204 " ideal model delta sigma weight residual 1.332 1.273 0.059 1.73e-02 3.34e+03 1.16e+01 bond pdb=" CB VAL A 473 " pdb=" CG2 VAL A 473 " ideal model delta sigma weight residual 1.521 1.411 0.110 3.30e-02 9.18e+02 1.10e+01 bond pdb=" C GLN A 573 " pdb=" N LYS A 574 " ideal model delta sigma weight residual 1.332 1.290 0.043 1.40e-02 5.10e+03 9.28e+00 bond pdb=" CA ILE B 120 " pdb=" C ILE B 120 " ideal model delta sigma weight residual 1.524 1.494 0.030 1.05e-02 9.07e+03 8.26e+00 bond pdb=" CB VAL A 637 " pdb=" CG2 VAL A 637 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.65e+00 ... (remaining 16524 not shown) Histogram of bond angle deviations from ideal: 93.98 - 102.16: 53 102.16 - 110.33: 14673 110.33 - 118.50: 7300 118.50 - 126.67: 7547 126.67 - 134.85: 156 Bond angle restraints: 29729 Sorted by residual: angle pdb=" N GLY A 503 " pdb=" CA GLY A 503 " pdb=" C GLY A 503 " ideal model delta sigma weight residual 111.85 117.17 -5.32 1.06e+00 8.90e-01 2.51e+01 angle pdb=" CA LEU A 241 " pdb=" CB LEU A 241 " pdb=" CG LEU A 241 " ideal model delta sigma weight residual 116.30 133.24 -16.94 3.50e+00 8.16e-02 2.34e+01 angle pdb=" CA LEU A 247 " pdb=" CB LEU A 247 " pdb=" CG LEU A 247 " ideal model delta sigma weight residual 116.30 131.87 -15.57 3.50e+00 8.16e-02 1.98e+01 angle pdb=" CA PRO A 830 " pdb=" C PRO A 830 " pdb=" N TYR A 831 " ideal model delta sigma weight residual 114.65 120.20 -5.55 1.27e+00 6.20e-01 1.91e+01 angle pdb=" N PHE A 321 " pdb=" CA PHE A 321 " pdb=" C PHE A 321 " ideal model delta sigma weight residual 110.36 104.55 5.81 1.34e+00 5.57e-01 1.88e+01 ... (remaining 29724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 5991 17.42 - 34.83: 574 34.83 - 52.25: 130 52.25 - 69.67: 41 69.67 - 87.08: 10 Dihedral angle restraints: 6746 sinusoidal: 3141 harmonic: 3605 Sorted by residual: dihedral pdb=" CA ASP A 465 " pdb=" C ASP A 465 " pdb=" N ILE A 466 " pdb=" CA ILE A 466 " ideal model delta harmonic sigma weight residual -180.00 -136.97 -43.03 0 5.00e+00 4.00e-02 7.41e+01 dihedral pdb=" CA VAL A 234 " pdb=" C VAL A 234 " pdb=" N ASP A 235 " pdb=" CA ASP A 235 " ideal model delta harmonic sigma weight residual -180.00 -139.49 -40.51 0 5.00e+00 4.00e-02 6.56e+01 dihedral pdb=" CA LEU B 180 " pdb=" C LEU B 180 " pdb=" N ALA B 181 " pdb=" CA ALA B 181 " ideal model delta harmonic sigma weight residual 180.00 141.10 38.90 0 5.00e+00 4.00e-02 6.05e+01 ... (remaining 6743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1052 0.076 - 0.152: 253 0.152 - 0.229: 27 0.229 - 0.305: 2 0.305 - 0.381: 1 Chirality restraints: 1335 Sorted by residual: chirality pdb=" CB VAL A 473 " pdb=" CA VAL A 473 " pdb=" CG1 VAL A 473 " pdb=" CG2 VAL A 473 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA PRO A 296 " pdb=" N PRO A 296 " pdb=" C PRO A 296 " pdb=" CB PRO A 296 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL A 763 " pdb=" CA VAL A 763 " pdb=" CG1 VAL A 763 " pdb=" CG2 VAL A 763 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1332 not shown) Planarity restraints: 2410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 166 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.19e+00 pdb=" C VAL A 166 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL A 166 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 167 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 134 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.11e+00 pdb=" C ASP B 134 " -0.052 2.00e-02 2.50e+03 pdb=" O ASP B 134 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR B 135 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 238 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C TYR A 238 " 0.050 2.00e-02 2.50e+03 pdb=" O TYR A 238 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A 239 " -0.017 2.00e-02 2.50e+03 ... (remaining 2407 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1295 2.19 - 2.79: 34516 2.79 - 3.39: 46566 3.39 - 4.00: 59821 4.00 - 4.60: 90605 Nonbonded interactions: 232803 Sorted by model distance: nonbonded pdb="HE21 GLN A 210 " pdb=" O GLY A 214 " model vdw 1.583 1.850 nonbonded pdb=" OD1 ASP A 194 " pdb=" HH TYR A 289 " model vdw 1.601 1.850 nonbonded pdb=" O ASP A 454 " pdb=" H ARG A 457 " model vdw 1.648 1.850 nonbonded pdb=" O VAL A 234 " pdb=" H TYR A 237 " model vdw 1.650 1.850 nonbonded pdb=" O PHE A 480 " pdb=" HZ1 LYS A 641 " model vdw 1.655 1.850 ... (remaining 232798 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 'E' and resid 3 through 8) selection = (chain 'F' and resid 3 through 8) } 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 15 5.49 5 Mg 1 5.21 5 S 61 5.16 5 C 5262 2.51 5 N 1392 2.21 5 O 1603 1.98 5 H 7987 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 0.240 Extract box with map and model: 3.820 Check model and map are aligned: 0.250 Convert atoms to be neutral: 0.130 Process input model: 64.700 Find NCS groups from input model: 0.290 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: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 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 : 0.012 0.110 8542 Z= 0.771 Angle : 1.277 16.942 11661 Z= 0.711 Chirality : 0.064 0.381 1335 Planarity : 0.008 0.059 1427 Dihedral : 12.243 78.509 3104 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.72 % 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: -5.15 (0.20), residues: 990 helix: -3.28 (0.17), residues: 427 sheet: -2.91 (0.47), residues: 86 loop : -3.65 (0.24), residues: 477 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 1.229 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 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: 2 outliers final: 1 residues processed: 171 average time/residue: 0.4086 time to fit residues: 96.5735 Evaluate side-chains 132 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.258 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2336 time to fit residues: 1.9797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN A 491 ASN A 492 GLN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN A 705 ASN ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5540 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8542 Z= 0.192 Angle : 0.671 9.183 11661 Z= 0.356 Chirality : 0.040 0.145 1335 Planarity : 0.005 0.053 1427 Dihedral : 8.345 59.407 1267 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.82 (0.23), residues: 990 helix: -2.14 (0.21), residues: 443 sheet: -2.47 (0.51), residues: 86 loop : -2.90 (0.26), residues: 461 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 154 time to evaluate : 1.433 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 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: 12 outliers final: 11 residues processed: 159 average time/residue: 0.4108 time to fit residues: 92.5001 Evaluate side-chains 149 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2806 time to fit residues: 6.3987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5749 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 8542 Z= 0.297 Angle : 0.710 8.040 11661 Z= 0.386 Chirality : 0.042 0.145 1335 Planarity : 0.005 0.061 1427 Dihedral : 8.042 58.443 1267 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 22.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.72 % Favored : 88.28 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.23), residues: 990 helix: -1.73 (0.21), residues: 439 sheet: -2.56 (0.46), residues: 95 loop : -2.94 (0.27), residues: 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 1.438 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 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: 13 outliers final: 9 residues processed: 151 average time/residue: 0.4332 time to fit residues: 93.3250 Evaluate side-chains 143 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 1.330 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.2195 time to fit residues: 5.1000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5732 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 8542 Z= 0.239 Angle : 0.638 6.242 11661 Z= 0.345 Chirality : 0.039 0.135 1335 Planarity : 0.005 0.066 1427 Dihedral : 7.785 58.851 1267 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.24), residues: 990 helix: -1.39 (0.22), residues: 436 sheet: -2.59 (0.46), residues: 96 loop : -2.80 (0.27), residues: 458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 1.361 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 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: 7 outliers final: 6 residues processed: 135 average time/residue: 0.4291 time to fit residues: 81.8747 Evaluate side-chains 135 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 1.430 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.2094 time to fit residues: 4.0315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 GLN ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5830 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 8542 Z= 0.287 Angle : 0.686 8.998 11661 Z= 0.370 Chirality : 0.041 0.141 1335 Planarity : 0.005 0.060 1427 Dihedral : 7.731 58.758 1267 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 25.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.03 % Favored : 86.97 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.24), residues: 990 helix: -1.24 (0.23), residues: 431 sheet: -2.56 (0.47), residues: 91 loop : -2.81 (0.27), residues: 468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.333 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 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: 14 outliers final: 9 residues processed: 147 average time/residue: 0.3948 time to fit residues: 81.9292 Evaluate side-chains 141 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 1.418 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.2184 time to fit residues: 4.9909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN A 439 HIS ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6033 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.091 8542 Z= 0.499 Angle : 0.888 8.767 11661 Z= 0.489 Chirality : 0.048 0.177 1335 Planarity : 0.007 0.055 1427 Dihedral : 8.583 64.091 1267 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 45.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.16 % Favored : 83.84 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.13 (0.22), residues: 990 helix: -2.08 (0.21), residues: 437 sheet: -2.99 (0.50), residues: 74 loop : -3.37 (0.24), residues: 479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 1.410 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 22 residues processed: 150 average time/residue: 0.4022 time to fit residues: 85.3145 Evaluate side-chains 146 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.283 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 2 residues processed: 22 average time/residue: 0.2332 time to fit residues: 10.1206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5768 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8542 Z= 0.185 Angle : 0.626 6.978 11661 Z= 0.333 Chirality : 0.039 0.150 1335 Planarity : 0.005 0.076 1427 Dihedral : 7.521 61.833 1267 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.09 (0.24), residues: 990 helix: -1.18 (0.23), residues: 442 sheet: -2.98 (0.46), residues: 86 loop : -2.75 (0.26), residues: 462 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.292 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 145 average time/residue: 0.4058 time to fit residues: 82.7678 Evaluate side-chains 136 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2135 time to fit residues: 3.4874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 8542 Z= 0.267 Angle : 0.666 7.685 11661 Z= 0.360 Chirality : 0.040 0.143 1335 Planarity : 0.005 0.064 1427 Dihedral : 7.516 61.608 1267 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 25.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.24), residues: 990 helix: -1.13 (0.23), residues: 430 sheet: -2.93 (0.48), residues: 79 loop : -2.85 (0.25), residues: 481 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.326 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 133 average time/residue: 0.4094 time to fit residues: 76.7274 Evaluate side-chains 135 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1835 time to fit residues: 3.0357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 8542 Z= 0.218 Angle : 0.626 7.462 11661 Z= 0.334 Chirality : 0.039 0.144 1335 Planarity : 0.004 0.057 1427 Dihedral : 7.362 61.592 1267 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 23.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.24), residues: 990 helix: -0.92 (0.23), residues: 437 sheet: -2.87 (0.48), residues: 86 loop : -2.76 (0.26), residues: 467 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 137 time to evaluate : 1.359 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 139 average time/residue: 0.4064 time to fit residues: 80.1382 Evaluate side-chains 137 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2249 time to fit residues: 3.5662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 moved from start: 0.6483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.088 8542 Z= 0.229 Angle : 0.632 7.602 11661 Z= 0.338 Chirality : 0.040 0.196 1335 Planarity : 0.005 0.087 1427 Dihedral : 7.246 60.456 1267 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.24), residues: 990 helix: -0.74 (0.23), residues: 431 sheet: -2.84 (0.49), residues: 86 loop : -2.75 (0.26), residues: 473 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 1.326 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 136 average time/residue: 0.4216 time to fit residues: 80.8483 Evaluate side-chains 135 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 1.329 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1860 time to fit residues: 2.4414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 69 optimal weight: 0.1980 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.152622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.135699 restraints weight = 90118.258| |-----------------------------------------------------------------------------| r_work (start): 0.4482 rms_B_bonded: 5.91 r_work: 0.4469 rms_B_bonded: 5.60 restraints_weight: 2.0000 r_work: 0.4463 rms_B_bonded: 5.03 restraints_weight: 4.0000 r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.6696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 8542 Z= 0.202 Angle : 0.608 7.603 11661 Z= 0.323 Chirality : 0.039 0.216 1335 Planarity : 0.004 0.087 1427 Dihedral : 7.071 59.296 1267 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % 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: -2.55 (0.25), residues: 990 helix: -0.56 (0.24), residues: 446 sheet: -2.59 (0.54), residues: 76 loop : -2.70 (0.26), residues: 468 =============================================================================== Job complete usr+sys time: 3617.29 seconds wall clock time: 65 minutes 17.98 seconds (3917.98 seconds total)