Starting phenix.real_space_refine on Fri May 16 17:38:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b9i_15932/05_2025/8b9i_15932.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b9i_15932/05_2025/8b9i_15932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b9i_15932/05_2025/8b9i_15932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b9i_15932/05_2025/8b9i_15932.map" model { file = "/net/cci-nas-00/data/ceres_data/8b9i_15932/05_2025/8b9i_15932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b9i_15932/05_2025/8b9i_15932.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7861 atoms to isotropic. 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 Al 1 5.89 5 P 13 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 5043 2.51 5 N 1381 2.21 5 O 1535 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.29s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8026 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7784 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 984, 7781 Classifications: {'peptide': 984} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 49, 'TRANS': 932} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 984, 7781 Classifications: {'peptide': 984} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 49, 'TRANS': 932} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 7927 Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Classifications: {'RNA': 11} Modifications used: {'rna3p_pyr': 10} Link IDs: {'rna3p': 10} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 37 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3, 'water': 4} Link IDs: {None: 6} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.73, per 1000 atoms: 1.09 Number of scatterers: 8026 At special positions: 0 Unit cell: (83.022, 96.174, 104.394, 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) S 48 16.00 P 13 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1535 8.00 N 1381 7.00 C 5043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.10 Conformation dependent library (CDL) restraints added in 1.9 seconds 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1880 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 7 sheets defined 52.3% alpha, 12.8% beta 0 base pairs and 3 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 166 through 182 removed outlier: 4.193A pdb=" N LYS A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLU A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 242 Processing helix chain 'A' and resid 268 through 282 Processing helix chain 'A' and resid 288 through 292 removed outlier: 3.880A pdb=" N ASN A 291 " --> pdb=" O ASN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 371 Processing helix chain 'A' and resid 371 through 382 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.765A pdb=" N ALA A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 412 through 428 removed outlier: 4.589A pdb=" N ALA A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLN A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 509 through 512 removed outlier: 3.746A pdb=" N ARG A 512 " --> pdb=" O ILE A 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 512' Processing helix chain 'A' and resid 513 through 530 Processing helix chain 'A' and resid 543 through 551 Processing helix chain 'A' and resid 570 through 579 Processing helix chain 'A' and resid 583 through 591 removed outlier: 4.104A pdb=" N ARG A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 636 through 650 Processing helix chain 'A' and resid 662 through 676 removed outlier: 3.582A pdb=" N THR A 676 " --> pdb=" O PHE A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 681 removed outlier: 4.096A pdb=" N ASP A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 700 Processing helix chain 'A' and resid 701 through 703 No H-bonds generated for 'chain 'A' and resid 701 through 703' Processing helix chain 'A' and resid 745 through 748 Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 782 through 789 Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 802 through 813 Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 829 through 843 Processing helix chain 'A' and resid 853 through 861 Processing helix chain 'A' and resid 865 through 879 Processing helix chain 'A' and resid 880 through 892 Processing helix chain 'A' and resid 908 through 914 Processing helix chain 'A' and resid 920 through 939 Processing helix chain 'A' and resid 939 through 951 Processing helix chain 'A' and resid 953 through 975 Processing helix chain 'A' and resid 977 through 981 Processing helix chain 'A' and resid 994 through 1008 removed outlier: 3.722A pdb=" N CYS A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1026 No H-bonds generated for 'chain 'A' and resid 1024 through 1026' Processing helix chain 'A' and resid 1070 through 1077 Processing helix chain 'A' and resid 1101 through 1110 Processing helix chain 'A' and resid 1110 through 1125 removed outlier: 4.042A pdb=" N ALA A1114 " --> pdb=" O ALA A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1129 removed outlier: 3.906A pdb=" N ILE A1129 " --> pdb=" O PRO A1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1126 through 1129' Processing helix chain 'A' and resid 1133 through 1148 Processing helix chain 'A' and resid 1149 through 1153 removed outlier: 4.474A pdb=" N GLY A1152 " --> pdb=" O LYS A1149 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 192 removed outlier: 3.702A pdb=" N ARG A 213 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 264 removed outlier: 5.895A pdb=" N TYR A 263 " --> pdb=" O ASP A1099 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 474 removed outlier: 6.743A pdb=" N GLY A 466 " --> pdb=" O PHE A 484 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N THR A 486 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N SER A 468 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASN A 435 " --> pdb=" O HIS A 503 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE A 505 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR A 437 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP A 507 " --> pdb=" O TYR A 437 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR A 439 " --> pdb=" O ASP A 507 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 407 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LEU A 557 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 404 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL A 559 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG A 406 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 566 through 569 removed outlier: 6.133A pdb=" N GLN A 567 " --> pdb=" O CYS A 777 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N THR A 779 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE A 569 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL A 730 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHE A 778 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A 732 " --> pdb=" O PHE A 778 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ALA A 655 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 656 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N SER A 716 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL A 658 " --> pdb=" O SER A 716 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 737 through 744 Processing sheet with id=AA7, first strand: chain 'A' and resid 1054 through 1057 removed outlier: 3.671A pdb=" N GLU A1054 " --> pdb=" O LYS A1064 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL A1061 " --> pdb=" O ALA A1028 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS A1020 " --> pdb=" O LYS A1016 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 3 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.42: 3326 1.42 - 1.62: 4786 1.62 - 1.83: 78 1.83 - 2.03: 0 2.03 - 2.23: 1 Bond restraints: 8191 Sorted by residual: bond pdb=" C GLY A 346 " pdb=" N LEU A 348 " ideal model delta sigma weight residual 1.329 2.234 -0.905 1.40e-02 5.10e+03 4.17e+03 bond pdb=" F3 ALF A1203 " pdb="AL ALF A1203 " ideal model delta sigma weight residual 1.685 1.782 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" F2 ALF A1203 " pdb="AL ALF A1203 " ideal model delta sigma weight residual 1.685 1.781 -0.096 2.00e-02 2.50e+03 2.33e+01 bond pdb=" F1 ALF A1203 " pdb="AL ALF A1203 " ideal model delta sigma weight residual 1.684 1.779 -0.095 2.00e-02 2.50e+03 2.28e+01 bond pdb=" F4 ALF A1203 " pdb="AL ALF A1203 " ideal model delta sigma weight residual 1.686 1.779 -0.093 2.00e-02 2.50e+03 2.18e+01 ... (remaining 8186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.15: 11139 14.15 - 28.31: 4 28.31 - 42.46: 0 42.46 - 56.62: 0 56.62 - 70.77: 2 Bond angle restraints: 11145 Sorted by residual: angle pdb=" F1 ALF A1203 " pdb="AL ALF A1203 " pdb=" F2 ALF A1203 " ideal model delta sigma weight residual 108.68 179.45 -70.77 3.00e+00 1.11e-01 5.57e+02 angle pdb=" F3 ALF A1203 " pdb="AL ALF A1203 " pdb=" F4 ALF A1203 " ideal model delta sigma weight residual 109.63 179.86 -70.23 3.00e+00 1.11e-01 5.48e+02 angle pdb=" CA PRO A 560 " pdb=" N PRO A 560 " pdb=" CD PRO A 560 " ideal model delta sigma weight residual 112.00 98.49 13.51 1.40e+00 5.10e-01 9.32e+01 angle pdb=" CA GLY A 346 " pdb=" C GLY A 346 " pdb=" N LEU A 348 " ideal model delta sigma weight residual 115.32 103.41 11.91 1.42e+00 4.96e-01 7.03e+01 angle pdb=" C GLY A 346 " pdb=" N LEU A 348 " pdb=" CA LEU A 348 " ideal model delta sigma weight residual 121.70 135.74 -14.04 1.80e+00 3.09e-01 6.08e+01 ... (remaining 11140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.51: 4768 33.51 - 67.02: 252 67.02 - 100.52: 26 100.52 - 134.03: 1 134.03 - 167.54: 3 Dihedral angle restraints: 5050 sinusoidal: 2164 harmonic: 2886 Sorted by residual: dihedral pdb=" O4' U C 6 " pdb=" C1' U C 6 " pdb=" N1 U C 6 " pdb=" C2 U C 6 " ideal model delta sinusoidal sigma weight residual -160.00 7.54 -167.54 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" C5' ADP A1201 " pdb=" O5' ADP A1201 " pdb=" PA ADP A1201 " pdb=" O2A ADP A1201 " ideal model delta sinusoidal sigma weight residual 300.00 144.92 155.08 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O2A ADP A1201 " pdb=" O3A ADP A1201 " pdb=" PA ADP A1201 " pdb=" PB ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 90.48 -150.48 1 2.00e+01 2.50e-03 4.49e+01 ... (remaining 5047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 994 0.050 - 0.100: 226 0.100 - 0.150: 62 0.150 - 0.200: 3 0.200 - 0.251: 2 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CB ILE A 719 " pdb=" CA ILE A 719 " pdb=" CG1 ILE A 719 " pdb=" CG2 ILE A 719 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CG LEU A 201 " pdb=" CB LEU A 201 " pdb=" CD1 LEU A 201 " pdb=" CD2 LEU A 201 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ILE A 343 " pdb=" N ILE A 343 " pdb=" C ILE A 343 " pdb=" CB ILE A 343 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 1284 not shown) Planarity restraints: 1401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 346 " -0.113 2.00e-02 2.50e+03 1.97e-01 3.90e+02 pdb=" C GLY A 346 " 0.337 2.00e-02 2.50e+03 pdb=" O GLY A 346 " -0.159 2.00e-02 2.50e+03 pdb=" N LEU A 348 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 559 " 0.068 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO A 560 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 342 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C ASN A 342 " -0.049 2.00e-02 2.50e+03 pdb=" O ASN A 342 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE A 343 " 0.016 2.00e-02 2.50e+03 ... (remaining 1398 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 68 2.55 - 3.14: 6179 3.14 - 3.73: 13209 3.73 - 4.31: 18362 4.31 - 4.90: 29800 Nonbonded interactions: 67618 Sorted by model distance: nonbonded pdb="MG MG A1202 " pdb=" O HOH A1302 " model vdw 1.963 2.170 nonbonded pdb=" F2 ALF A1203 " pdb=" O HOH A1301 " model vdw 2.099 2.990 nonbonded pdb=" F2 ALF A1203 " pdb=" O HOH A1302 " model vdw 2.146 2.990 nonbonded pdb=" OE1 GLN A 576 " pdb=" OG1 THR A 623 " model vdw 2.187 3.040 nonbonded pdb=" O3B ADP A1201 " pdb=" O HOH A1301 " model vdw 2.196 3.040 ... (remaining 67613 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.050 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 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 : 0.011 0.905 8191 Z= 0.742 Angle : 1.242 70.773 11145 Z= 0.516 Chirality : 0.046 0.251 1287 Planarity : 0.008 0.197 1401 Dihedral : 19.476 167.540 3170 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 2.31 % Allowed : 30.40 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.28), residues: 977 helix: 1.73 (0.24), residues: 457 sheet: -0.38 (0.42), residues: 161 loop : -0.21 (0.36), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 663 HIS 0.004 0.001 HIS A 746 PHE 0.016 0.002 PHE A 878 TYR 0.012 0.001 TYR A 890 ARG 0.007 0.000 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.13279 ( 392) hydrogen bonds : angle 5.29879 ( 1122) covalent geometry : bond 0.01100 ( 8191) covalent geometry : angle 1.24246 (11145) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8107 (pp) outliers start: 20 outliers final: 9 residues processed: 150 average time/residue: 1.2164 time to fit residues: 193.7089 Evaluate side-chains 77 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1058 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 332 GLN A 339 HIS A 510 HIS A 567 GLN A 621 GLN A 911 GLN A 973 GLN A1032 HIS A1037 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.089341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.065401 restraints weight = 34220.003| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 5.23 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 8191 Z= 0.153 Angle : 0.700 11.995 11145 Z= 0.344 Chirality : 0.045 0.201 1287 Planarity : 0.006 0.055 1401 Dihedral : 12.647 163.665 1254 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.32 % Rotamer: Outliers : 4.97 % Allowed : 28.67 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.28), residues: 979 helix: 1.84 (0.24), residues: 458 sheet: -0.27 (0.39), residues: 179 loop : -0.46 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 335 HIS 0.004 0.001 HIS A 691 PHE 0.015 0.001 PHE A 667 TYR 0.008 0.001 TYR A 619 ARG 0.012 0.001 ARG A 844 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 392) hydrogen bonds : angle 4.60539 ( 1122) covalent geometry : bond 0.00365 ( 8191) covalent geometry : angle 0.69993 (11145) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 75 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8459 (mt) REVERT: A 176 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8963 (mp) REVERT: A 229 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.8785 (mtpp) REVERT: A 297 ASP cc_start: 0.6027 (OUTLIER) cc_final: 0.5188 (p0) REVERT: A 358 MET cc_start: 0.9153 (mtp) cc_final: 0.8915 (mmp) REVERT: A 389 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8217 (tpp) REVERT: A 585 GLU cc_start: 0.9446 (pm20) cc_final: 0.9038 (tp30) REVERT: A 896 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7086 (mm-30) REVERT: A 954 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8533 (mmt) REVERT: A 1018 LYS cc_start: 0.9072 (mttt) cc_final: 0.8777 (mmmm) outliers start: 43 outliers final: 12 residues processed: 111 average time/residue: 1.1738 time to fit residues: 138.7168 Evaluate side-chains 86 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1150 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 41 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 911 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.089103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.065584 restraints weight = 31950.359| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 5.06 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8191 Z= 0.132 Angle : 0.659 9.528 11145 Z= 0.324 Chirality : 0.044 0.240 1287 Planarity : 0.005 0.052 1401 Dihedral : 12.154 156.842 1246 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.17 % Favored : 96.73 % Rotamer: Outliers : 3.47 % Allowed : 28.21 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.28), residues: 979 helix: 1.97 (0.24), residues: 457 sheet: -0.20 (0.39), residues: 179 loop : -0.46 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 335 HIS 0.002 0.001 HIS A 691 PHE 0.014 0.001 PHE A 667 TYR 0.049 0.001 TYR A1009 ARG 0.008 0.001 ARG A 844 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 392) hydrogen bonds : angle 4.40668 ( 1122) covalent geometry : bond 0.00316 ( 8191) covalent geometry : angle 0.65921 (11145) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8366 (mt) REVERT: A 176 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8997 (mp) REVERT: A 229 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.8812 (mtpp) REVERT: A 297 ASP cc_start: 0.6103 (OUTLIER) cc_final: 0.5305 (p0) REVERT: A 358 MET cc_start: 0.9122 (mtp) cc_final: 0.8906 (mmp) REVERT: A 585 GLU cc_start: 0.9444 (pm20) cc_final: 0.9057 (tp30) REVERT: A 896 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7138 (mm-30) REVERT: A 905 ARG cc_start: 0.8085 (mmp-170) cc_final: 0.7874 (mmp-170) REVERT: A 954 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8440 (mmt) REVERT: A 1009 TYR cc_start: 0.8543 (t80) cc_final: 0.8213 (t80) REVERT: A 1018 LYS cc_start: 0.9096 (mttt) cc_final: 0.8734 (mmmm) outliers start: 29 outliers final: 9 residues processed: 96 average time/residue: 1.1597 time to fit residues: 118.8009 Evaluate side-chains 79 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 911 GLN Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1148 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 96 optimal weight: 0.7980 chunk 80 optimal weight: 0.4980 chunk 62 optimal weight: 0.0980 chunk 44 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 911 GLN ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.089329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.066947 restraints weight = 22536.870| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.31 r_work: 0.2829 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8191 Z= 0.124 Angle : 0.632 10.121 11145 Z= 0.310 Chirality : 0.043 0.183 1287 Planarity : 0.005 0.052 1401 Dihedral : 11.839 154.897 1240 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.27 % Favored : 96.63 % Rotamer: Outliers : 3.58 % Allowed : 28.21 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.28), residues: 979 helix: 2.01 (0.24), residues: 457 sheet: -0.18 (0.39), residues: 179 loop : -0.45 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 335 HIS 0.004 0.001 HIS A 910 PHE 0.013 0.001 PHE A 667 TYR 0.026 0.001 TYR A1009 ARG 0.007 0.001 ARG A 443 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 392) hydrogen bonds : angle 4.31723 ( 1122) covalent geometry : bond 0.00290 ( 8191) covalent geometry : angle 0.63236 (11145) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.9002 (mp) REVERT: A 229 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.9078 (mtpp) REVERT: A 297 ASP cc_start: 0.6221 (OUTLIER) cc_final: 0.5432 (p0) REVERT: A 358 MET cc_start: 0.9274 (mtp) cc_final: 0.8965 (mmp) REVERT: A 585 GLU cc_start: 0.9400 (pm20) cc_final: 0.9003 (tp30) REVERT: A 617 ASP cc_start: 0.9121 (m-30) cc_final: 0.8902 (p0) REVERT: A 634 ASP cc_start: 0.8310 (t0) cc_final: 0.7821 (p0) REVERT: A 698 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8868 (mm-30) REVERT: A 701 LYS cc_start: 0.9450 (OUTLIER) cc_final: 0.8994 (mtmm) REVERT: A 896 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7375 (mm-30) REVERT: A 905 ARG cc_start: 0.8222 (mmp-170) cc_final: 0.7996 (mmp-170) REVERT: A 942 MET cc_start: 0.8759 (mpp) cc_final: 0.8386 (pmm) REVERT: A 954 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8594 (mmt) REVERT: A 1018 LYS cc_start: 0.9205 (mttt) cc_final: 0.8893 (mmmm) outliers start: 30 outliers final: 7 residues processed: 93 average time/residue: 1.1249 time to fit residues: 111.9446 Evaluate side-chains 77 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 701 LYS Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1148 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 3 optimal weight: 2.9990 chunk 86 optimal weight: 0.0770 chunk 4 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.088683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.065020 restraints weight = 34569.982| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 5.29 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8191 Z= 0.125 Angle : 0.628 10.146 11145 Z= 0.309 Chirality : 0.043 0.172 1287 Planarity : 0.005 0.048 1401 Dihedral : 11.656 153.663 1240 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.17 % Favored : 96.73 % Rotamer: Outliers : 3.24 % Allowed : 27.86 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.28), residues: 979 helix: 2.02 (0.24), residues: 456 sheet: -0.05 (0.40), residues: 174 loop : -0.45 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 335 HIS 0.003 0.001 HIS A 746 PHE 0.013 0.001 PHE A 155 TYR 0.019 0.001 TYR A1009 ARG 0.009 0.001 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 392) hydrogen bonds : angle 4.26544 ( 1122) covalent geometry : bond 0.00298 ( 8191) covalent geometry : angle 0.62786 (11145) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8996 (mp) REVERT: A 297 ASP cc_start: 0.6281 (OUTLIER) cc_final: 0.5523 (p0) REVERT: A 358 MET cc_start: 0.9169 (mtp) cc_final: 0.8885 (mmp) REVERT: A 585 GLU cc_start: 0.9438 (pm20) cc_final: 0.9038 (OUTLIER) REVERT: A 634 ASP cc_start: 0.8073 (t0) cc_final: 0.7786 (p0) REVERT: A 698 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8533 (mm-30) REVERT: A 701 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.8864 (mtmm) REVERT: A 792 ASN cc_start: 0.9144 (p0) cc_final: 0.8642 (p0) REVERT: A 942 MET cc_start: 0.8868 (mpp) cc_final: 0.8529 (pmm) REVERT: A 954 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8405 (mmt) REVERT: A 998 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7798 (p0) REVERT: A 1018 LYS cc_start: 0.9128 (mttt) cc_final: 0.8783 (mmmm) outliers start: 27 outliers final: 10 residues processed: 83 average time/residue: 1.0178 time to fit residues: 90.9715 Evaluate side-chains 70 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 701 LYS Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1148 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 60 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.088032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.064781 restraints weight = 26145.993| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 4.71 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8191 Z= 0.128 Angle : 0.622 10.765 11145 Z= 0.303 Chirality : 0.043 0.165 1287 Planarity : 0.005 0.045 1401 Dihedral : 11.558 152.925 1240 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.32 % Rotamer: Outliers : 3.01 % Allowed : 28.55 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.28), residues: 979 helix: 2.04 (0.24), residues: 460 sheet: 0.03 (0.42), residues: 164 loop : -0.49 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 335 HIS 0.003 0.001 HIS A 746 PHE 0.017 0.001 PHE A 155 TYR 0.024 0.001 TYR A1009 ARG 0.006 0.001 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 392) hydrogen bonds : angle 4.21933 ( 1122) covalent geometry : bond 0.00305 ( 8191) covalent geometry : angle 0.62155 (11145) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.9002 (mp) REVERT: A 297 ASP cc_start: 0.6239 (OUTLIER) cc_final: 0.5508 (p0) REVERT: A 358 MET cc_start: 0.9166 (mtp) cc_final: 0.8885 (mmp) REVERT: A 585 GLU cc_start: 0.9436 (pm20) cc_final: 0.9008 (tp30) REVERT: A 634 ASP cc_start: 0.8089 (t0) cc_final: 0.7817 (p0) REVERT: A 792 ASN cc_start: 0.9139 (p0) cc_final: 0.8669 (p0) REVERT: A 896 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7355 (mm-30) REVERT: A 942 MET cc_start: 0.8869 (mpp) cc_final: 0.8560 (pmm) REVERT: A 954 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8380 (mmt) REVERT: A 998 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7750 (p0) REVERT: A 1018 LYS cc_start: 0.9135 (mttt) cc_final: 0.8790 (mmmm) outliers start: 25 outliers final: 9 residues processed: 82 average time/residue: 0.9915 time to fit residues: 87.9845 Evaluate side-chains 70 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1148 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 664 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.087276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.063862 restraints weight = 31660.085| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 4.99 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8191 Z= 0.132 Angle : 0.630 11.447 11145 Z= 0.305 Chirality : 0.043 0.164 1287 Planarity : 0.004 0.043 1401 Dihedral : 11.509 152.666 1240 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.68 % Favored : 96.22 % Rotamer: Outliers : 2.54 % Allowed : 28.90 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.28), residues: 979 helix: 2.05 (0.24), residues: 460 sheet: -0.02 (0.41), residues: 164 loop : -0.44 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 335 HIS 0.002 0.001 HIS A 691 PHE 0.016 0.001 PHE A 155 TYR 0.025 0.001 TYR A1009 ARG 0.007 0.001 ARG A 455 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 392) hydrogen bonds : angle 4.20444 ( 1122) covalent geometry : bond 0.00316 ( 8191) covalent geometry : angle 0.63033 (11145) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.9025 (mp) REVERT: A 297 ASP cc_start: 0.6228 (OUTLIER) cc_final: 0.5496 (p0) REVERT: A 358 MET cc_start: 0.9179 (mtp) cc_final: 0.8882 (mmp) REVERT: A 585 GLU cc_start: 0.9459 (pm20) cc_final: 0.9014 (tp30) REVERT: A 792 ASN cc_start: 0.9139 (p0) cc_final: 0.8710 (p0) REVERT: A 942 MET cc_start: 0.8890 (mpp) cc_final: 0.8572 (pmm) REVERT: A 954 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8371 (mmt) REVERT: A 998 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.7797 (p0) REVERT: A 1009 TYR cc_start: 0.8362 (t80) cc_final: 0.8148 (t80) REVERT: A 1018 LYS cc_start: 0.9164 (mttt) cc_final: 0.8821 (mmmm) outliers start: 21 outliers final: 9 residues processed: 76 average time/residue: 1.0462 time to fit residues: 85.9439 Evaluate side-chains 71 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1148 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 82 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.087276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.065119 restraints weight = 23642.374| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.43 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8191 Z= 0.121 Angle : 0.636 12.097 11145 Z= 0.307 Chirality : 0.043 0.224 1287 Planarity : 0.004 0.042 1401 Dihedral : 11.460 150.211 1240 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.32 % Rotamer: Outliers : 2.77 % Allowed : 28.67 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.28), residues: 979 helix: 2.07 (0.24), residues: 459 sheet: 0.03 (0.42), residues: 164 loop : -0.40 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 335 HIS 0.002 0.000 HIS A 691 PHE 0.012 0.001 PHE A 667 TYR 0.021 0.001 TYR A1009 ARG 0.006 0.001 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.03199 ( 392) hydrogen bonds : angle 4.16506 ( 1122) covalent geometry : bond 0.00291 ( 8191) covalent geometry : angle 0.63589 (11145) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6136 (OUTLIER) cc_final: 0.5450 (p0) REVERT: A 358 MET cc_start: 0.9317 (mtp) cc_final: 0.8947 (mmp) REVERT: A 585 GLU cc_start: 0.9465 (pm20) cc_final: 0.8998 (tp30) REVERT: A 792 ASN cc_start: 0.9184 (p0) cc_final: 0.8703 (p0) REVERT: A 896 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7412 (mm-30) REVERT: A 942 MET cc_start: 0.8857 (mpp) cc_final: 0.8527 (pmm) REVERT: A 954 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8345 (mmt) REVERT: A 998 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7612 (p0) REVERT: A 1018 LYS cc_start: 0.9102 (mttt) cc_final: 0.8754 (mmmm) outliers start: 23 outliers final: 13 residues processed: 77 average time/residue: 1.0693 time to fit residues: 88.5956 Evaluate side-chains 73 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1148 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 58 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 91 optimal weight: 0.0370 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.087597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.066143 restraints weight = 19248.741| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.97 r_work: 0.2859 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8191 Z= 0.124 Angle : 0.646 12.637 11145 Z= 0.313 Chirality : 0.043 0.247 1287 Planarity : 0.005 0.047 1401 Dihedral : 11.425 149.396 1240 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 2.20 % Allowed : 29.02 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.28), residues: 979 helix: 2.02 (0.24), residues: 459 sheet: 0.00 (0.43), residues: 154 loop : -0.35 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 335 HIS 0.002 0.001 HIS A 691 PHE 0.012 0.001 PHE A 667 TYR 0.021 0.001 TYR A1009 ARG 0.005 0.001 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.03206 ( 392) hydrogen bonds : angle 4.20759 ( 1122) covalent geometry : bond 0.00301 ( 8191) covalent geometry : angle 0.64598 (11145) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6106 (OUTLIER) cc_final: 0.5425 (p0) REVERT: A 358 MET cc_start: 0.9314 (mtp) cc_final: 0.8961 (mmp) REVERT: A 585 GLU cc_start: 0.9416 (pm20) cc_final: 0.8975 (OUTLIER) REVERT: A 792 ASN cc_start: 0.9266 (p0) cc_final: 0.8817 (p0) REVERT: A 896 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7688 (mm-30) REVERT: A 942 MET cc_start: 0.8831 (mpp) cc_final: 0.8526 (pmm) REVERT: A 954 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8532 (mmt) REVERT: A 998 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7686 (p0) REVERT: A 1018 LYS cc_start: 0.9225 (mttt) cc_final: 0.8933 (mmmm) outliers start: 18 outliers final: 13 residues processed: 70 average time/residue: 1.1336 time to fit residues: 84.9666 Evaluate side-chains 70 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1148 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.0070 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.087693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.066324 restraints weight = 18835.508| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.92 r_work: 0.2865 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8191 Z= 0.124 Angle : 0.653 13.030 11145 Z= 0.316 Chirality : 0.043 0.242 1287 Planarity : 0.005 0.048 1401 Dihedral : 11.410 148.658 1240 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.89 % Favored : 96.01 % Rotamer: Outliers : 1.97 % Allowed : 29.13 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.28), residues: 979 helix: 2.00 (0.24), residues: 459 sheet: 0.02 (0.43), residues: 154 loop : -0.38 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 335 HIS 0.002 0.000 HIS A 691 PHE 0.012 0.001 PHE A 667 TYR 0.020 0.001 TYR A1009 ARG 0.005 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 392) hydrogen bonds : angle 4.19108 ( 1122) covalent geometry : bond 0.00301 ( 8191) covalent geometry : angle 0.65277 (11145) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6202 (OUTLIER) cc_final: 0.5507 (p0) REVERT: A 358 MET cc_start: 0.9310 (mtp) cc_final: 0.8956 (mmp) REVERT: A 585 GLU cc_start: 0.9422 (pm20) cc_final: 0.8978 (OUTLIER) REVERT: A 792 ASN cc_start: 0.9250 (p0) cc_final: 0.8811 (p0) REVERT: A 896 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7707 (mm-30) REVERT: A 942 MET cc_start: 0.8836 (mpp) cc_final: 0.8533 (pmm) REVERT: A 954 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8536 (mmt) REVERT: A 998 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7693 (p0) REVERT: A 1009 TYR cc_start: 0.8689 (t80) cc_final: 0.8476 (t80) REVERT: A 1018 LYS cc_start: 0.9229 (mttt) cc_final: 0.8940 (mmmm) outliers start: 16 outliers final: 14 residues processed: 69 average time/residue: 1.1336 time to fit residues: 83.7674 Evaluate side-chains 72 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1148 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 0.0070 chunk 82 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 0.0070 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 95 optimal weight: 0.0040 overall best weight: 0.3628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.088198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.066168 restraints weight = 22673.352| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 4.32 r_work: 0.2857 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8191 Z= 0.116 Angle : 0.650 12.991 11145 Z= 0.315 Chirality : 0.043 0.251 1287 Planarity : 0.004 0.046 1401 Dihedral : 11.400 147.297 1240 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.99 % Favored : 95.91 % Rotamer: Outliers : 1.85 % Allowed : 29.25 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.28), residues: 979 helix: 1.98 (0.24), residues: 459 sheet: 0.05 (0.42), residues: 164 loop : -0.45 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 335 HIS 0.002 0.000 HIS A 746 PHE 0.017 0.001 PHE A 155 TYR 0.019 0.001 TYR A1009 ARG 0.005 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 392) hydrogen bonds : angle 4.16793 ( 1122) covalent geometry : bond 0.00282 ( 8191) covalent geometry : angle 0.65020 (11145) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5146.16 seconds wall clock time: 89 minutes 26.20 seconds (5366.20 seconds total)