Starting phenix.real_space_refine on Sun Mar 17 01:11:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqb_22288/03_2024/6xqb_22288.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqb_22288/03_2024/6xqb_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_22288/03_2024/6xqb_22288.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqb_22288/03_2024/6xqb_22288.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqb_22288/03_2024/6xqb_22288.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqb_22288/03_2024/6xqb_22288.pdb" } resolution = 3.4 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= 0.002 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 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. Process input model Symmetric amino acids flipped Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 285": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 533": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 583": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 595": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 836": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 858": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 147": "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-5265/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: {'3*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 3} 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_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} 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: 8.02, per 1000 atoms: 0.49 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: 13.02 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal 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: 7.81 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: 6.53 Time building geometry restraints manager: 13.53 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: 6972 17.42 - 34.83: 634 34.83 - 52.25: 177 52.25 - 69.67: 81 69.67 - 87.08: 16 Dihedral angle restraints: 7880 sinusoidal: 4275 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 7877 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 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: 0.520 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: 0.250 Extract box with map and model: 3.040 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 65.300 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5560 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 : 13.837 78.509 3174 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Rotamer: Outliers : 0.23 % Allowed : 3.97 % Favored : 95.80 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP A 290 HIS 0.022 0.005 HIS A 613 PHE 0.044 0.005 PHE A 326 TYR 0.031 0.005 TYR A 788 ARG 0.020 0.003 ARG A 132 *********************** 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 : 1.235 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 revert: symmetry clash REVERT: A 859 PHE cc_start: 0.7511 (t80) cc_final: 0.6713 (t80) REVERT: A 884 TYR cc_start: 0.8757 (m-10) cc_final: 0.8551 (m-10) REVERT: A 885 LEU cc_start: 0.8528 (mt) cc_final: 0.8304 (tp) REVERT: B 104 ASN cc_start: 0.6760 (t160) cc_final: 0.6326 (m110) REVERT: C 47 GLU cc_start: 0.8062 (mp0) cc_final: 0.7726 (mp0) REVERT: D 87 MET cc_start: 0.6526 (ttm) cc_final: 0.5334 (mmp) outliers start: 2 outliers final: 1 residues processed: 171 average time/residue: 0.4473 time to fit residues: 105.3465 Evaluate side-chains 134 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 MET 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: 4.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 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 B 104 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: 0.5404 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8542 Z= 0.191 Angle : 0.665 8.925 11661 Z= 0.353 Chirality : 0.040 0.141 1335 Planarity : 0.005 0.050 1427 Dihedral : 13.013 73.981 1340 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 1.48 % Allowed : 8.97 % Favored : 89.56 % 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: -3.70 (0.23), residues: 990 helix: -2.06 (0.21), residues: 444 sheet: -2.46 (0.51), residues: 86 loop : -2.82 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 617 HIS 0.007 0.002 HIS A 309 PHE 0.018 0.001 PHE A 471 TYR 0.018 0.002 TYR A 289 ARG 0.003 0.000 ARG A 735 *********************** 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 169 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 156 time to evaluate : 1.165 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 revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.7033 (m-30) cc_final: 0.6700 (p0) REVERT: A 479 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.6566 (t80) REVERT: A 519 MET cc_start: 0.2084 (mtp) cc_final: 0.1501 (mtp) REVERT: A 859 PHE cc_start: 0.7266 (t80) cc_final: 0.6415 (t80) REVERT: A 884 TYR cc_start: 0.8438 (m-10) cc_final: 0.8105 (m-10) REVERT: A 885 LEU cc_start: 0.8409 (mt) cc_final: 0.7942 (tt) REVERT: A 886 GLN cc_start: 0.9008 (mm110) cc_final: 0.8253 (mm-40) REVERT: A 888 ILE cc_start: 0.7382 (mt) cc_final: 0.7149 (mt) REVERT: B 104 ASN cc_start: 0.6839 (t0) cc_final: 0.6401 (m110) REVERT: C 40 LEU cc_start: 0.6340 (mt) cc_final: 0.6125 (mt) outliers start: 13 outliers final: 12 residues processed: 161 average time/residue: 0.4166 time to fit residues: 93.4558 Evaluate side-chains 157 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 55 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 705 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5668 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 : 0.005 0.052 8542 Z= 0.299 Angle : 0.709 8.579 11661 Z= 0.385 Chirality : 0.041 0.145 1335 Planarity : 0.005 0.059 1427 Dihedral : 12.850 73.884 1340 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 2.38 % Allowed : 11.24 % Favored : 86.38 % 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: -3.53 (0.24), residues: 990 helix: -1.72 (0.22), residues: 445 sheet: -2.54 (0.46), residues: 97 loop : -2.90 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 598 HIS 0.008 0.002 HIS C 36 PHE 0.021 0.002 PHE A 753 TYR 0.020 0.002 TYR A 674 ARG 0.002 0.000 ARG A 183 *********************** 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 165 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 1.208 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 REVERT: A 479 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.6741 (t80) REVERT: A 859 PHE cc_start: 0.7564 (t80) cc_final: 0.6656 (t80) REVERT: A 884 TYR cc_start: 0.8749 (m-10) cc_final: 0.8412 (m-10) REVERT: A 885 LEU cc_start: 0.8545 (mt) cc_final: 0.8094 (tt) REVERT: A 886 GLN cc_start: 0.9111 (mm110) cc_final: 0.8439 (mm-40) REVERT: A 888 ILE cc_start: 0.7646 (mt) cc_final: 0.7342 (mt) REVERT: B 104 ASN cc_start: 0.6880 (t0) cc_final: 0.6241 (m110) outliers start: 21 outliers final: 16 residues processed: 156 average time/residue: 0.4301 time to fit residues: 93.8636 Evaluate side-chains 153 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 521 TYR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 749 LEU 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: 2.9990 chunk 10 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN ** 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: 0.5792 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8542 Z= 0.346 Angle : 0.728 6.819 11661 Z= 0.401 Chirality : 0.042 0.146 1335 Planarity : 0.005 0.058 1427 Dihedral : 12.873 73.974 1340 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 29.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 3.06 % Allowed : 12.71 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.23), residues: 990 helix: -1.68 (0.22), residues: 442 sheet: -2.61 (0.48), residues: 91 loop : -3.11 (0.25), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 617 HIS 0.011 0.002 HIS A 309 PHE 0.027 0.002 PHE A 753 TYR 0.022 0.002 TYR A 674 ARG 0.003 0.000 ARG A 858 *********************** 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 169 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 1.368 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 revert: symmetry clash REVERT: A 350 GLU cc_start: 0.8347 (mp0) cc_final: 0.7939 (mm-30) REVERT: A 381 HIS cc_start: 0.7920 (m-70) cc_final: 0.7371 (m-70) REVERT: A 617 TRP cc_start: 0.4359 (p-90) cc_final: 0.3275 (p-90) REVERT: A 674 TYR cc_start: 0.8106 (m-80) cc_final: 0.7680 (m-80) REVERT: A 859 PHE cc_start: 0.7677 (t80) cc_final: 0.6870 (t80) REVERT: A 884 TYR cc_start: 0.8733 (m-10) cc_final: 0.8458 (m-10) REVERT: A 885 LEU cc_start: 0.8567 (mt) cc_final: 0.8339 (tp) REVERT: A 888 ILE cc_start: 0.7604 (mt) cc_final: 0.7361 (mt) REVERT: B 130 VAL cc_start: 0.0923 (OUTLIER) cc_final: 0.0619 (t) outliers start: 27 outliers final: 23 residues processed: 158 average time/residue: 0.4073 time to fit residues: 90.7472 Evaluate side-chains 162 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain D residue 90 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5828 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8542 Z= 0.334 Angle : 0.721 8.789 11661 Z= 0.392 Chirality : 0.042 0.147 1335 Planarity : 0.005 0.053 1427 Dihedral : 12.781 73.897 1340 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 29.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 3.97 % Allowed : 13.28 % Favored : 82.75 % 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: -3.53 (0.23), residues: 990 helix: -1.53 (0.22), residues: 433 sheet: -2.67 (0.47), residues: 91 loop : -3.09 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 598 HIS 0.010 0.002 HIS A 309 PHE 0.027 0.002 PHE A 753 TYR 0.020 0.002 TYR A 515 ARG 0.007 0.001 ARG A 858 *********************** 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 179 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 144 time to evaluate : 1.313 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: A 350 GLU cc_start: 0.8397 (mp0) cc_final: 0.8092 (mm-30) REVERT: A 674 TYR cc_start: 0.8072 (m-80) cc_final: 0.7642 (m-80) REVERT: A 859 PHE cc_start: 0.7757 (t80) cc_final: 0.7086 (t80) REVERT: A 884 TYR cc_start: 0.8726 (m-10) cc_final: 0.8455 (m-10) REVERT: A 885 LEU cc_start: 0.8596 (mt) cc_final: 0.8230 (tt) REVERT: A 886 GLN cc_start: 0.9206 (mm110) cc_final: 0.8536 (mm-40) REVERT: A 888 ILE cc_start: 0.7686 (mt) cc_final: 0.7436 (mt) REVERT: B 130 VAL cc_start: 0.0930 (OUTLIER) cc_final: 0.0644 (t) outliers start: 35 outliers final: 29 residues processed: 166 average time/residue: 0.4049 time to fit residues: 94.7739 Evaluate side-chains 166 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 92 PHE 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: 2.9990 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8542 Z= 0.265 Angle : 0.665 8.288 11661 Z= 0.359 Chirality : 0.040 0.151 1335 Planarity : 0.004 0.050 1427 Dihedral : 12.654 73.713 1340 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 25.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.03 % Favored : 86.97 % Rotamer: Outliers : 3.63 % Allowed : 14.30 % Favored : 82.07 % 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: -3.29 (0.24), residues: 990 helix: -1.30 (0.22), residues: 441 sheet: -2.98 (0.52), residues: 71 loop : -2.96 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 598 HIS 0.007 0.002 HIS C 36 PHE 0.024 0.002 PHE A 753 TYR 0.019 0.002 TYR A 515 ARG 0.002 0.000 ARG A 624 *********************** 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 173 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.272 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: A 157 PHE cc_start: 0.6911 (m-10) cc_final: 0.6696 (m-80) REVERT: A 350 GLU cc_start: 0.8303 (mp0) cc_final: 0.8019 (mm-30) REVERT: A 519 MET cc_start: 0.4020 (mtp) cc_final: 0.3816 (mtp) REVERT: A 859 PHE cc_start: 0.7774 (t80) cc_final: 0.6942 (t80) REVERT: A 884 TYR cc_start: 0.8679 (m-10) cc_final: 0.8392 (m-10) REVERT: A 885 LEU cc_start: 0.8647 (mt) cc_final: 0.8248 (tt) REVERT: A 886 GLN cc_start: 0.9187 (mm110) cc_final: 0.8524 (mm-40) REVERT: A 888 ILE cc_start: 0.7704 (mt) cc_final: 0.7490 (mt) REVERT: B 130 VAL cc_start: 0.0906 (OUTLIER) cc_final: 0.0605 (t) outliers start: 32 outliers final: 27 residues processed: 159 average time/residue: 0.3956 time to fit residues: 89.0442 Evaluate side-chains 163 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 92 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.5781 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8542 Z= 0.219 Angle : 0.626 8.190 11661 Z= 0.334 Chirality : 0.039 0.132 1335 Planarity : 0.004 0.042 1427 Dihedral : 12.442 73.528 1340 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 3.06 % Allowed : 15.21 % Favored : 81.73 % 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: -2.96 (0.25), residues: 990 helix: -0.98 (0.23), residues: 440 sheet: -2.93 (0.51), residues: 69 loop : -2.81 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 598 HIS 0.007 0.001 HIS A 381 PHE 0.020 0.002 PHE A 753 TYR 0.018 0.002 TYR A 515 ARG 0.006 0.000 ARG A 858 *********************** 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 166 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.242 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: A 350 GLU cc_start: 0.8240 (mp0) cc_final: 0.7951 (mm-30) REVERT: A 674 TYR cc_start: 0.7847 (m-80) cc_final: 0.7476 (m-80) REVERT: A 859 PHE cc_start: 0.7792 (t80) cc_final: 0.7016 (t80) REVERT: A 884 TYR cc_start: 0.8613 (m-10) cc_final: 0.8340 (m-10) outliers start: 27 outliers final: 23 residues processed: 157 average time/residue: 0.4110 time to fit residues: 90.9171 Evaluate side-chains 157 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 92 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.5810 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8542 Z= 0.241 Angle : 0.641 7.980 11661 Z= 0.343 Chirality : 0.039 0.138 1335 Planarity : 0.004 0.044 1427 Dihedral : 12.370 73.402 1340 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 24.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 3.06 % Allowed : 15.21 % Favored : 81.73 % 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: -2.88 (0.25), residues: 990 helix: -0.87 (0.23), residues: 436 sheet: -2.72 (0.54), residues: 71 loop : -2.84 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 617 HIS 0.007 0.002 HIS C 36 PHE 0.021 0.002 PHE A 753 TYR 0.015 0.002 TYR A 515 ARG 0.006 0.000 ARG A 858 *********************** 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 168 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 1.068 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: A 350 GLU cc_start: 0.8248 (mp0) cc_final: 0.8022 (mm-30) REVERT: A 674 TYR cc_start: 0.7888 (m-80) cc_final: 0.7543 (m-80) REVERT: A 859 PHE cc_start: 0.7734 (t80) cc_final: 0.6974 (t80) REVERT: A 884 TYR cc_start: 0.8544 (m-10) cc_final: 0.8171 (m-10) REVERT: A 888 ILE cc_start: 0.7608 (mt) cc_final: 0.7304 (mt) REVERT: B 130 VAL cc_start: 0.1158 (OUTLIER) cc_final: 0.0841 (t) outliers start: 27 outliers final: 25 residues processed: 159 average time/residue: 0.3950 time to fit residues: 88.9710 Evaluate side-chains 162 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 92 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 6.9990 chunk 54 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 ASN C 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5702 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8542 Z= 0.161 Angle : 0.583 7.611 11661 Z= 0.306 Chirality : 0.037 0.137 1335 Planarity : 0.004 0.043 1427 Dihedral : 12.152 73.293 1337 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 2.27 % Allowed : 16.69 % Favored : 81.04 % 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: -2.38 (0.25), residues: 990 helix: -0.44 (0.24), residues: 442 sheet: -2.75 (0.51), residues: 76 loop : -2.54 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 290 HIS 0.005 0.001 HIS C 36 PHE 0.012 0.001 PHE A 753 TYR 0.015 0.001 TYR A 515 ARG 0.004 0.000 ARG A 858 *********************** 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 156 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 1.290 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: A 45 PHE cc_start: 0.1855 (OUTLIER) cc_final: 0.1369 (t80) REVERT: A 674 TYR cc_start: 0.7482 (m-80) cc_final: 0.7208 (m-80) REVERT: A 756 MET cc_start: 0.5470 (tmm) cc_final: 0.4720 (ttp) REVERT: A 859 PHE cc_start: 0.7731 (t80) cc_final: 0.7014 (t80) REVERT: A 884 TYR cc_start: 0.8525 (m-10) cc_final: 0.8176 (m-10) outliers start: 20 outliers final: 17 residues processed: 149 average time/residue: 0.3899 time to fit residues: 82.6069 Evaluate side-chains 150 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 92 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 79 optimal weight: 0.0970 chunk 8 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5793 moved from start: 0.6239 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= 0.224 Angle : 0.619 7.942 11661 Z= 0.328 Chirality : 0.039 0.131 1335 Planarity : 0.004 0.038 1427 Dihedral : 12.102 73.294 1337 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 23.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 2.16 % Allowed : 17.14 % Favored : 80.70 % 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: -2.40 (0.25), residues: 990 helix: -0.40 (0.24), residues: 436 sheet: -2.81 (0.51), residues: 76 loop : -2.57 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 617 HIS 0.006 0.001 HIS A 309 PHE 0.028 0.002 PHE A 471 TYR 0.016 0.002 TYR A 238 ARG 0.004 0.000 ARG A 858 ********************** 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 156 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.111 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: A 859 PHE cc_start: 0.7816 (t80) cc_final: 0.7082 (t80) REVERT: A 884 TYR cc_start: 0.8604 (m-10) cc_final: 0.8257 (m-10) REVERT: B 163 ASP cc_start: 0.8365 (m-30) cc_final: 0.7927 (m-30) outliers start: 19 outliers final: 19 residues processed: 152 average time/residue: 0.3813 time to fit residues: 82.4010 Evaluate side-chains 153 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 92 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.142469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.127337 restraints weight = 101095.269| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 5.41 r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6086 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8542 Z= 0.357 Angle : 0.747 11.655 11661 Z= 0.404 Chirality : 0.043 0.168 1335 Planarity : 0.005 0.039 1427 Dihedral : 12.391 73.206 1337 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 33.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.74 % Favored : 86.26 % Rotamer: Outliers : 2.95 % Allowed : 17.03 % Favored : 80.02 % 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: -2.96 (0.24), residues: 990 helix: -0.93 (0.23), residues: 431 sheet: -2.66 (0.52), residues: 76 loop : -2.88 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 617 HIS 0.011 0.002 HIS A 309 PHE 0.030 0.002 PHE A 753 TYR 0.020 0.002 TYR A 238 ARG 0.006 0.001 ARG A 858 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3746.09 seconds wall clock time: 67 minutes 2.54 seconds (4022.54 seconds total)