Starting phenix.real_space_refine on Fri Sep 11 09:07:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nsk_0499/09_2026/6nsk_0499.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nsk_0499/09_2026/6nsk_0499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nsk_0499/09_2026/6nsk_0499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nsk_0499/09_2026/6nsk_0499.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nsk_0499/09_2026/6nsk_0499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nsk_0499/09_2026/6nsk_0499.map" } resolution = 2.7 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= 0.017 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 30 5.16 5 C 6234 2.51 5 N 1332 2.21 5 O 1494 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9096 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "B" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "C" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "D" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "E" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "F" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'XP4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-1': 1, 'XP4:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'XP4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-1': 1, 'XP4:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'XP4': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-1': 1, 'XP4:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'XP4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-1': 1, 'XP4:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'XP4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-1': 1, 'XP4:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'XP4': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 2.32, per 1000 atoms: 0.26 Number of scatterers: 9096 At special positions: 0 Unit cell: (101.65, 97.37, 62.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 6 15.00 O 1494 8.00 N 1332 7.00 C 6234 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: 0.91 Conformation dependent library (CDL) restraints added in 274.7 milliseconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2004 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 1 through 23 removed outlier: 3.947A pdb=" N LEU A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR A 8 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 21 " --> pdb=" O GLY A 17 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 23 " --> pdb=" O CYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 54 removed outlier: 4.237A pdb=" N ASN A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 47 " --> pdb=" O CYS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 81 through 98 removed outlier: 3.704A pdb=" N GLY A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 124 Proline residue: A 117 - end of helix removed outlier: 3.665A pdb=" N ILE A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 161 Processing helix chain 'A' and resid 168 through 189 removed outlier: 4.174A pdb=" N TRP A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Proline residue: A 185 - end of helix Processing helix chain 'B' and resid 2 through 23 removed outlier: 3.904A pdb=" N LEU B 7 " --> pdb=" O GLY B 3 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 54 removed outlier: 4.302A pdb=" N ASN B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL B 47 " --> pdb=" O CYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 81 through 98 removed outlier: 3.733A pdb=" N GLY B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 124 Proline residue: B 117 - end of helix removed outlier: 3.577A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR B 124 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 161 Processing helix chain 'B' and resid 168 through 189 removed outlier: 3.933A pdb=" N TRP B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Proline residue: B 185 - end of helix Processing helix chain 'C' and resid 2 through 22 removed outlier: 3.876A pdb=" N LEU C 7 " --> pdb=" O GLY C 3 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR C 8 " --> pdb=" O LEU C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 54 removed outlier: 4.152A pdb=" N ASN C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 98 removed outlier: 3.938A pdb=" N LEU C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N PHE C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 124 Proline residue: C 117 - end of helix removed outlier: 3.644A pdb=" N ILE C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR C 124 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 161 Processing helix chain 'C' and resid 168 through 183 removed outlier: 4.185A pdb=" N TRP C 172 " --> pdb=" O LYS C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 191 removed outlier: 3.693A pdb=" N TRP C 187 " --> pdb=" O TRP C 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 23 removed outlier: 3.947A pdb=" N LEU D 7 " --> pdb=" O GLY D 3 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR D 8 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 21 " --> pdb=" O GLY D 17 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS D 23 " --> pdb=" O CYS D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 54 removed outlier: 4.237A pdb=" N ASN D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL D 47 " --> pdb=" O CYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 81 through 98 removed outlier: 3.704A pdb=" N GLY D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 124 Proline residue: D 117 - end of helix removed outlier: 3.665A pdb=" N ILE D 120 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 161 Processing helix chain 'D' and resid 168 through 189 removed outlier: 4.174A pdb=" N TRP D 172 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Proline residue: D 185 - end of helix Processing helix chain 'E' and resid 2 through 23 removed outlier: 3.904A pdb=" N LEU E 7 " --> pdb=" O GLY E 3 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR E 8 " --> pdb=" O LEU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 54 removed outlier: 4.302A pdb=" N ASN E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL E 47 " --> pdb=" O CYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 80 Processing helix chain 'E' and resid 81 through 98 removed outlier: 3.733A pdb=" N GLY E 85 " --> pdb=" O GLY E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 124 Proline residue: E 117 - end of helix removed outlier: 3.577A pdb=" N ILE E 120 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 161 Processing helix chain 'E' and resid 168 through 189 removed outlier: 3.932A pdb=" N TRP E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Proline residue: E 185 - end of helix Processing helix chain 'F' and resid 2 through 22 removed outlier: 3.875A pdb=" N LEU F 7 " --> pdb=" O GLY F 3 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 54 removed outlier: 4.158A pdb=" N ASN F 33 " --> pdb=" O THR F 29 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL F 47 " --> pdb=" O CYS F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 98 removed outlier: 3.938A pdb=" N LEU F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N PHE F 84 " --> pdb=" O THR F 80 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 124 Proline residue: F 117 - end of helix removed outlier: 3.644A pdb=" N ILE F 120 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR F 124 " --> pdb=" O ILE F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 161 Processing helix chain 'F' and resid 168 through 183 removed outlier: 4.187A pdb=" N TRP F 172 " --> pdb=" O LYS F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 191 removed outlier: 3.693A pdb=" N TRP F 187 " --> pdb=" O TRP F 183 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1809 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: 1.35 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1266 1.31 - 1.43: 2876 1.43 - 1.56: 5200 1.56 - 1.68: 6 1.68 - 1.81: 48 Bond restraints: 9396 Sorted by residual: bond pdb=" C4 XP4 D 202 " pdb=" O5 XP4 D 202 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C4 XP4 A 202 " pdb=" O5 XP4 A 202 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C4 XP4 B 203 " pdb=" O5 XP4 B 203 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C4 XP4 E 203 " pdb=" O5 XP4 E 203 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C4 XP4 C 204 " pdb=" O5 XP4 C 204 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 9391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 11842 1.91 - 3.82: 740 3.82 - 5.73: 138 5.73 - 7.65: 43 7.65 - 9.56: 41 Bond angle restraints: 12804 Sorted by residual: angle pdb=" C PHE C 169 " pdb=" N THR C 170 " pdb=" CA THR C 170 " ideal model delta sigma weight residual 120.09 125.21 -5.12 1.25e+00 6.40e-01 1.67e+01 angle pdb=" C PHE F 169 " pdb=" N THR F 170 " pdb=" CA THR F 170 " ideal model delta sigma weight residual 120.09 125.21 -5.12 1.25e+00 6.40e-01 1.67e+01 angle pdb=" C THR D 181 " pdb=" N ALA D 182 " pdb=" CA ALA D 182 " ideal model delta sigma weight residual 122.15 112.59 9.56 2.83e+00 1.25e-01 1.14e+01 angle pdb=" C THR A 181 " pdb=" N ALA A 182 " pdb=" CA ALA A 182 " ideal model delta sigma weight residual 122.15 112.59 9.56 2.83e+00 1.25e-01 1.14e+01 angle pdb=" CA TYR F 90 " pdb=" CB TYR F 90 " pdb=" CG TYR F 90 " ideal model delta sigma weight residual 113.90 119.82 -5.92 1.80e+00 3.09e-01 1.08e+01 ... (remaining 12799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.91: 4439 11.91 - 23.82: 471 23.82 - 35.73: 160 35.73 - 47.64: 65 47.64 - 59.56: 43 Dihedral angle restraints: 5178 sinusoidal: 2046 harmonic: 3132 Sorted by residual: dihedral pdb=" CA LEU F 128 " pdb=" C LEU F 128 " pdb=" N ASP F 129 " pdb=" CA ASP F 129 " ideal model delta harmonic sigma weight residual -180.00 -156.63 -23.37 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LEU C 128 " pdb=" C LEU C 128 " pdb=" N ASP C 129 " pdb=" CA ASP C 129 " ideal model delta harmonic sigma weight residual -180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA LEU D 128 " pdb=" C LEU D 128 " pdb=" N ASP D 129 " pdb=" CA ASP D 129 " ideal model delta harmonic sigma weight residual 180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 5175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 598 0.034 - 0.068: 460 0.068 - 0.102: 241 0.102 - 0.136: 96 0.136 - 0.169: 45 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CA TRP F 183 " pdb=" N TRP F 183 " pdb=" C TRP F 183 " pdb=" CB TRP F 183 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA ARG A 102 " pdb=" N ARG A 102 " pdb=" C ARG A 102 " pdb=" CB ARG A 102 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.04e-01 chirality pdb=" CA ARG D 102 " pdb=" N ARG D 102 " pdb=" C ARG D 102 " pdb=" CB ARG D 102 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.04e-01 ... (remaining 1437 not shown) Planarity restraints: 1470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 90 " 0.037 2.00e-02 2.50e+03 3.05e-02 1.86e+01 pdb=" CG TYR D 90 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR D 90 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR D 90 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 90 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 90 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR D 90 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 90 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 90 " 0.037 2.00e-02 2.50e+03 3.05e-02 1.86e+01 pdb=" CG TYR A 90 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR A 90 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 90 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 90 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 90 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 90 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 90 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 90 " 0.037 2.00e-02 2.50e+03 3.01e-02 1.82e+01 pdb=" CG TYR E 90 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR E 90 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR E 90 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 90 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR E 90 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR E 90 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 90 " 0.005 2.00e-02 2.50e+03 ... (remaining 1467 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1074 2.75 - 3.29: 8422 3.29 - 3.83: 14894 3.83 - 4.36: 18086 4.36 - 4.90: 32197 Nonbonded interactions: 74673 Sorted by model distance: nonbonded pdb=" O GLU B 177 " pdb=" OG1 THR B 181 " model vdw 2.213 3.040 nonbonded pdb=" O GLU E 177 " pdb=" OG1 THR E 181 " model vdw 2.213 3.040 nonbonded pdb=" O GLU F 177 " pdb=" OG1 THR F 181 " model vdw 2.219 3.040 nonbonded pdb=" O GLU C 177 " pdb=" OG1 THR C 181 " model vdw 2.219 3.040 nonbonded pdb=" O GLU D 177 " pdb=" OG1 THR D 181 " model vdw 2.230 3.040 ... (remaining 74668 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 201) selection = (chain 'B' and (resid 1 through 195 or (resid 201 and (name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or name O \ 7 or name O8 )))) selection = (chain 'C' and (resid 1 through 195 or (resid 201 and (name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or name O \ 7 or name O8 )))) selection = (chain 'D' and resid 1 through 201) selection = (chain 'E' and (resid 1 through 195 or (resid 201 and (name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or name O \ 7 or name O8 )))) selection = (chain 'F' and (resid 1 through 195 or (resid 201 and (name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or name O \ 7 or name O8 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.500 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:7.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 : 0.010 0.075 9396 Z= 0.418 Angle : 1.190 9.557 12804 Z= 0.593 Chirality : 0.061 0.169 1440 Planarity : 0.008 0.045 1470 Dihedral : 13.468 59.556 3174 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.23 (0.20), residues: 1068 helix: -1.94 (0.14), residues: 810 sheet: None (None), residues: 0 loop : -2.09 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 102 TYR 0.073 0.005 TYR D 90 PHE 0.031 0.003 PHE B 34 TRP 0.031 0.003 TRP C 153 HIS 0.013 0.003 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00953 / 0.42 ( 9396) covalent geometry : angle 1.18996 / 0.59 (12804) hydrogen bonds : bond 0.13312 / 8.78 ( 603) hydrogen bonds : angle 8.75530 / 6.33 ( 1809) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.299 Fit side-chains REVERT: A 15 SER cc_start: 0.8629 (t) cc_final: 0.8293 (m) REVERT: A 88 TYR cc_start: 0.8657 (m-80) cc_final: 0.8377 (m-80) REVERT: D 15 SER cc_start: 0.8645 (t) cc_final: 0.8321 (m) REVERT: D 88 TYR cc_start: 0.8677 (m-80) cc_final: 0.8400 (m-80) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.4140 time to fit residues: 68.2548 Evaluate side-chains 108 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 HIS A 114 ASN B 114 ASN C 95 HIS D 95 HIS D 114 ASN E 114 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.148800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117953 restraints weight = 10123.496| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.69 r_work: 0.3330 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9396 Z= 0.135 Angle : 0.590 7.193 12804 Z= 0.307 Chirality : 0.043 0.166 1440 Planarity : 0.005 0.035 1470 Dihedral : 13.047 59.803 1410 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.09 % Allowed : 10.02 % Favored : 88.89 % 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: -0.24 (0.25), residues: 1068 helix: 0.33 (0.17), residues: 840 sheet: None (None), residues: 0 loop : -1.68 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 102 TYR 0.026 0.002 TYR F 90 PHE 0.016 0.002 PHE E 34 TRP 0.010 0.001 TRP E 153 HIS 0.004 0.001 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 9396) covalent geometry : angle 0.59041 / 0.31 (12804) hydrogen bonds : bond 0.05483 / 3.56 ( 603) hydrogen bonds : angle 4.61522 / 3.33 ( 1809) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.343 Fit side-chains REVERT: A 40 SER cc_start: 0.8028 (t) cc_final: 0.7699 (m) REVERT: A 88 TYR cc_start: 0.8872 (m-80) cc_final: 0.8516 (m-80) REVERT: B 32 MET cc_start: 0.8562 (tpt) cc_final: 0.8172 (tpt) REVERT: B 40 SER cc_start: 0.8199 (t) cc_final: 0.7791 (m) REVERT: B 126 ASP cc_start: 0.6700 (m-30) cc_final: 0.6457 (m-30) REVERT: C 126 ASP cc_start: 0.6652 (m-30) cc_final: 0.6296 (m-30) REVERT: C 159 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7548 (mt-10) REVERT: D 40 SER cc_start: 0.8025 (t) cc_final: 0.7700 (m) REVERT: D 88 TYR cc_start: 0.8876 (m-80) cc_final: 0.8522 (m-80) REVERT: E 32 MET cc_start: 0.8567 (tpt) cc_final: 0.8177 (tpt) REVERT: E 40 SER cc_start: 0.8194 (t) cc_final: 0.7784 (m) REVERT: E 126 ASP cc_start: 0.6672 (m-30) cc_final: 0.6444 (m-30) REVERT: F 15 SER cc_start: 0.8482 (t) cc_final: 0.8278 (m) REVERT: F 126 ASP cc_start: 0.6626 (m-30) cc_final: 0.6289 (m-30) REVERT: F 159 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7556 (mt-10) outliers start: 10 outliers final: 0 residues processed: 134 average time/residue: 0.3350 time to fit residues: 49.7079 Evaluate side-chains 112 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 30 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 5 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.144729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113941 restraints weight = 10206.234| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.67 r_work: 0.3276 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9396 Z= 0.144 Angle : 0.575 7.053 12804 Z= 0.296 Chirality : 0.043 0.150 1440 Planarity : 0.005 0.037 1470 Dihedral : 12.403 59.303 1410 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.72 % Allowed : 12.20 % Favored : 85.08 % 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: 0.92 (0.26), residues: 1068 helix: 1.17 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -1.38 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 102 TYR 0.029 0.002 TYR C 90 PHE 0.014 0.001 PHE A 110 TRP 0.008 0.001 TRP C 187 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9396) covalent geometry : angle 0.57511 / 0.30 (12804) hydrogen bonds : bond 0.05728 / 3.70 ( 603) hydrogen bonds : angle 4.33831 / 3.12 ( 1809) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.306 Fit side-chains REVERT: A 1 MET cc_start: 0.5489 (ttp) cc_final: 0.5270 (tmm) REVERT: A 88 TYR cc_start: 0.8876 (m-80) cc_final: 0.8608 (m-80) REVERT: C 126 ASP cc_start: 0.6696 (m-30) cc_final: 0.6112 (m-30) REVERT: D 88 TYR cc_start: 0.8875 (m-80) cc_final: 0.8605 (m-80) REVERT: F 126 ASP cc_start: 0.6670 (m-30) cc_final: 0.6103 (m-30) REVERT: F 159 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7636 (mt-10) outliers start: 25 outliers final: 10 residues processed: 129 average time/residue: 0.3405 time to fit residues: 48.6258 Evaluate side-chains 116 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN C 44 ASN C 54 HIS D 160 ASN F 54 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.146437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115855 restraints weight = 10392.389| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.68 r_work: 0.3288 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9396 Z= 0.129 Angle : 0.544 6.853 12804 Z= 0.278 Chirality : 0.042 0.131 1440 Planarity : 0.004 0.038 1470 Dihedral : 11.826 59.936 1410 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.72 % Allowed : 13.18 % Favored : 84.10 % 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: 1.66 (0.26), residues: 1068 helix: 1.69 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -1.08 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 102 TYR 0.020 0.002 TYR C 90 PHE 0.013 0.001 PHE A 110 TRP 0.006 0.001 TRP C 187 HIS 0.004 0.001 HIS E 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 9396) covalent geometry : angle 0.54362 / 0.28 (12804) hydrogen bonds : bond 0.05123 / 3.31 ( 603) hydrogen bonds : angle 4.07171 / 2.93 ( 1809) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.197 Fit side-chains REVERT: A 88 TYR cc_start: 0.8858 (m-80) cc_final: 0.8556 (m-80) REVERT: C 126 ASP cc_start: 0.6603 (m-30) cc_final: 0.6047 (m-30) REVERT: D 88 TYR cc_start: 0.8868 (m-80) cc_final: 0.8561 (m-80) REVERT: F 4 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8675 (tt) REVERT: F 126 ASP cc_start: 0.6583 (m-30) cc_final: 0.6034 (m-30) outliers start: 25 outliers final: 11 residues processed: 127 average time/residue: 0.3636 time to fit residues: 50.4893 Evaluate side-chains 128 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 168 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN C 54 HIS D 160 ASN F 54 HIS F 95 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.142551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111647 restraints weight = 10405.667| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.68 r_work: 0.3251 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9396 Z= 0.160 Angle : 0.578 7.252 12804 Z= 0.297 Chirality : 0.043 0.133 1440 Planarity : 0.005 0.039 1470 Dihedral : 11.656 58.248 1410 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.05 % Allowed : 13.18 % Favored : 83.77 % 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: 1.75 (0.26), residues: 1068 helix: 1.64 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -0.68 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 102 TYR 0.022 0.002 TYR C 90 PHE 0.012 0.001 PHE D 110 TRP 0.008 0.001 TRP C 187 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 9396) covalent geometry : angle 0.57786 / 0.30 (12804) hydrogen bonds : bond 0.05969 / 3.87 ( 603) hydrogen bonds : angle 4.17790 / 3.00 ( 1809) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.307 Fit side-chains REVERT: A 88 TYR cc_start: 0.8924 (m-80) cc_final: 0.8655 (m-80) REVERT: C 159 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7604 (mt-10) REVERT: D 88 TYR cc_start: 0.8926 (m-80) cc_final: 0.8654 (m-80) REVERT: F 4 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8811 (tt) outliers start: 28 outliers final: 19 residues processed: 134 average time/residue: 0.3432 time to fit residues: 50.7951 Evaluate side-chains 139 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 168 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN B 44 ASN C 54 HIS D 160 ASN E 44 ASN F 54 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.146260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115921 restraints weight = 10391.045| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.67 r_work: 0.3300 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9396 Z= 0.121 Angle : 0.527 6.925 12804 Z= 0.269 Chirality : 0.041 0.129 1440 Planarity : 0.004 0.037 1470 Dihedral : 11.092 58.673 1410 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.05 % Allowed : 13.18 % Favored : 83.77 % 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: 2.19 (0.27), residues: 1068 helix: 1.96 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -0.50 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 102 TYR 0.013 0.002 TYR C 90 PHE 0.013 0.001 PHE D 110 TRP 0.007 0.001 TRP C 187 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 9396) covalent geometry : angle 0.52744 / 0.27 (12804) hydrogen bonds : bond 0.04851 / 3.14 ( 603) hydrogen bonds : angle 3.96453 / 2.85 ( 1809) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.326 Fit side-chains REVERT: A 88 TYR cc_start: 0.8922 (m-80) cc_final: 0.8646 (m-80) REVERT: A 127 MET cc_start: 0.4449 (OUTLIER) cc_final: 0.2980 (tpt) REVERT: B 44 ASN cc_start: 0.8505 (m-40) cc_final: 0.8081 (m110) REVERT: C 168 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.6897 (mtpm) REVERT: C 180 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8265 (mt) REVERT: D 88 TYR cc_start: 0.8924 (m-80) cc_final: 0.8649 (m-80) REVERT: D 127 MET cc_start: 0.4444 (OUTLIER) cc_final: 0.2976 (tpt) REVERT: E 44 ASN cc_start: 0.8519 (m-40) cc_final: 0.8098 (m110) REVERT: F 4 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8775 (tt) REVERT: F 159 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7458 (mt-10) REVERT: F 168 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.6912 (mtpm) outliers start: 28 outliers final: 14 residues processed: 138 average time/residue: 0.3454 time to fit residues: 52.5979 Evaluate side-chains 141 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 168 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 71 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN C 54 HIS D 160 ASN E 95 HIS F 54 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.144150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.113921 restraints weight = 10388.666| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.62 r_work: 0.3273 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9396 Z= 0.142 Angle : 0.553 7.060 12804 Z= 0.283 Chirality : 0.043 0.207 1440 Planarity : 0.005 0.039 1470 Dihedral : 10.953 59.974 1410 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.27 % Allowed : 13.18 % Favored : 83.55 % 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: 2.23 (0.26), residues: 1068 helix: 1.94 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -0.30 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 102 TYR 0.016 0.002 TYR F 90 PHE 0.011 0.001 PHE A 110 TRP 0.007 0.001 TRP C 153 HIS 0.004 0.001 HIS E 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 9396) covalent geometry : angle 0.55335 / 0.28 (12804) hydrogen bonds : bond 0.05492 / 3.55 ( 603) hydrogen bonds : angle 4.05418 / 2.91 ( 1809) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.306 Fit side-chains REVERT: A 88 TYR cc_start: 0.8834 (m-80) cc_final: 0.8461 (m-80) REVERT: A 127 MET cc_start: 0.4376 (OUTLIER) cc_final: 0.2979 (tpt) REVERT: B 44 ASN cc_start: 0.8415 (m-40) cc_final: 0.8016 (m110) REVERT: B 180 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8464 (mt) REVERT: C 159 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7485 (mt-10) REVERT: C 168 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7243 (mtpm) REVERT: C 180 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8209 (mt) REVERT: D 88 TYR cc_start: 0.8837 (m-80) cc_final: 0.8542 (m-80) REVERT: D 127 MET cc_start: 0.4423 (OUTLIER) cc_final: 0.2991 (tpt) REVERT: E 44 ASN cc_start: 0.8405 (m-40) cc_final: 0.8002 (m110) REVERT: E 180 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8468 (mt) REVERT: F 4 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8764 (tt) REVERT: F 159 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7443 (mt-10) REVERT: F 168 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.6832 (mtpm) outliers start: 30 outliers final: 16 residues processed: 136 average time/residue: 0.3470 time to fit residues: 52.2697 Evaluate side-chains 143 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 168 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 2 optimal weight: 0.0370 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 26 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN C 54 HIS D 160 ASN F 54 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.149492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119462 restraints weight = 10361.737| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.66 r_work: 0.3347 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9396 Z= 0.107 Angle : 0.504 6.626 12804 Z= 0.255 Chirality : 0.041 0.167 1440 Planarity : 0.004 0.039 1470 Dihedral : 10.145 57.632 1410 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.94 % Allowed : 13.73 % Favored : 83.33 % 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: 2.74 (0.27), residues: 1068 helix: 2.32 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -0.14 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 102 TYR 0.013 0.001 TYR B 88 PHE 0.013 0.001 PHE A 110 TRP 0.007 0.001 TRP F 153 HIS 0.003 0.001 HIS E 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.11 ( 9396) covalent geometry : angle 0.50393 / 0.26 (12804) hydrogen bonds : bond 0.04146 / 2.68 ( 603) hydrogen bonds : angle 3.81373 / 2.74 ( 1809) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.213 Fit side-chains REVERT: A 88 TYR cc_start: 0.8915 (m-80) cc_final: 0.8624 (m-80) REVERT: A 127 MET cc_start: 0.4312 (OUTLIER) cc_final: 0.2829 (tpt) REVERT: B 44 ASN cc_start: 0.8501 (m-40) cc_final: 0.8132 (m110) REVERT: B 126 ASP cc_start: 0.6533 (m-30) cc_final: 0.6219 (m-30) REVERT: B 180 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8493 (mt) REVERT: C 159 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7391 (mt-10) REVERT: C 168 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.6825 (mtpm) REVERT: C 180 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8212 (mt) REVERT: D 88 TYR cc_start: 0.8917 (m-80) cc_final: 0.8633 (m-80) REVERT: D 127 MET cc_start: 0.4282 (OUTLIER) cc_final: 0.2798 (tpt) REVERT: E 44 ASN cc_start: 0.8481 (m-40) cc_final: 0.8128 (m110) REVERT: E 180 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8500 (mt) REVERT: F 4 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8726 (tt) REVERT: F 27 LYS cc_start: 0.7570 (ttmm) cc_final: 0.7337 (mtpt) REVERT: F 159 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7195 (mt-10) outliers start: 27 outliers final: 12 residues processed: 135 average time/residue: 0.3483 time to fit residues: 51.7360 Evaluate side-chains 135 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 20 optimal weight: 0.0070 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN D 114 ASN D 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.149364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119212 restraints weight = 10322.865| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.65 r_work: 0.3335 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9396 Z= 0.109 Angle : 0.505 6.619 12804 Z= 0.256 Chirality : 0.042 0.211 1440 Planarity : 0.004 0.041 1470 Dihedral : 9.498 54.758 1410 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.72 % Allowed : 14.60 % Favored : 82.68 % 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: 2.93 (0.27), residues: 1068 helix: 2.44 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -0.05 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 102 TYR 0.012 0.001 TYR E 88 PHE 0.012 0.001 PHE B 110 TRP 0.010 0.001 TRP A 153 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 ( 9396) covalent geometry : angle 0.50531 / 0.26 (12804) hydrogen bonds : bond 0.04297 / 2.78 ( 603) hydrogen bonds : angle 3.80406 / 2.72 ( 1809) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.290 Fit side-chains REVERT: A 88 TYR cc_start: 0.8934 (m-80) cc_final: 0.8648 (m-80) REVERT: A 127 MET cc_start: 0.4316 (OUTLIER) cc_final: 0.2862 (tpt) REVERT: B 44 ASN cc_start: 0.8489 (m-40) cc_final: 0.8181 (m-40) REVERT: B 180 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8511 (mt) REVERT: C 159 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7472 (mt-10) REVERT: C 168 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.6804 (mtpm) REVERT: D 88 TYR cc_start: 0.8931 (m-80) cc_final: 0.8642 (m-80) REVERT: D 127 MET cc_start: 0.4313 (OUTLIER) cc_final: 0.2846 (tpt) REVERT: E 44 ASN cc_start: 0.8487 (m-40) cc_final: 0.8182 (m-40) REVERT: E 180 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8510 (mt) REVERT: F 4 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8712 (tt) REVERT: F 159 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7360 (mt-10) outliers start: 25 outliers final: 16 residues processed: 136 average time/residue: 0.3410 time to fit residues: 51.3078 Evaluate side-chains 140 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN D 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.143344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.112501 restraints weight = 10369.883| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.67 r_work: 0.3253 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9396 Z= 0.157 Angle : 0.569 7.303 12804 Z= 0.291 Chirality : 0.045 0.253 1440 Planarity : 0.005 0.041 1470 Dihedral : 9.769 51.797 1410 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.61 % Allowed : 14.60 % Favored : 82.79 % 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: 2.63 (0.27), residues: 1068 helix: 2.18 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -0.01 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 102 TYR 0.016 0.002 TYR F 90 PHE 0.010 0.001 PHE B 110 TRP 0.011 0.001 TRP D 153 HIS 0.004 0.001 HIS E 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 9396) covalent geometry : angle 0.56923 / 0.29 (12804) hydrogen bonds : bond 0.05709 / 3.71 ( 603) hydrogen bonds : angle 4.08259 / 2.92 ( 1809) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.325 Fit side-chains REVERT: A 88 TYR cc_start: 0.8962 (m-80) cc_final: 0.8660 (m-80) REVERT: A 127 MET cc_start: 0.4558 (OUTLIER) cc_final: 0.3042 (tpt) REVERT: B 44 ASN cc_start: 0.8501 (m-40) cc_final: 0.8134 (m110) REVERT: B 180 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8592 (mt) REVERT: C 4 LEU cc_start: 0.9037 (tm) cc_final: 0.8779 (tt) REVERT: C 159 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7663 (mt-10) REVERT: C 168 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.6919 (mtpm) REVERT: D 88 TYR cc_start: 0.8952 (m-80) cc_final: 0.8649 (m-80) REVERT: D 127 MET cc_start: 0.4571 (OUTLIER) cc_final: 0.3045 (tpt) REVERT: E 44 ASN cc_start: 0.8495 (m-40) cc_final: 0.8125 (m110) REVERT: F 4 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8793 (tt) REVERT: F 159 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7547 (mt-10) outliers start: 24 outliers final: 15 residues processed: 128 average time/residue: 0.3855 time to fit residues: 54.4028 Evaluate side-chains 128 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 13 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 20 optimal weight: 0.0010 chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN D 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.145499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.114977 restraints weight = 10333.442| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.66 r_work: 0.3282 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9396 Z= 0.127 Angle : 0.539 7.001 12804 Z= 0.274 Chirality : 0.043 0.191 1440 Planarity : 0.004 0.042 1470 Dihedral : 9.434 52.399 1410 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.51 % Allowed : 14.60 % Favored : 82.90 % 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: 2.78 (0.27), residues: 1068 helix: 2.29 (0.18), residues: 852 sheet: None (None), residues: 0 loop : 0.06 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 102 TYR 0.012 0.001 TYR F 90 PHE 0.011 0.001 PHE A 110 TRP 0.014 0.001 TRP C 153 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 9396) covalent geometry : angle 0.53861 / 0.27 (12804) hydrogen bonds : bond 0.04974 / 3.22 ( 603) hydrogen bonds : angle 3.98667 / 2.85 ( 1809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2589.99 seconds wall clock time: 44 minutes 55.70 seconds (2695.70 seconds total)