Starting phenix.real_space_refine on Tue Feb 3 18:44:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mha_48271/02_2026/9mha_48271.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mha_48271/02_2026/9mha_48271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mha_48271/02_2026/9mha_48271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mha_48271/02_2026/9mha_48271.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mha_48271/02_2026/9mha_48271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mha_48271/02_2026/9mha_48271.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 3959 2.51 5 N 1072 2.21 5 O 1134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6188 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 749 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 90} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 749 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 90} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 752 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1277 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1271 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 2, 'GLU:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 45 Chain: "D" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1273 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 2, 'GLU:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.69, per 1000 atoms: 0.27 Number of scatterers: 6188 At special positions: 0 Unit cell: (91.56, 85.68, 77.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1134 8.00 N 1072 7.00 C 3959 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.04 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 135 " distance=2.03 Simple disulfide: pdb=" SG CYS D 121 " - pdb=" SG CYS D 147 " distance=2.03 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG G 1 " - " ASN C 563 " " NAG H 1 " - " ASN E 563 " " NAG I 1 " - " ASN F 563 " Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 243.4 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1482 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 15 sheets defined 24.9% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'C' and resid 538 through 542 removed outlier: 4.146A pdb=" N ILE C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 576 removed outlier: 4.226A pdb=" N GLY C 557 " --> pdb=" O GLY C 553 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLN C 567 " --> pdb=" O ASN C 563 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA C 568 " --> pdb=" O GLU C 564 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 596 Processing helix chain 'E' and resid 527 through 532 removed outlier: 4.337A pdb=" N TRP E 531 " --> pdb=" O GLY E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 4.165A pdb=" N ILE E 542 " --> pdb=" O ALA E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 576 removed outlier: 4.452A pdb=" N GLY E 557 " --> pdb=" O GLY E 553 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 596 removed outlier: 3.772A pdb=" N ARG E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 532 removed outlier: 4.400A pdb=" N TRP F 531 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 4.086A pdb=" N ILE F 542 " --> pdb=" O ALA F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 551 through 576 removed outlier: 4.306A pdb=" N GLY F 557 " --> pdb=" O GLY F 553 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 595 removed outlier: 3.707A pdb=" N GLN F 595 " --> pdb=" O ASP F 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.550A pdb=" N LEU B 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.720A pdb=" N SER B 196 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 74 Processing helix chain 'D' and resid 78 through 84 removed outlier: 3.652A pdb=" N LYS D 84 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 196 removed outlier: 4.141A pdb=" N SER D 196 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 516 through 517 removed outlier: 3.555A pdb=" N GLY C 546 " --> pdb=" O TYR C 517 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.541A pdb=" N THR C 581 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.541A pdb=" N THR C 581 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 544 through 547 removed outlier: 3.619A pdb=" N TRP E 518 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 580 through 581 removed outlier: 7.652A pdb=" N THR E 581 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 38 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 580 through 581 removed outlier: 7.652A pdb=" N THR E 581 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 544 through 545 removed outlier: 3.696A pdb=" N TRP F 518 " --> pdb=" O GLY D 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 580 through 581 removed outlier: 3.511A pdb=" N ILE D 38 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D 35 " --> pdb=" O SER D 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 580 through 581 Processing sheet with id=AB1, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AB2, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.654A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AB4, first strand: chain 'B' and resid 108 through 114 removed outlier: 6.502A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 142 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 144 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 86 through 89 Processing sheet with id=AB6, first strand: chain 'D' and resid 108 through 113 removed outlier: 6.405A pdb=" N CYS D 108 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL D 141 " --> pdb=" O CYS D 108 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN D 110 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLY D 143 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU D 112 " --> pdb=" O GLY D 143 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 564 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1999 1.34 - 1.46: 1471 1.46 - 1.58: 2839 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 6335 Sorted by residual: bond pdb=" N ALA E 503 " pdb=" CA ALA E 503 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N ALA F 503 " pdb=" CA ALA F 503 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" N ALA C 503 " pdb=" CA ALA C 503 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.56e+00 bond pdb=" C CYS D 121 " pdb=" N LEU D 122 " ideal model delta sigma weight residual 1.329 1.306 0.023 1.86e-02 2.89e+03 1.48e+00 bond pdb=" C TYR C 517 " pdb=" N TRP C 518 " ideal model delta sigma weight residual 1.332 1.347 -0.016 1.42e-02 4.96e+03 1.25e+00 ... (remaining 6330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 8081 1.03 - 2.06: 433 2.06 - 3.09: 64 3.09 - 4.11: 47 4.11 - 5.14: 7 Bond angle restraints: 8632 Sorted by residual: angle pdb=" C ASP A 78 " pdb=" N VAL A 79 " pdb=" CA VAL A 79 " ideal model delta sigma weight residual 120.33 122.44 -2.11 8.00e-01 1.56e+00 6.96e+00 angle pdb=" C HIS C 549 " pdb=" N ASN C 550 " pdb=" CA ASN C 550 " ideal model delta sigma weight residual 122.08 125.49 -3.41 1.47e+00 4.63e-01 5.38e+00 angle pdb=" C VAL A 79 " pdb=" CA VAL A 79 " pdb=" CB VAL A 79 " ideal model delta sigma weight residual 114.00 110.98 3.02 1.31e+00 5.83e-01 5.33e+00 angle pdb=" N LYS B 56 " pdb=" CA LYS B 56 " pdb=" C LYS B 56 " ideal model delta sigma weight residual 109.15 112.42 -3.27 1.44e+00 4.82e-01 5.14e+00 angle pdb=" CA GLY D 131 " pdb=" C GLY D 131 " pdb=" N PHE D 132 " ideal model delta sigma weight residual 115.11 117.23 -2.12 9.50e-01 1.11e+00 4.98e+00 ... (remaining 8627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3537 17.70 - 35.39: 224 35.39 - 53.09: 51 53.09 - 70.79: 11 70.79 - 88.48: 11 Dihedral angle restraints: 3834 sinusoidal: 1527 harmonic: 2307 Sorted by residual: dihedral pdb=" CA LEU D 184 " pdb=" C LEU D 184 " pdb=" N ILE D 185 " pdb=" CA ILE D 185 " ideal model delta harmonic sigma weight residual 180.00 163.09 16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA LYS A 56 " pdb=" C LYS A 56 " pdb=" N LEU A 57 " pdb=" CA LEU A 57 " ideal model delta harmonic sigma weight residual 180.00 163.33 16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA HIS F 549 " pdb=" C HIS F 549 " pdb=" N ASN F 550 " pdb=" CA ASN F 550 " ideal model delta harmonic sigma weight residual 180.00 163.56 16.44 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 3831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 563 0.028 - 0.057: 275 0.057 - 0.085: 67 0.085 - 0.113: 63 0.113 - 0.141: 29 Chirality restraints: 997 Sorted by residual: chirality pdb=" CA ILE A 33 " pdb=" N ILE A 33 " pdb=" C ILE A 33 " pdb=" CB ILE A 33 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA ILE A 129 " pdb=" N ILE A 129 " pdb=" C ILE A 129 " pdb=" CB ILE A 129 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE F 532 " pdb=" N ILE F 532 " pdb=" C ILE F 532 " pdb=" CB ILE F 532 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 994 not shown) Planarity restraints: 1111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 93 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO D 94 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 94 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 94 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 145 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO B 146 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 145 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO A 146 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.019 5.00e-02 4.00e+02 ... (remaining 1108 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1337 2.78 - 3.31: 5422 3.31 - 3.84: 9218 3.84 - 4.37: 11116 4.37 - 4.90: 19537 Nonbonded interactions: 46630 Sorted by model distance: nonbonded pdb=" OE1 GLU F 523 " pdb=" OG SER A 32 " model vdw 2.251 3.040 nonbonded pdb=" O SER D 32 " pdb=" OG SER D 32 " model vdw 2.281 3.040 nonbonded pdb=" OE1 GLU D 106 " pdb=" ND2 ASN D 107 " model vdw 2.307 3.120 nonbonded pdb=" NZ LYS A 56 " pdb=" OE1 GLN A 188 " model vdw 2.315 3.120 nonbonded pdb=" OD1 ASN B 98 " pdb=" N TYR B 99 " model vdw 2.368 3.120 ... (remaining 46625 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 or (resid 52 through 56 and (name N or nam \ e CA or name C or name O or name CB )) or resid 57 through 149 or (resid 150 and \ (name N or name CA or name C or name O or name CB )) or resid 151 through 223)) \ selection = (chain 'B' and (resid 32 through 46 or (resid 47 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 52 or (resid 53 through 56 and (na \ me N or name CA or name C or name O or name CB )) or resid 57 through 105 or (re \ sid 106 and (name N or name CA or name C or name O or name CB )) or resid 107 th \ rough 223)) selection = (chain 'D' and (resid 32 through 46 or (resid 47 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 105 or (resid 106 and (name N or n \ ame CA or name C or name O or name CB )) or resid 107 through 149 or (resid 150 \ and (name N or name CA or name C or name O or name CB )) or resid 151 through 22 \ 3)) } ncs_group { reference = (chain 'C' and (resid 503 through 549 or (resid 550 and (name N or name CA or na \ me C or name O or name CB )) or resid 551 through 597)) selection = (chain 'E' and (resid 503 through 551 or (resid 552 and (name N or name CA or na \ me C or name O or name CB )) or resid 553 through 597)) selection = (chain 'F' and (resid 503 through 549 or (resid 550 and (name N or name CA or na \ me C or name O or name CB )) or resid 551 or (resid 552 and (name N or name CA o \ r name C or name O or name CB )) or resid 553 through 597)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.780 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 0.004 0.033 6350 Z= 0.186 Angle : 0.616 5.932 8671 Z= 0.327 Chirality : 0.045 0.141 997 Planarity : 0.004 0.040 1108 Dihedral : 13.581 88.482 2334 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.34 % Allowed : 8.38 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.28), residues: 792 helix: -0.10 (0.45), residues: 147 sheet: 0.42 (0.44), residues: 111 loop : -0.57 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 130 TYR 0.020 0.002 TYR F 517 PHE 0.010 0.001 PHE F 582 TRP 0.008 0.001 TRP B 104 HIS 0.006 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 6335) covalent geometry : angle 0.58932 ( 8632) SS BOND : bond 0.00367 ( 6) SS BOND : angle 0.90137 ( 12) hydrogen bonds : bond 0.25104 ( 201) hydrogen bonds : angle 8.03039 ( 564) link_BETA1-4 : bond 0.00537 ( 6) link_BETA1-4 : angle 3.59307 ( 18) link_NAG-ASN : bond 0.00652 ( 3) link_NAG-ASN : angle 2.43824 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.226 Fit side-chains REVERT: B 115 LYS cc_start: 0.8315 (ptpt) cc_final: 0.7976 (mtmt) outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.0881 time to fit residues: 6.0417 Evaluate side-chains 44 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 597 TRP Chi-restraints excluded: chain A residue 77 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.122979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110844 restraints weight = 8770.527| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.18 r_work: 0.3314 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6350 Z= 0.162 Angle : 0.605 7.916 8671 Z= 0.309 Chirality : 0.048 0.146 997 Planarity : 0.004 0.038 1108 Dihedral : 6.730 58.796 1050 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.84 % Allowed : 7.04 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.28), residues: 792 helix: 0.29 (0.45), residues: 147 sheet: 0.22 (0.35), residues: 189 loop : -0.37 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 596 TYR 0.012 0.002 TYR F 517 PHE 0.009 0.001 PHE A 159 TRP 0.013 0.001 TRP C 518 HIS 0.006 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6335) covalent geometry : angle 0.58007 ( 8632) SS BOND : bond 0.00406 ( 6) SS BOND : angle 2.81164 ( 12) hydrogen bonds : bond 0.06638 ( 201) hydrogen bonds : angle 4.92173 ( 564) link_BETA1-4 : bond 0.00527 ( 6) link_BETA1-4 : angle 3.04963 ( 18) link_NAG-ASN : bond 0.01261 ( 3) link_NAG-ASN : angle 0.90464 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: D 119 SER cc_start: 0.8673 (t) cc_final: 0.8435 (p) outliers start: 11 outliers final: 8 residues processed: 61 average time/residue: 0.0736 time to fit residues: 6.3002 Evaluate side-chains 62 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 597 TRP Chi-restraints excluded: chain F residue 545 GLU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 58 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 19 optimal weight: 0.0270 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.123623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111470 restraints weight = 8887.232| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.23 r_work: 0.3324 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6350 Z= 0.135 Angle : 0.530 6.701 8671 Z= 0.271 Chirality : 0.045 0.142 997 Planarity : 0.004 0.034 1108 Dihedral : 5.545 51.865 1049 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.35 % Allowed : 7.04 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.28), residues: 792 helix: 0.83 (0.46), residues: 147 sheet: 0.94 (0.45), residues: 111 loop : -0.43 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 85 TYR 0.010 0.001 TYR B 99 PHE 0.009 0.001 PHE D 153 TRP 0.012 0.001 TRP C 518 HIS 0.005 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6335) covalent geometry : angle 0.51209 ( 8632) SS BOND : bond 0.00308 ( 6) SS BOND : angle 1.64195 ( 12) hydrogen bonds : bond 0.05348 ( 201) hydrogen bonds : angle 4.24081 ( 564) link_BETA1-4 : bond 0.00492 ( 6) link_BETA1-4 : angle 2.66125 ( 18) link_NAG-ASN : bond 0.00893 ( 3) link_NAG-ASN : angle 1.10912 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.220 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 55 average time/residue: 0.0698 time to fit residues: 5.4415 Evaluate side-chains 54 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 597 TRP Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 122 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.124032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.111547 restraints weight = 8786.238| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.26 r_work: 0.3323 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6350 Z= 0.154 Angle : 0.534 6.837 8671 Z= 0.272 Chirality : 0.045 0.140 997 Planarity : 0.004 0.033 1108 Dihedral : 5.439 49.246 1049 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.68 % Allowed : 6.53 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.28), residues: 792 helix: 0.93 (0.47), residues: 147 sheet: 0.94 (0.46), residues: 111 loop : -0.44 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 596 TYR 0.012 0.001 TYR A 162 PHE 0.009 0.001 PHE D 153 TRP 0.012 0.001 TRP C 518 HIS 0.005 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6335) covalent geometry : angle 0.51862 ( 8632) SS BOND : bond 0.00259 ( 6) SS BOND : angle 1.65210 ( 12) hydrogen bonds : bond 0.05104 ( 201) hydrogen bonds : angle 4.11105 ( 564) link_BETA1-4 : bond 0.00382 ( 6) link_BETA1-4 : angle 2.37875 ( 18) link_NAG-ASN : bond 0.00738 ( 3) link_NAG-ASN : angle 1.24452 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.168 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 56 average time/residue: 0.0626 time to fit residues: 5.0084 Evaluate side-chains 59 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 597 TRP Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 122 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.123445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.110921 restraints weight = 8910.628| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.28 r_work: 0.3311 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6350 Z= 0.174 Angle : 0.539 6.864 8671 Z= 0.275 Chirality : 0.045 0.141 997 Planarity : 0.004 0.033 1108 Dihedral : 5.523 46.523 1049 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.51 % Allowed : 7.37 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.28), residues: 792 helix: 0.97 (0.47), residues: 147 sheet: 0.87 (0.46), residues: 111 loop : -0.49 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 596 TYR 0.013 0.002 TYR A 162 PHE 0.011 0.002 PHE D 153 TRP 0.012 0.001 TRP C 518 HIS 0.005 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 6335) covalent geometry : angle 0.52448 ( 8632) SS BOND : bond 0.00256 ( 6) SS BOND : angle 1.56911 ( 12) hydrogen bonds : bond 0.05158 ( 201) hydrogen bonds : angle 4.06507 ( 564) link_BETA1-4 : bond 0.00366 ( 6) link_BETA1-4 : angle 2.32767 ( 18) link_NAG-ASN : bond 0.00677 ( 3) link_NAG-ASN : angle 1.29397 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.148 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 54 average time/residue: 0.0623 time to fit residues: 4.7551 Evaluate side-chains 59 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 597 TRP Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 122 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.124380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.111954 restraints weight = 8805.844| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.26 r_work: 0.3322 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6350 Z= 0.128 Angle : 0.503 6.844 8671 Z= 0.256 Chirality : 0.044 0.136 997 Planarity : 0.004 0.034 1108 Dihedral : 5.305 43.058 1049 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.01 % Allowed : 8.04 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.28), residues: 792 helix: 1.04 (0.47), residues: 147 sheet: 0.91 (0.46), residues: 111 loop : -0.43 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 85 TYR 0.011 0.001 TYR A 99 PHE 0.009 0.001 PHE D 153 TRP 0.011 0.001 TRP C 518 HIS 0.004 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6335) covalent geometry : angle 0.48945 ( 8632) SS BOND : bond 0.00188 ( 6) SS BOND : angle 1.45929 ( 12) hydrogen bonds : bond 0.04568 ( 201) hydrogen bonds : angle 3.84099 ( 564) link_BETA1-4 : bond 0.00418 ( 6) link_BETA1-4 : angle 2.18849 ( 18) link_NAG-ASN : bond 0.00700 ( 3) link_NAG-ASN : angle 1.13707 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.136 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 12 residues processed: 50 average time/residue: 0.0610 time to fit residues: 4.2804 Evaluate side-chains 53 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 597 TRP Chi-restraints excluded: chain F residue 545 GLU Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 122 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 77 optimal weight: 0.0970 chunk 7 optimal weight: 0.0870 chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.125291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.112793 restraints weight = 8832.191| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.28 r_work: 0.3331 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6350 Z= 0.105 Angle : 0.476 6.793 8671 Z= 0.241 Chirality : 0.043 0.136 997 Planarity : 0.003 0.032 1108 Dihedral : 5.095 41.622 1049 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.35 % Allowed : 7.87 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.29), residues: 792 helix: 1.22 (0.47), residues: 147 sheet: 0.33 (0.42), residues: 147 loop : -0.11 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 596 TYR 0.009 0.001 TYR D 99 PHE 0.007 0.001 PHE D 153 TRP 0.011 0.001 TRP C 518 HIS 0.003 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 6335) covalent geometry : angle 0.46405 ( 8632) SS BOND : bond 0.00171 ( 6) SS BOND : angle 1.24141 ( 12) hydrogen bonds : bond 0.03998 ( 201) hydrogen bonds : angle 3.60697 ( 564) link_BETA1-4 : bond 0.00450 ( 6) link_BETA1-4 : angle 2.05730 ( 18) link_NAG-ASN : bond 0.00595 ( 3) link_NAG-ASN : angle 1.15169 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.174 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 13 residues processed: 50 average time/residue: 0.0605 time to fit residues: 4.4052 Evaluate side-chains 54 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 545 GLU Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 122 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 2 optimal weight: 0.2980 chunk 27 optimal weight: 0.0050 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.125167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.112551 restraints weight = 8956.897| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.31 r_work: 0.3331 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6350 Z= 0.113 Angle : 0.478 6.788 8671 Z= 0.242 Chirality : 0.043 0.134 997 Planarity : 0.003 0.032 1108 Dihedral : 4.780 32.870 1047 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.84 % Allowed : 8.88 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.29), residues: 792 helix: 1.29 (0.47), residues: 147 sheet: 0.35 (0.42), residues: 147 loop : -0.10 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 596 TYR 0.009 0.001 TYR A 162 PHE 0.008 0.001 PHE D 153 TRP 0.009 0.001 TRP C 518 HIS 0.003 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6335) covalent geometry : angle 0.46528 ( 8632) SS BOND : bond 0.00174 ( 6) SS BOND : angle 1.24544 ( 12) hydrogen bonds : bond 0.04064 ( 201) hydrogen bonds : angle 3.59355 ( 564) link_BETA1-4 : bond 0.00403 ( 6) link_BETA1-4 : angle 2.05228 ( 18) link_NAG-ASN : bond 0.00530 ( 3) link_NAG-ASN : angle 1.26118 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.152 Fit side-chains REVERT: B 147 CYS cc_start: 0.7611 (p) cc_final: 0.7303 (p) outliers start: 11 outliers final: 11 residues processed: 50 average time/residue: 0.0692 time to fit residues: 4.8094 Evaluate side-chains 52 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 122 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 0.0070 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 0.0770 chunk 33 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.125501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112857 restraints weight = 8920.313| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.31 r_work: 0.3348 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6350 Z= 0.103 Angle : 0.468 6.768 8671 Z= 0.237 Chirality : 0.043 0.135 997 Planarity : 0.003 0.031 1108 Dihedral : 4.723 32.745 1047 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.51 % Allowed : 9.38 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.29), residues: 792 helix: 1.34 (0.47), residues: 147 sheet: 0.33 (0.42), residues: 147 loop : -0.07 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 596 TYR 0.009 0.001 TYR B 162 PHE 0.007 0.001 PHE D 153 TRP 0.009 0.001 TRP C 518 HIS 0.003 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 6335) covalent geometry : angle 0.45620 ( 8632) SS BOND : bond 0.00172 ( 6) SS BOND : angle 1.17959 ( 12) hydrogen bonds : bond 0.03864 ( 201) hydrogen bonds : angle 3.53273 ( 564) link_BETA1-4 : bond 0.00426 ( 6) link_BETA1-4 : angle 2.00312 ( 18) link_NAG-ASN : bond 0.00545 ( 3) link_NAG-ASN : angle 1.21362 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.222 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 47 average time/residue: 0.0790 time to fit residues: 5.1833 Evaluate side-chains 50 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.124476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111881 restraints weight = 8857.741| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.30 r_work: 0.3322 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6350 Z= 0.139 Angle : 0.493 6.841 8671 Z= 0.250 Chirality : 0.044 0.135 997 Planarity : 0.004 0.030 1108 Dihedral : 4.843 32.869 1047 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.34 % Allowed : 9.72 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.28), residues: 792 helix: 1.28 (0.47), residues: 147 sheet: 0.28 (0.42), residues: 147 loop : -0.12 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 596 TYR 0.012 0.001 TYR A 162 PHE 0.009 0.001 PHE D 153 TRP 0.008 0.001 TRP D 104 HIS 0.004 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6335) covalent geometry : angle 0.48063 ( 8632) SS BOND : bond 0.00212 ( 6) SS BOND : angle 1.29339 ( 12) hydrogen bonds : bond 0.04354 ( 201) hydrogen bonds : angle 3.64936 ( 564) link_BETA1-4 : bond 0.00357 ( 6) link_BETA1-4 : angle 2.08109 ( 18) link_NAG-ASN : bond 0.00464 ( 3) link_NAG-ASN : angle 1.38987 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.132 Fit side-chains REVERT: B 147 CYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7272 (p) outliers start: 8 outliers final: 7 residues processed: 47 average time/residue: 0.0651 time to fit residues: 4.3398 Evaluate side-chains 51 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 42 optimal weight: 0.0670 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.124633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.112213 restraints weight = 8784.700| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.25 r_work: 0.3331 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6350 Z= 0.130 Angle : 0.486 6.828 8671 Z= 0.246 Chirality : 0.043 0.136 997 Planarity : 0.004 0.030 1108 Dihedral : 4.831 32.794 1047 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.01 % Allowed : 9.05 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.29), residues: 792 helix: 1.27 (0.47), residues: 147 sheet: 0.29 (0.42), residues: 147 loop : -0.08 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 596 TYR 0.011 0.001 TYR A 162 PHE 0.009 0.001 PHE D 153 TRP 0.008 0.001 TRP C 518 HIS 0.004 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6335) covalent geometry : angle 0.47402 ( 8632) SS BOND : bond 0.00199 ( 6) SS BOND : angle 1.26190 ( 12) hydrogen bonds : bond 0.04253 ( 201) hydrogen bonds : angle 3.63142 ( 564) link_BETA1-4 : bond 0.00388 ( 6) link_BETA1-4 : angle 2.06780 ( 18) link_NAG-ASN : bond 0.00533 ( 3) link_NAG-ASN : angle 1.27980 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1433.63 seconds wall clock time: 25 minutes 6.09 seconds (1506.09 seconds total)