Starting phenix.real_space_refine on Wed Sep 17 19:26:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fp9_29360/09_2025/8fp9_29360.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fp9_29360/09_2025/8fp9_29360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fp9_29360/09_2025/8fp9_29360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fp9_29360/09_2025/8fp9_29360.map" model { file = "/net/cci-nas-00/data/ceres_data/8fp9_29360/09_2025/8fp9_29360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fp9_29360/09_2025/8fp9_29360.cif" } resolution = 2.44 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= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 76 5.16 5 Cl 4 4.86 5 C 7002 2.51 5 N 1708 2.21 5 O 2060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10851 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1177 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Chain: "B" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 bond proxies already assigned to first conformer: 1253 Chain: "C" Number of atoms: 1177 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Chain: "D" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 bond proxies already assigned to first conformer: 1253 Chain: "E" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1451 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1451 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1467 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1467 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ACYS A 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 589 " occ=0.50 residue: pdb=" N ASER A 615 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 615 " occ=0.50 residue: pdb=" N ACYS B 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 589 " occ=0.50 residue: pdb=" N ACYS C 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 589 " occ=0.50 residue: pdb=" N ASER C 615 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 615 " occ=0.50 residue: pdb=" N ACYS D 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 589 " occ=0.50 Time building chain proxies: 4.20, per 1000 atoms: 0.39 Number of scatterers: 10851 At special positions: 0 Unit cell: (113.911, 113.911, 91.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 Cl 4 17.00 S 76 16.00 O 2060 8.00 N 1708 7.00 C 7002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " 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 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 819.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 73.8% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 625 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 826 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 618 Processing helix chain 'B' and resid 619 through 626 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 826 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 549 No H-bonds generated for 'chain 'C' and resid 547 through 549' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 625 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 826 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 618 Processing helix chain 'D' and resid 619 through 626 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 826 Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 128 Processing helix chain 'E' and resid 132 through 162 removed outlier: 3.709A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.508A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 92 through 105 removed outlier: 3.521A pdb=" N TYR G 96 " --> pdb=" O ASP G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 128 removed outlier: 3.794A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 162 removed outlier: 3.691A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.673A pdb=" N TYR F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 129 Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.591A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 216 removed outlier: 3.529A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 30 Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.596A pdb=" N TYR H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 129 Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.572A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 216 removed outlier: 3.529A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 551 through 552 Processing sheet with id=AA2, first strand: chain 'C' and resid 551 through 552 Processing sheet with id=AA3, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AA5, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AA6, first strand: chain 'H' and resid 77 through 79 864 hydrogen bonds defined for protein. 2510 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: 2.09 Time building geometry restraints manager: 1.30 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: 3226 1.34 - 1.46: 2541 1.46 - 1.58: 5041 1.58 - 1.70: 0 1.70 - 1.81: 116 Bond restraints: 10924 Sorted by residual: bond pdb=" CG GLU G 191 " pdb=" CD GLU G 191 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.51e-01 bond pdb=" CG GLU E 191 " pdb=" CD GLU E 191 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.44e-01 bond pdb=" N ASN B 619 " pdb=" CA ASN B 619 " ideal model delta sigma weight residual 1.458 1.468 -0.010 1.44e-02 4.82e+03 4.90e-01 bond pdb=" CB PRO B 520 " pdb=" CG PRO B 520 " ideal model delta sigma weight residual 1.492 1.457 0.035 5.00e-02 4.00e+02 4.84e-01 bond pdb=" CB PRO D 520 " pdb=" CG PRO D 520 " ideal model delta sigma weight residual 1.492 1.457 0.035 5.00e-02 4.00e+02 4.81e-01 ... (remaining 10919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 14441 1.13 - 2.27: 292 2.27 - 3.40: 42 3.40 - 4.53: 17 4.53 - 5.67: 6 Bond angle restraints: 14798 Sorted by residual: angle pdb=" N ASP D 519 " pdb=" CA ASP D 519 " pdb=" C ASP D 519 " ideal model delta sigma weight residual 109.81 115.48 -5.67 2.21e+00 2.05e-01 6.57e+00 angle pdb=" N ASP B 519 " pdb=" CA ASP B 519 " pdb=" C ASP B 519 " ideal model delta sigma weight residual 109.81 115.46 -5.65 2.21e+00 2.05e-01 6.54e+00 angle pdb=" N ASP E 88 " pdb=" CA ASP E 88 " pdb=" CB ASP E 88 " ideal model delta sigma weight residual 113.65 110.10 3.55 1.47e+00 4.63e-01 5.82e+00 angle pdb=" CA ASP B 519 " pdb=" C ASP B 519 " pdb=" N PRO B 520 " ideal model delta sigma weight residual 118.44 122.10 -3.66 1.59e+00 3.96e-01 5.31e+00 angle pdb=" CA ASP D 519 " pdb=" C ASP D 519 " pdb=" N PRO D 520 " ideal model delta sigma weight residual 118.44 122.10 -3.66 1.59e+00 3.96e-01 5.30e+00 ... (remaining 14793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5403 17.89 - 35.79: 619 35.79 - 53.68: 168 53.68 - 71.58: 26 71.58 - 89.47: 16 Dihedral angle restraints: 6232 sinusoidal: 2298 harmonic: 3934 Sorted by residual: dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual -86.00 -121.10 35.10 1 1.00e+01 1.00e-02 1.75e+01 dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual -86.00 -120.87 34.87 1 1.00e+01 1.00e-02 1.72e+01 dihedral pdb=" CA ALA E 87 " pdb=" C ALA E 87 " pdb=" N ASP E 88 " pdb=" CA ASP E 88 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 6229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1105 0.028 - 0.056: 338 0.056 - 0.085: 188 0.085 - 0.113: 37 0.113 - 0.141: 6 Chirality restraints: 1674 Sorted by residual: chirality pdb=" CA PHE E 107 " pdb=" N PHE E 107 " pdb=" C PHE E 107 " pdb=" CB PHE E 107 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA PHE G 107 " pdb=" N PHE G 107 " pdb=" C PHE G 107 " pdb=" CB PHE G 107 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA VAL H 57 " pdb=" N VAL H 57 " pdb=" C VAL H 57 " pdb=" CB VAL H 57 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1671 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 107 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO H 108 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO H 108 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 108 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 107 " -0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO F 108 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO F 108 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO F 108 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 519 " 0.019 5.00e-02 4.00e+02 2.90e-02 1.34e+00 pdb=" N PRO B 520 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 520 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 520 " 0.016 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 726 2.74 - 3.28: 10800 3.28 - 3.82: 20325 3.82 - 4.36: 21626 4.36 - 4.90: 37809 Nonbonded interactions: 91286 Sorted by model distance: nonbonded pdb=" OG1 THR G 30 " pdb=" OG SER G 179 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR E 30 " pdb=" OG SER E 179 " model vdw 2.200 3.040 nonbonded pdb=" NE2 GLN D 586 " pdb=" O HOH D 901 " model vdw 2.221 3.120 nonbonded pdb=" O HOH B1001 " pdb=" O HOH B1008 " model vdw 2.228 3.040 nonbonded pdb=" OG SER C 564 " pdb=" N SER C 565 " model vdw 2.229 3.120 ... (remaining 91281 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 511 through 552 or resid 564 through 588 or resid 590 thro \ ugh 614 or resid 616 through 826)) selection = (chain 'B' and (resid 511 through 588 or resid 590 through 614 or resid 616 thro \ ugh 626 or resid 784 through 824 or (resid 825 and (name N or name CA or name C \ or name O or name CB )) or resid 826)) selection = (chain 'C' and (resid 511 through 552 or resid 564 through 588 or resid 590 thro \ ugh 614 or resid 616 through 826)) selection = (chain 'D' and (resid 511 through 588 or resid 590 through 614 or resid 616 thro \ ugh 626 or resid 784 through 824 or (resid 825 and (name N or name CA or name C \ or name O or name CB )) or resid 826)) } ncs_group { reference = (chain 'E' and (resid 5 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 401)) selection = (chain 'F' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 214 or resid 401)) selection = (chain 'G' and (resid 5 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 401)) selection = (chain 'H' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 214 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.910 Find NCS groups from input model: 0.250 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:8.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.003 0.035 10932 Z= 0.126 Angle : 0.427 5.666 14814 Z= 0.242 Chirality : 0.036 0.141 1674 Planarity : 0.003 0.030 1808 Dihedral : 16.651 89.473 3688 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.98 % Allowed : 19.68 % Favored : 79.34 % 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 aren not related in a simple way. whole: 4.36 (0.23), residues: 1336 helix: 4.00 (0.16), residues: 950 sheet: 0.37 (0.78), residues: 48 loop : -0.27 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 65 TYR 0.014 0.001 TYR G 89 PHE 0.010 0.001 PHE F 107 TRP 0.007 0.001 TRP G 33 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00255 (10924) covalent geometry : angle 0.42701 (14798) SS BOND : bond 0.00176 ( 8) SS BOND : angle 0.34502 ( 16) hydrogen bonds : bond 0.12066 ( 864) hydrogen bonds : angle 4.12499 ( 2510) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.408 Fit side-chains REVERT: D 629 MET cc_start: 0.6605 (tpt) cc_final: 0.6293 (tpp) REVERT: G 10 MET cc_start: 0.7887 (mmm) cc_final: 0.7662 (mmm) outliers start: 10 outliers final: 8 residues processed: 146 average time/residue: 0.6329 time to fit residues: 99.3916 Evaluate side-chains 144 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 791 ASN D 791 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.193353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129599 restraints weight = 33243.679| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.83 r_work: 0.2965 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.0626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10932 Z= 0.117 Angle : 0.414 5.796 14814 Z= 0.232 Chirality : 0.035 0.126 1674 Planarity : 0.003 0.030 1808 Dihedral : 3.900 27.669 1479 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.33 % Allowed : 17.98 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.60 (0.23), residues: 1336 helix: 4.16 (0.16), residues: 956 sheet: 0.08 (0.91), residues: 38 loop : -0.12 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 65 TYR 0.011 0.001 TYR G 89 PHE 0.009 0.001 PHE E 107 TRP 0.006 0.001 TRP E 178 HIS 0.003 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00224 (10924) covalent geometry : angle 0.41380 (14798) SS BOND : bond 0.00174 ( 8) SS BOND : angle 0.34127 ( 16) hydrogen bonds : bond 0.04876 ( 864) hydrogen bonds : angle 3.30538 ( 2510) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.452 Fit side-chains REVERT: D 586 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7937 (mm-40) REVERT: D 629 MET cc_start: 0.6369 (tpt) cc_final: 0.6161 (tpp) REVERT: E 31 ASP cc_start: 0.8222 (m-30) cc_final: 0.7926 (m-30) REVERT: G 31 ASP cc_start: 0.8214 (m-30) cc_final: 0.7981 (m-30) REVERT: G 74 LYS cc_start: 0.6487 (OUTLIER) cc_final: 0.6195 (ttpt) REVERT: H 65 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6667 (ptm-80) outliers start: 26 outliers final: 9 residues processed: 169 average time/residue: 0.5776 time to fit residues: 105.7794 Evaluate side-chains 153 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain D residue 586 GLN Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 65 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.192082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.129311 restraints weight = 36875.661| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.80 r_work: 0.2927 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10932 Z= 0.129 Angle : 0.424 6.003 14814 Z= 0.238 Chirality : 0.036 0.135 1674 Planarity : 0.003 0.031 1808 Dihedral : 3.719 27.665 1472 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.04 % Allowed : 17.53 % Favored : 79.43 % 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 aren not related in a simple way. whole: 4.52 (0.23), residues: 1336 helix: 4.10 (0.16), residues: 954 sheet: 0.70 (1.01), residues: 28 loop : -0.22 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 545 TYR 0.011 0.001 TYR G 89 PHE 0.010 0.001 PHE G 107 TRP 0.007 0.001 TRP E 33 HIS 0.003 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00260 (10924) covalent geometry : angle 0.42367 (14798) SS BOND : bond 0.00172 ( 8) SS BOND : angle 0.33975 ( 16) hydrogen bonds : bond 0.05188 ( 864) hydrogen bonds : angle 3.30972 ( 2510) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.438 Fit side-chains REVERT: B 629 MET cc_start: 0.6847 (tpp) cc_final: 0.6554 (tpt) REVERT: E 31 ASP cc_start: 0.8273 (m-30) cc_final: 0.7982 (m-30) REVERT: G 31 ASP cc_start: 0.8261 (m-30) cc_final: 0.8008 (m-30) REVERT: G 65 ARG cc_start: 0.7777 (ptm-80) cc_final: 0.7378 (ptm-80) REVERT: G 74 LYS cc_start: 0.6590 (OUTLIER) cc_final: 0.6272 (ttpt) REVERT: G 122 ILE cc_start: 0.7479 (mm) cc_final: 0.7242 (mm) REVERT: G 204 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6614 (mtt90) REVERT: F 58 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6770 (tpp) REVERT: F 65 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.6818 (ptm-80) REVERT: F 126 GLU cc_start: 0.5277 (OUTLIER) cc_final: 0.4911 (tm-30) outliers start: 34 outliers final: 16 residues processed: 166 average time/residue: 0.6026 time to fit residues: 107.8996 Evaluate side-chains 167 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 821 GLU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 175 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 18 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.188446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.125987 restraints weight = 27354.798| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.65 r_work: 0.2880 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 10932 Z= 0.279 Angle : 0.586 7.063 14814 Z= 0.329 Chirality : 0.044 0.164 1674 Planarity : 0.004 0.033 1808 Dihedral : 4.420 33.310 1472 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.38 % Allowed : 16.10 % Favored : 79.52 % 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 aren not related in a simple way. whole: 3.75 (0.23), residues: 1336 helix: 3.55 (0.16), residues: 952 sheet: 0.07 (0.69), residues: 48 loop : -0.51 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 545 TYR 0.015 0.003 TYR A 616 PHE 0.017 0.002 PHE G 107 TRP 0.020 0.003 TRP E 33 HIS 0.004 0.001 HIS B 552 Details of bonding type rmsd covalent geometry : bond 0.00639 (10924) covalent geometry : angle 0.58636 (14798) SS BOND : bond 0.00347 ( 8) SS BOND : angle 0.36927 ( 16) hydrogen bonds : bond 0.07346 ( 864) hydrogen bonds : angle 3.69491 ( 2510) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 133 time to evaluate : 0.416 Fit side-chains REVERT: A 570 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: B 586 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8113 (mm110) REVERT: C 570 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: E 10 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.7013 (mmm) REVERT: E 204 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6544 (mtt180) REVERT: E 207 GLN cc_start: 0.6318 (tt0) cc_final: 0.6018 (mt0) REVERT: G 122 ILE cc_start: 0.7650 (mm) cc_final: 0.7419 (mm) REVERT: G 204 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6555 (mtt180) REVERT: G 207 GLN cc_start: 0.6258 (tt0) cc_final: 0.5946 (tm-30) REVERT: F 12 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7252 (mp) REVERT: F 58 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6756 (tpt) REVERT: F 65 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6697 (ptm-80) REVERT: F 126 GLU cc_start: 0.5439 (OUTLIER) cc_final: 0.4831 (tm-30) REVERT: H 58 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6750 (tpt) REVERT: H 65 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6747 (ptm-80) outliers start: 49 outliers final: 17 residues processed: 165 average time/residue: 0.6075 time to fit residues: 108.3167 Evaluate side-chains 159 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 586 GLN Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 821 GLU Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 204 ARG Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 175 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 89 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.192539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130421 restraints weight = 30867.087| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.74 r_work: 0.2947 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10932 Z= 0.117 Angle : 0.417 7.107 14814 Z= 0.233 Chirality : 0.036 0.131 1674 Planarity : 0.003 0.031 1808 Dihedral : 3.794 27.879 1472 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.68 % Allowed : 18.25 % Favored : 79.07 % 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 aren not related in a simple way. whole: 4.44 (0.23), residues: 1336 helix: 4.05 (0.15), residues: 954 sheet: 1.18 (1.01), residues: 28 loop : -0.32 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 65 TYR 0.010 0.001 TYR B 523 PHE 0.009 0.001 PHE G 107 TRP 0.009 0.001 TRP G 178 HIS 0.004 0.000 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00229 (10924) covalent geometry : angle 0.41706 (14798) SS BOND : bond 0.00143 ( 8) SS BOND : angle 0.37279 ( 16) hydrogen bonds : bond 0.04899 ( 864) hydrogen bonds : angle 3.25351 ( 2510) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.407 Fit side-chains REVERT: E 10 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6909 (mmm) REVERT: E 31 ASP cc_start: 0.8220 (m-30) cc_final: 0.7773 (m-30) REVERT: E 204 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6639 (mtt180) REVERT: E 207 GLN cc_start: 0.6218 (tt0) cc_final: 0.5911 (tm-30) REVERT: G 31 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: G 65 ARG cc_start: 0.7849 (ptm-80) cc_final: 0.7392 (ptm-80) REVERT: G 122 ILE cc_start: 0.7565 (mm) cc_final: 0.7335 (mm) REVERT: G 204 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6631 (mtt90) REVERT: G 207 GLN cc_start: 0.6206 (tt0) cc_final: 0.5931 (tm-30) REVERT: F 58 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6825 (tpp) REVERT: F 65 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6789 (ptm-80) REVERT: H 58 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6929 (tpp) outliers start: 30 outliers final: 10 residues processed: 158 average time/residue: 0.6371 time to fit residues: 108.0925 Evaluate side-chains 160 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 204 ARG Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 58 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 78 optimal weight: 0.0670 chunk 117 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 586 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.190410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.128529 restraints weight = 29271.611| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.73 r_work: 0.2904 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10932 Z= 0.168 Angle : 0.474 8.014 14814 Z= 0.264 Chirality : 0.038 0.130 1674 Planarity : 0.003 0.031 1808 Dihedral : 4.019 28.875 1472 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.13 % Allowed : 17.53 % Favored : 79.34 % 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 aren not related in a simple way. whole: 4.25 (0.23), residues: 1336 helix: 3.89 (0.15), residues: 954 sheet: 1.21 (0.96), residues: 28 loop : -0.36 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 545 TYR 0.012 0.002 TYR B 523 PHE 0.012 0.002 PHE G 107 TRP 0.012 0.002 TRP E 33 HIS 0.003 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00363 (10924) covalent geometry : angle 0.47393 (14798) SS BOND : bond 0.00212 ( 8) SS BOND : angle 0.34950 ( 16) hydrogen bonds : bond 0.05892 ( 864) hydrogen bonds : angle 3.39151 ( 2510) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.427 Fit side-chains REVERT: A 570 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8019 (tt0) REVERT: C 570 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8016 (tt0) REVERT: E 31 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7868 (m-30) REVERT: E 204 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.6620 (mtt180) REVERT: E 207 GLN cc_start: 0.6280 (tt0) cc_final: 0.5948 (tm-30) REVERT: G 31 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7868 (m-30) REVERT: G 65 ARG cc_start: 0.7848 (ptm-80) cc_final: 0.7482 (ptm-80) REVERT: G 122 ILE cc_start: 0.7603 (mm) cc_final: 0.7359 (mm) REVERT: G 204 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6620 (mtt90) REVERT: G 207 GLN cc_start: 0.6300 (tt0) cc_final: 0.5979 (tm-30) REVERT: F 58 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.6757 (tpp) REVERT: F 65 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6810 (ptm-80) REVERT: H 65 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.6754 (ptm-80) outliers start: 35 outliers final: 16 residues processed: 159 average time/residue: 0.6312 time to fit residues: 107.8467 Evaluate side-chains 159 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 204 ARG Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 134 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 24 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 586 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.192347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.130376 restraints weight = 33043.790| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.70 r_work: 0.2932 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10932 Z= 0.120 Angle : 0.423 8.190 14814 Z= 0.234 Chirality : 0.036 0.138 1674 Planarity : 0.003 0.031 1808 Dihedral : 3.763 27.776 1472 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.68 % Allowed : 17.89 % Favored : 79.43 % 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 aren not related in a simple way. whole: 4.53 (0.23), residues: 1336 helix: 4.12 (0.15), residues: 954 sheet: 1.46 (1.02), residues: 28 loop : -0.33 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 99 TYR 0.010 0.001 TYR B 523 PHE 0.009 0.001 PHE G 107 TRP 0.008 0.001 TRP G 178 HIS 0.003 0.000 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00237 (10924) covalent geometry : angle 0.42349 (14798) SS BOND : bond 0.00157 ( 8) SS BOND : angle 0.33057 ( 16) hydrogen bonds : bond 0.04917 ( 864) hydrogen bonds : angle 3.21769 ( 2510) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.427 Fit side-chains REVERT: E 31 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: E 204 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6689 (mtt180) REVERT: G 31 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: G 65 ARG cc_start: 0.7882 (ptm-80) cc_final: 0.7527 (ptm-80) REVERT: G 122 ILE cc_start: 0.7582 (mm) cc_final: 0.7334 (mm) REVERT: G 204 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6663 (mtt90) REVERT: F 58 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6823 (tpp) REVERT: F 65 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6810 (ptm-80) REVERT: F 206 LYS cc_start: 0.6813 (mttt) cc_final: 0.6606 (mttt) REVERT: H 58 MET cc_start: 0.7103 (tpt) cc_final: 0.6823 (tpp) REVERT: H 206 LYS cc_start: 0.6819 (mttt) cc_final: 0.6609 (mttt) outliers start: 30 outliers final: 14 residues processed: 157 average time/residue: 0.6140 time to fit residues: 103.8806 Evaluate side-chains 160 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 204 ARG Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 134 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 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 = 0.4086 r_free = 0.4086 target = 0.192379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.130497 restraints weight = 32675.690| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.71 r_work: 0.2934 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10932 Z= 0.120 Angle : 0.424 8.245 14814 Z= 0.234 Chirality : 0.036 0.136 1674 Planarity : 0.003 0.030 1808 Dihedral : 3.728 27.641 1472 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.68 % Allowed : 18.07 % Favored : 79.25 % 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 aren not related in a simple way. whole: 4.59 (0.23), residues: 1336 helix: 4.17 (0.15), residues: 954 sheet: 1.40 (1.03), residues: 28 loop : -0.32 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 99 TYR 0.011 0.001 TYR B 523 PHE 0.010 0.001 PHE C 607 TRP 0.008 0.001 TRP F 178 HIS 0.003 0.000 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00238 (10924) covalent geometry : angle 0.42458 (14798) SS BOND : bond 0.00158 ( 8) SS BOND : angle 0.31614 ( 16) hydrogen bonds : bond 0.04892 ( 864) hydrogen bonds : angle 3.19007 ( 2510) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.423 Fit side-chains REVERT: E 31 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7842 (m-30) REVERT: E 204 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6697 (mtt180) REVERT: G 31 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: G 65 ARG cc_start: 0.7897 (ptm-80) cc_final: 0.7558 (ptm-80) REVERT: G 122 ILE cc_start: 0.7555 (mm) cc_final: 0.7312 (mm) REVERT: G 204 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6684 (mtt90) REVERT: F 10 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7444 (tpt) REVERT: F 58 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6859 (tpp) REVERT: F 65 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.6820 (ptm-80) REVERT: F 206 LYS cc_start: 0.6861 (mttt) cc_final: 0.6656 (mttt) REVERT: H 58 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6952 (tpp) REVERT: H 65 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.6824 (ptm-80) REVERT: H 206 LYS cc_start: 0.6877 (mttt) cc_final: 0.6663 (mttt) outliers start: 30 outliers final: 17 residues processed: 155 average time/residue: 0.6453 time to fit residues: 107.4468 Evaluate side-chains 164 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 204 ARG Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 175 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 79 optimal weight: 0.3980 chunk 130 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.193971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132410 restraints weight = 33128.961| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.79 r_work: 0.2967 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10932 Z= 0.105 Angle : 0.404 8.282 14814 Z= 0.222 Chirality : 0.035 0.132 1674 Planarity : 0.003 0.030 1808 Dihedral : 3.575 26.800 1472 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.88 % Allowed : 18.78 % Favored : 79.34 % 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 aren not related in a simple way. whole: 4.73 (0.23), residues: 1336 helix: 4.27 (0.15), residues: 956 sheet: 1.44 (1.07), residues: 28 loop : -0.29 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 99 TYR 0.010 0.001 TYR A 523 PHE 0.009 0.001 PHE C 607 TRP 0.009 0.001 TRP G 178 HIS 0.003 0.000 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00198 (10924) covalent geometry : angle 0.40392 (14798) SS BOND : bond 0.00141 ( 8) SS BOND : angle 0.29802 ( 16) hydrogen bonds : bond 0.04387 ( 864) hydrogen bonds : angle 3.10203 ( 2510) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.432 Fit side-chains REVERT: E 10 MET cc_start: 0.7249 (tpt) cc_final: 0.6677 (mmm) REVERT: E 204 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6649 (mtt180) REVERT: G 31 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: G 65 ARG cc_start: 0.7879 (ptm-80) cc_final: 0.7578 (ptm-80) REVERT: G 122 ILE cc_start: 0.7384 (mm) cc_final: 0.7136 (mm) REVERT: F 58 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6765 (tpp) REVERT: H 37 ARG cc_start: 0.6924 (mtp85) cc_final: 0.6360 (mtp-110) REVERT: H 58 MET cc_start: 0.7131 (tpt) cc_final: 0.6857 (tpp) REVERT: H 206 LYS cc_start: 0.6756 (mttt) cc_final: 0.6550 (mttt) outliers start: 21 outliers final: 12 residues processed: 157 average time/residue: 0.6202 time to fit residues: 104.8472 Evaluate side-chains 155 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 204 ARG Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 134 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.192501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130582 restraints weight = 31214.187| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.73 r_work: 0.2940 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10932 Z= 0.124 Angle : 0.431 8.273 14814 Z= 0.237 Chirality : 0.036 0.135 1674 Planarity : 0.003 0.031 1808 Dihedral : 3.697 27.447 1472 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.79 % Allowed : 18.78 % Favored : 79.43 % 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 aren not related in a simple way. whole: 4.60 (0.23), residues: 1336 helix: 4.17 (0.15), residues: 956 sheet: 1.39 (1.06), residues: 28 loop : -0.29 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 99 TYR 0.012 0.001 TYR A 523 PHE 0.010 0.001 PHE G 107 TRP 0.008 0.001 TRP E 33 HIS 0.003 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00251 (10924) covalent geometry : angle 0.43091 (14798) SS BOND : bond 0.00162 ( 8) SS BOND : angle 0.29726 ( 16) hydrogen bonds : bond 0.04921 ( 864) hydrogen bonds : angle 3.17825 ( 2510) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.433 Fit side-chains REVERT: E 10 MET cc_start: 0.7303 (tpt) cc_final: 0.6724 (mmm) REVERT: E 31 ASP cc_start: 0.8180 (m-30) cc_final: 0.7897 (m-30) REVERT: E 204 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6628 (mtt180) REVERT: G 31 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7798 (m-30) REVERT: G 65 ARG cc_start: 0.7886 (ptm-80) cc_final: 0.7536 (ptm-80) REVERT: G 122 ILE cc_start: 0.7473 (mm) cc_final: 0.7221 (mm) REVERT: F 10 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7437 (tpt) REVERT: F 58 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6826 (tpp) REVERT: H 206 LYS cc_start: 0.6774 (mttt) cc_final: 0.6558 (mttt) outliers start: 20 outliers final: 14 residues processed: 153 average time/residue: 0.6302 time to fit residues: 103.5506 Evaluate side-chains 157 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 204 ARG Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 175 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 120 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 119 optimal weight: 0.4980 chunk 4 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.192639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130456 restraints weight = 30824.125| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.74 r_work: 0.2949 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10932 Z= 0.121 Angle : 0.425 8.253 14814 Z= 0.234 Chirality : 0.036 0.134 1674 Planarity : 0.003 0.031 1808 Dihedral : 3.680 27.379 1472 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.97 % Allowed : 18.34 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.62 (0.23), residues: 1336 helix: 4.19 (0.15), residues: 956 sheet: 1.41 (1.07), residues: 28 loop : -0.30 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 99 TYR 0.011 0.001 TYR C 523 PHE 0.010 0.001 PHE G 107 TRP 0.008 0.001 TRP F 178 HIS 0.003 0.000 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00240 (10924) covalent geometry : angle 0.42553 (14798) SS BOND : bond 0.00161 ( 8) SS BOND : angle 0.29656 ( 16) hydrogen bonds : bond 0.04836 ( 864) hydrogen bonds : angle 3.16417 ( 2510) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5031.57 seconds wall clock time: 86 minutes 18.58 seconds (5178.58 seconds total)