Starting phenix.real_space_refine on Tue Dec 31 03:44:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b9i_15932/12_2024/8b9i_15932.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b9i_15932/12_2024/8b9i_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_15932/12_2024/8b9i_15932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b9i_15932/12_2024/8b9i_15932.map" model { file = "/net/cci-nas-00/data/ceres_data/8b9i_15932/12_2024/8b9i_15932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b9i_15932/12_2024/8b9i_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 8.87, per 1000 atoms: 1.11 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: 2.20 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: 2.97 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: 3.22 Time building geometry restraints manager: 2.46 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: 0.710 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: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 29.650 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.060 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:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.230 ------------------------------------------------------------------------------- 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= 0.692 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 *********************** 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 : 0.976 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: 1.2872 time to fit residues: 204.5921 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 : 0.932 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 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= 0.233 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 *********************** 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 : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8143 (mt) REVERT: A 297 ASP cc_start: 0.6946 (OUTLIER) cc_final: 0.6163 (p0) outliers start: 43 outliers final: 12 residues processed: 111 average time/residue: 1.2612 time to fit residues: 148.9807 Evaluate side-chains 80 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 235 LEU Chi-restraints excluded: chain A residue 293 LYS 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 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 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 49 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 80 optimal weight: 0.0970 chunk 89 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8191 Z= 0.206 Angle : 0.672 9.660 11145 Z= 0.332 Chirality : 0.044 0.237 1287 Planarity : 0.005 0.052 1401 Dihedral : 12.189 157.463 1246 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.52 % Rotamer: Outliers : 2.89 % Allowed : 28.55 % 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: 1.00 (0.28), residues: 979 helix: 1.90 (0.24), residues: 457 sheet: -0.20 (0.39), residues: 179 loop : -0.48 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 335 HIS 0.003 0.001 HIS A 746 PHE 0.014 0.001 PHE A 667 TYR 0.044 0.001 TYR A1009 ARG 0.009 0.001 ARG A 844 *********************** 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 93 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6262 (p0) outliers start: 24 outliers final: 9 residues processed: 91 average time/residue: 1.2125 time to fit residues: 118.6385 Evaluate side-chains 71 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 88 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN A 911 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8191 Z= 0.308 Angle : 0.681 9.845 11145 Z= 0.337 Chirality : 0.045 0.182 1287 Planarity : 0.005 0.051 1401 Dihedral : 12.014 161.212 1240 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.99 % Favored : 95.91 % Rotamer: Outliers : 3.58 % Allowed : 28.09 % 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: 1.02 (0.28), residues: 979 helix: 1.92 (0.24), residues: 459 sheet: -0.13 (0.40), residues: 174 loop : -0.52 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 335 HIS 0.004 0.001 HIS A 746 PHE 0.014 0.001 PHE A 667 TYR 0.065 0.002 TYR A1009 ARG 0.007 0.001 ARG A 844 *********************** 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 91 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6343 (p0) outliers start: 30 outliers final: 12 residues processed: 88 average time/residue: 1.1095 time to fit residues: 104.8905 Evaluate side-chains 67 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 235 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 449 VAL 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 792 ASN Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1076 LEU 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 79 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8191 Z= 0.258 Angle : 0.670 10.206 11145 Z= 0.331 Chirality : 0.044 0.179 1287 Planarity : 0.005 0.047 1401 Dihedral : 11.866 159.234 1240 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.32 % Rotamer: Outliers : 3.12 % Allowed : 28.44 % 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: 1.03 (0.28), residues: 979 helix: 1.94 (0.24), residues: 460 sheet: -0.18 (0.39), residues: 174 loop : -0.52 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 335 HIS 0.003 0.001 HIS A 691 PHE 0.014 0.001 PHE A 667 TYR 0.056 0.002 TYR A1009 ARG 0.006 0.001 ARG A 367 *********************** 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 85 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6482 (p0) outliers start: 26 outliers final: 14 residues processed: 81 average time/residue: 0.9981 time to fit residues: 87.6846 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 : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE 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 634 ASP 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 871 MET Chi-restraints excluded: chain A residue 911 GLN Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1076 LEU 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 32 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 0.0010 chunk 7 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 ASN A 911 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3395 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= 0.212 Angle : 0.662 11.030 11145 Z= 0.325 Chirality : 0.044 0.197 1287 Planarity : 0.005 0.068 1401 Dihedral : 11.742 156.180 1240 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 3.12 % Allowed : 28.79 % Favored : 68.09 % 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: 1.08 (0.28), residues: 979 helix: 1.97 (0.24), residues: 461 sheet: -0.16 (0.40), residues: 174 loop : -0.48 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 335 HIS 0.003 0.001 HIS A 910 PHE 0.018 0.001 PHE A 155 TYR 0.047 0.001 TYR A1009 ARG 0.008 0.001 ARG A 184 *********************** 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: 26 poor density : 58 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6456 (p0) outliers start: 26 outliers final: 9 residues processed: 83 average time/residue: 1.1026 time to fit residues: 98.4473 Evaluate side-chains 63 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 911 GLN 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 92 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 746 HIS A 911 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3544 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= 0.201 Angle : 0.667 11.468 11145 Z= 0.325 Chirality : 0.043 0.215 1287 Planarity : 0.005 0.043 1401 Dihedral : 11.661 153.729 1240 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.89 % Favored : 96.01 % Rotamer: Outliers : 2.20 % Allowed : 29.83 % Favored : 67.98 % 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: 1.08 (0.28), residues: 979 helix: 1.96 (0.24), residues: 461 sheet: -0.09 (0.41), residues: 164 loop : -0.50 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 663 HIS 0.002 0.000 HIS A 691 PHE 0.018 0.001 PHE A 155 TYR 0.044 0.001 TYR A1009 ARG 0.006 0.001 ARG A 367 *********************** 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 71 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6947 (OUTLIER) cc_final: 0.6443 (p0) outliers start: 18 outliers final: 9 residues processed: 70 average time/residue: 1.1668 time to fit residues: 88.1630 Evaluate side-chains 60 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 911 GLN Chi-restraints excluded: chain A residue 1076 LEU 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 56 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 91 optimal weight: 0.0870 chunk 83 optimal weight: 1.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8191 Z= 0.229 Angle : 0.671 12.107 11145 Z= 0.327 Chirality : 0.044 0.223 1287 Planarity : 0.004 0.043 1401 Dihedral : 11.636 154.732 1240 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 1.73 % Allowed : 30.06 % 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: 1.96 (0.24), residues: 461 sheet: -0.17 (0.43), residues: 154 loop : -0.40 (0.35), residues: 364 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 0.013 0.001 PHE A 667 TYR 0.036 0.001 TYR A1009 ARG 0.006 0.001 ARG A 367 *********************** 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 66 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6913 (OUTLIER) cc_final: 0.6476 (p0) outliers start: 14 outliers final: 10 residues processed: 65 average time/residue: 1.1704 time to fit residues: 81.9438 Evaluate side-chains 62 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 911 GLN 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 88 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 57 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 911 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3699 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= 0.224 Angle : 0.678 13.911 11145 Z= 0.329 Chirality : 0.044 0.248 1287 Planarity : 0.004 0.042 1401 Dihedral : 11.592 153.311 1240 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 1.62 % Allowed : 30.52 % Favored : 67.86 % 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: 1.08 (0.28), residues: 979 helix: 1.94 (0.24), residues: 461 sheet: -0.18 (0.43), residues: 154 loop : -0.41 (0.35), residues: 364 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 0.013 0.001 PHE A 667 TYR 0.007 0.001 TYR A 890 ARG 0.006 0.001 ARG A 367 *********************** 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 65 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.6405 (p0) outliers start: 13 outliers final: 9 residues processed: 64 average time/residue: 1.1331 time to fit residues: 78.2049 Evaluate side-chains 63 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 911 GLN 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 44 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8191 Z= 0.299 Angle : 0.709 15.535 11145 Z= 0.346 Chirality : 0.045 0.245 1287 Planarity : 0.005 0.042 1401 Dihedral : 11.616 157.163 1240 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.19 % Favored : 95.71 % Rotamer: Outliers : 1.73 % Allowed : 30.52 % Favored : 67.75 % 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: 0.99 (0.28), residues: 979 helix: 1.83 (0.25), residues: 461 sheet: -0.19 (0.42), residues: 154 loop : -0.43 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 335 HIS 0.004 0.001 HIS A 691 PHE 0.013 0.001 PHE A 667 TYR 0.035 0.001 TYR A1009 ARG 0.006 0.001 ARG A 367 ********************** 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 65 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6815 (OUTLIER) cc_final: 0.6418 (p0) outliers start: 14 outliers final: 8 residues processed: 64 average time/residue: 1.3022 time to fit residues: 89.4304 Evaluate side-chains 60 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 911 GLN 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 72 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 14 optimal weight: 0.0770 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.088198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.065887 restraints weight = 22050.328| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.25 r_work: 0.2834 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8191 Z= 0.201 Angle : 0.699 14.278 11145 Z= 0.341 Chirality : 0.044 0.242 1287 Planarity : 0.005 0.041 1401 Dihedral : 11.554 151.118 1240 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 1.16 % Allowed : 31.33 % Favored : 67.51 % 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: 0.93 (0.28), residues: 979 helix: 1.77 (0.24), residues: 461 sheet: -0.16 (0.43), residues: 154 loop : -0.46 (0.34), residues: 364 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 0.013 0.001 PHE A 667 TYR 0.005 0.001 TYR A 619 ARG 0.007 0.001 ARG A 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2814.14 seconds wall clock time: 51 minutes 28.37 seconds (3088.37 seconds total)