Starting phenix.real_space_refine on Wed Mar 4 04:15:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fp4_29359/03_2026/8fp4_29359.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fp4_29359/03_2026/8fp4_29359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fp4_29359/03_2026/8fp4_29359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fp4_29359/03_2026/8fp4_29359.map" model { file = "/net/cci-nas-00/data/ceres_data/8fp4_29359/03_2026/8fp4_29359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fp4_29359/03_2026/8fp4_29359.cif" } resolution = 2.4 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 76 5.16 5 Cl 2 4.86 5 C 7002 2.51 5 N 1708 2.21 5 O 2088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10876 Number of models: 1 Model: "" Number of chains: 18 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: 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 Conformer: "C" Number of residues, atoms: 148, 1159 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Conformer: "A" Number of residues, atoms: 148, 1159 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 3 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: "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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} 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 BCYS C 589 " occ=0.38 ... (10 atoms not shown) pdb=" SG CCYS C 589 " occ=0.62 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: 3.49, per 1000 atoms: 0.32 Number of scatterers: 10876 At special positions: 0 Unit cell: (112.34, 113.98, 90.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 76 16.00 O 2088 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: 0.83 Conformation dependent library (CDL) restraints added in 711.0 milliseconds 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: 53 helices and 6 sheets defined 74.3% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 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 625 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 826 removed outlier: 3.552A pdb=" N LYS B 826 " --> pdb=" O ALA B 822 " (cutoff:3.500A) 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 624 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 624 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 84 through 89 removed outlier: 3.588A pdb=" N ASP E 88 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 127 Processing helix chain 'E' and resid 132 through 162 removed outlier: 3.784A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.536A 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 84 through 89 removed outlier: 3.580A pdb=" N ASP G 88 " --> pdb=" O PRO G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 125 Processing helix chain 'G' and resid 126 through 128 No H-bonds generated for 'chain 'G' and resid 126 through 128' Processing helix chain 'G' and resid 132 through 162 removed outlier: 3.699A 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: 4.159A 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: 3.702A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 216 removed outlier: 3.570A 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: 4.015A 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: 3.661A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 216 removed outlier: 3.569A 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 79 860 hydrogen bonds defined for protein. 2498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3232 1.34 - 1.46: 2910 1.46 - 1.58: 4666 1.58 - 1.70: 0 1.70 - 1.81: 116 Bond restraints: 10924 Sorted by residual: bond pdb=" CB MET D 825 " pdb=" CG MET D 825 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.61e-01 bond pdb=" C VAL A 792 " pdb=" O VAL A 792 " ideal model delta sigma weight residual 1.232 1.242 -0.010 1.30e-02 5.92e+03 5.94e-01 bond pdb=" N TYR E 128 " pdb=" CA TYR E 128 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.50e-02 4.44e+03 5.66e-01 bond pdb=" C ALA F 87 " pdb=" N ASP F 88 " ideal model delta sigma weight residual 1.328 1.337 -0.010 1.30e-02 5.92e+03 5.60e-01 bond pdb=" SD MET B 825 " pdb=" CE MET B 825 " ideal model delta sigma weight residual 1.791 1.772 0.019 2.50e-02 1.60e+03 5.58e-01 ... (remaining 10919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 14671 1.72 - 3.43: 106 3.43 - 5.15: 18 5.15 - 6.86: 2 6.86 - 8.58: 1 Bond angle restraints: 14798 Sorted by residual: angle pdb=" N VAL A 792 " pdb=" CA VAL A 792 " pdb=" C VAL A 792 " ideal model delta sigma weight residual 113.20 109.87 3.33 9.60e-01 1.09e+00 1.20e+01 angle pdb=" CA MET B 825 " pdb=" CB MET B 825 " pdb=" CG MET B 825 " ideal model delta sigma weight residual 114.10 120.30 -6.20 2.00e+00 2.50e-01 9.61e+00 angle pdb=" C ARG B 824 " pdb=" N MET B 825 " pdb=" CA MET B 825 " ideal model delta sigma weight residual 122.38 116.94 5.44 1.81e+00 3.05e-01 9.03e+00 angle pdb=" CB MET D 825 " pdb=" CG MET D 825 " pdb=" SD MET D 825 " ideal model delta sigma weight residual 112.70 121.28 -8.58 3.00e+00 1.11e-01 8.17e+00 angle pdb=" CA VAL A 792 " pdb=" C VAL A 792 " pdb=" N ALA A 793 " ideal model delta sigma weight residual 118.71 115.95 2.76 1.15e+00 7.56e-01 5.74e+00 ... (remaining 14793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5427 17.83 - 35.66: 591 35.66 - 53.49: 171 53.49 - 71.32: 29 71.32 - 89.15: 14 Dihedral angle restraints: 6232 sinusoidal: 2298 harmonic: 3934 Sorted by residual: dihedral pdb=" CA ASP D 590 " pdb=" CB ASP D 590 " pdb=" CG ASP D 590 " pdb=" OD1 ASP D 590 " ideal model delta sinusoidal sigma weight residual -30.00 -86.67 56.67 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP B 590 " pdb=" CB ASP B 590 " pdb=" CG ASP B 590 " pdb=" OD1 ASP B 590 " ideal model delta sinusoidal sigma weight residual -30.00 -86.55 56.55 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA PHE A 571 " pdb=" C PHE A 571 " pdb=" N GLY A 572 " pdb=" CA GLY A 572 " ideal model delta harmonic sigma weight residual 180.00 163.61 16.39 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 6229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1048 0.026 - 0.052: 369 0.052 - 0.077: 187 0.077 - 0.103: 56 0.103 - 0.129: 14 Chirality restraints: 1674 Sorted by residual: 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 chirality pdb=" CA VAL F 57 " pdb=" N VAL F 57 " pdb=" C VAL F 57 " pdb=" CB VAL F 57 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.08e-01 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 2.39 0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 1671 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 107 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO E 108 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 108 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 108 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 107 " -0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO G 108 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO G 108 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 108 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 107 " -0.018 5.00e-02 4.00e+02 2.70e-02 1.17e+00 pdb=" N PRO F 108 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO F 108 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO F 108 " -0.015 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 450 2.72 - 3.27: 11097 3.27 - 3.81: 20457 3.81 - 4.36: 22553 4.36 - 4.90: 38664 Nonbonded interactions: 93221 Sorted by model distance: nonbonded pdb=" OE1 GLN D 586 " pdb=" O HOH D 901 " model vdw 2.178 3.040 nonbonded pdb=" OE1 GLN B 586 " pdb=" O HOH B 901 " model vdw 2.182 3.040 nonbonded pdb=" O HOH D 902 " pdb=" O HOH D 910 " model vdw 2.198 3.040 nonbonded pdb=" O HOH B 902 " pdb=" O HOH B 910 " model vdw 2.199 3.040 nonbonded pdb=" O HOH B 906 " pdb=" O HOH B 914 " model vdw 2.208 3.040 ... (remaining 93216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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 214)) 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)) 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 214)) 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)) } 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=0.38 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.330 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 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 : 0.002 0.024 10932 Z= 0.118 Angle : 0.422 8.576 14814 Z= 0.240 Chirality : 0.035 0.129 1674 Planarity : 0.003 0.033 1808 Dihedral : 16.680 89.147 3688 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.43 % Allowed : 19.68 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.16 (0.24), residues: 1336 helix: 3.74 (0.16), residues: 953 sheet: 0.35 (1.10), residues: 28 loop : 0.01 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 204 TYR 0.011 0.001 TYR A 616 PHE 0.014 0.001 PHE E 127 TRP 0.006 0.001 TRP D 606 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00235 (10924) covalent geometry : angle 0.42220 (14798) SS BOND : bond 0.00221 ( 8) SS BOND : angle 0.53663 ( 16) hydrogen bonds : bond 0.09919 ( 860) hydrogen bonds : angle 3.95304 ( 2498) *********************** 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 178 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.345 Fit side-chains REVERT: F 191 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8573 (mm-30) outliers start: 16 outliers final: 12 residues processed: 174 average time/residue: 0.5233 time to fit residues: 98.6001 Evaluate side-chains 172 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 39 VAL Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN E 132 HIS G 132 HIS F 149 ASN H 149 ASN H 205 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.165555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.109985 restraints weight = 32960.807| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.54 r_work: 0.2727 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10932 Z= 0.158 Angle : 0.473 7.145 14814 Z= 0.267 Chirality : 0.038 0.131 1674 Planarity : 0.004 0.038 1808 Dihedral : 4.561 51.687 1482 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.70 % Allowed : 18.87 % 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 are not related in a simple way. whole: 4.00 (0.24), residues: 1336 helix: 3.63 (0.16), residues: 952 sheet: 0.03 (1.07), residues: 28 loop : -0.05 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 204 TYR 0.013 0.002 TYR G 181 PHE 0.015 0.002 PHE G 107 TRP 0.008 0.001 TRP D 606 HIS 0.005 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00338 (10924) covalent geometry : angle 0.47265 (14798) SS BOND : bond 0.00367 ( 8) SS BOND : angle 0.79726 ( 16) hydrogen bonds : bond 0.05200 ( 860) hydrogen bonds : angle 3.59629 ( 2498) *********************** 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 185 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.361 Fit side-chains REVERT: F 99 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6592 (tpp-160) REVERT: H 122 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.7024 (mm) REVERT: H 191 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8607 (mm-30) outliers start: 19 outliers final: 11 residues processed: 175 average time/residue: 0.5198 time to fit residues: 98.7865 Evaluate side-chains 171 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 203 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS E 149 ASN G 132 HIS G 149 ASN F 149 ASN H 149 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.167369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123708 restraints weight = 28840.109| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 4.72 r_work: 0.2724 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10932 Z= 0.116 Angle : 0.418 7.017 14814 Z= 0.235 Chirality : 0.036 0.132 1674 Planarity : 0.003 0.035 1808 Dihedral : 3.857 41.547 1476 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.97 % Allowed : 18.16 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.12 (0.24), residues: 1336 helix: 3.71 (0.16), residues: 956 sheet: -0.48 (1.05), residues: 30 loop : 0.04 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 204 TYR 0.010 0.001 TYR E 181 PHE 0.014 0.001 PHE E 127 TRP 0.007 0.001 TRP F 178 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00228 (10924) covalent geometry : angle 0.41744 (14798) SS BOND : bond 0.00210 ( 8) SS BOND : angle 0.61637 ( 16) hydrogen bonds : bond 0.04439 ( 860) hydrogen bonds : angle 3.39525 ( 2498) *********************** 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 188 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.420 Fit side-chains REVERT: A 514 VAL cc_start: 0.7378 (m) cc_final: 0.7050 (p) REVERT: B 619 ASN cc_start: 0.7485 (m-40) cc_final: 0.7229 (m-40) REVERT: C 514 VAL cc_start: 0.7375 (m) cc_final: 0.7073 (p) REVERT: E 9 GLN cc_start: 0.6840 (OUTLIER) cc_final: 0.6587 (tt0) REVERT: F 99 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6630 (tpp-160) REVERT: F 191 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8559 (mm-30) REVERT: H 122 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6947 (mm) REVERT: H 191 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8590 (mm-30) outliers start: 22 outliers final: 9 residues processed: 179 average time/residue: 0.5338 time to fit residues: 103.2862 Evaluate side-chains 174 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 9 GLN Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 203 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 128 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS F 149 ASN H 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.166081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.110763 restraints weight = 32069.818| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.55 r_work: 0.2762 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10932 Z= 0.132 Angle : 0.443 6.654 14814 Z= 0.247 Chirality : 0.036 0.132 1674 Planarity : 0.003 0.036 1808 Dihedral : 3.791 31.364 1469 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.61 % Allowed : 18.52 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.06 (0.24), residues: 1336 helix: 3.65 (0.16), residues: 955 sheet: -0.45 (1.07), residues: 30 loop : 0.08 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 204 TYR 0.013 0.001 TYR G 181 PHE 0.014 0.002 PHE E 127 TRP 0.007 0.001 TRP D 606 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00274 (10924) covalent geometry : angle 0.44227 (14798) SS BOND : bond 0.00243 ( 8) SS BOND : angle 0.69427 ( 16) hydrogen bonds : bond 0.04767 ( 860) hydrogen bonds : angle 3.44297 ( 2498) *********************** 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 181 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.386 Fit side-chains REVERT: A 514 VAL cc_start: 0.7402 (m) cc_final: 0.7129 (p) REVERT: B 619 ASN cc_start: 0.7502 (m-40) cc_final: 0.7264 (m-40) REVERT: C 514 VAL cc_start: 0.7401 (m) cc_final: 0.7149 (p) REVERT: D 825 MET cc_start: 0.5358 (ppp) cc_final: 0.4987 (pp-130) REVERT: E 9 GLN cc_start: 0.6789 (OUTLIER) cc_final: 0.6554 (tt0) REVERT: F 99 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.6592 (tpp-160) outliers start: 18 outliers final: 11 residues processed: 176 average time/residue: 0.5412 time to fit residues: 102.8592 Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 9 GLN Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 203 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 37 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 586 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN H 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.165561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.111835 restraints weight = 33686.536| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.33 r_work: 0.2747 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10932 Z= 0.144 Angle : 0.458 6.651 14814 Z= 0.256 Chirality : 0.037 0.135 1674 Planarity : 0.003 0.036 1808 Dihedral : 3.843 24.247 1469 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.97 % Allowed : 17.89 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.97 (0.24), residues: 1336 helix: 3.58 (0.16), residues: 954 sheet: -0.37 (1.07), residues: 30 loop : 0.06 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 204 TYR 0.014 0.002 TYR G 181 PHE 0.013 0.002 PHE G 107 TRP 0.007 0.001 TRP D 606 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00305 (10924) covalent geometry : angle 0.45735 (14798) SS BOND : bond 0.00284 ( 8) SS BOND : angle 0.73472 ( 16) hydrogen bonds : bond 0.04922 ( 860) hydrogen bonds : angle 3.47242 ( 2498) *********************** 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 185 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.451 Fit side-chains REVERT: A 514 VAL cc_start: 0.7373 (m) cc_final: 0.7081 (p) REVERT: B 619 ASN cc_start: 0.7504 (m-40) cc_final: 0.7250 (m-40) REVERT: C 514 VAL cc_start: 0.7391 (m) cc_final: 0.7116 (p) REVERT: D 825 MET cc_start: 0.5435 (ppp) cc_final: 0.5116 (pp-130) REVERT: E 9 GLN cc_start: 0.6772 (OUTLIER) cc_final: 0.6518 (tt0) REVERT: F 99 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6570 (tpp-160) outliers start: 22 outliers final: 15 residues processed: 176 average time/residue: 0.5167 time to fit residues: 98.4045 Evaluate side-chains 175 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 203 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 132 HIS ** 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 = 0.3859 r_free = 0.3859 target = 0.166819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.111675 restraints weight = 34668.315| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.63 r_work: 0.2771 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10932 Z= 0.119 Angle : 0.424 6.558 14814 Z= 0.237 Chirality : 0.036 0.136 1674 Planarity : 0.003 0.036 1808 Dihedral : 3.673 18.762 1469 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.70 % Allowed : 18.16 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.09 (0.24), residues: 1336 helix: 3.67 (0.16), residues: 956 sheet: -0.49 (1.05), residues: 30 loop : 0.09 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 204 TYR 0.011 0.001 TYR G 181 PHE 0.014 0.001 PHE E 127 TRP 0.007 0.001 TRP F 178 HIS 0.003 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00238 (10924) covalent geometry : angle 0.42385 (14798) SS BOND : bond 0.00222 ( 8) SS BOND : angle 0.66311 ( 16) hydrogen bonds : bond 0.04476 ( 860) hydrogen bonds : angle 3.36485 ( 2498) *********************** 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 181 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.435 Fit side-chains REVERT: A 514 VAL cc_start: 0.7391 (m) cc_final: 0.7118 (p) REVERT: B 619 ASN cc_start: 0.7412 (m-40) cc_final: 0.7156 (m-40) REVERT: C 514 VAL cc_start: 0.7347 (m) cc_final: 0.7099 (p) REVERT: D 825 MET cc_start: 0.5411 (ppp) cc_final: 0.5123 (pp-130) REVERT: F 191 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8550 (mm-30) outliers start: 19 outliers final: 12 residues processed: 175 average time/residue: 0.5537 time to fit residues: 104.6403 Evaluate side-chains 168 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 14 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 203 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 95 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 132 HIS ** 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 = 0.3843 r_free = 0.3843 target = 0.165509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.110420 restraints weight = 35719.238| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.52 r_work: 0.2749 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10932 Z= 0.145 Angle : 0.454 5.628 14814 Z= 0.254 Chirality : 0.037 0.135 1674 Planarity : 0.003 0.036 1808 Dihedral : 3.791 18.300 1468 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.43 % Allowed : 18.07 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.96 (0.24), residues: 1336 helix: 3.58 (0.16), residues: 954 sheet: -0.57 (1.01), residues: 30 loop : 0.05 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 204 TYR 0.014 0.002 TYR G 181 PHE 0.015 0.002 PHE E 127 TRP 0.007 0.001 TRP D 606 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00309 (10924) covalent geometry : angle 0.45318 (14798) SS BOND : bond 0.00273 ( 8) SS BOND : angle 0.76090 ( 16) hydrogen bonds : bond 0.04930 ( 860) hydrogen bonds : angle 3.46219 ( 2498) *********************** 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 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.389 Fit side-chains REVERT: A 514 VAL cc_start: 0.7398 (m) cc_final: 0.7109 (p) REVERT: B 619 ASN cc_start: 0.7497 (m-40) cc_final: 0.7222 (m-40) REVERT: B 825 MET cc_start: 0.5384 (ppp) cc_final: 0.4984 (pp-130) REVERT: C 514 VAL cc_start: 0.7416 (m) cc_final: 0.7143 (p) REVERT: D 825 MET cc_start: 0.5289 (ppp) cc_final: 0.5037 (pp-130) outliers start: 16 outliers final: 14 residues processed: 170 average time/residue: 0.5379 time to fit residues: 98.9287 Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 514 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 203 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 128 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 132 HIS ** 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 = 0.3857 r_free = 0.3857 target = 0.166673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.113069 restraints weight = 34109.117| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.37 r_work: 0.2768 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10932 Z= 0.120 Angle : 0.421 5.338 14814 Z= 0.237 Chirality : 0.036 0.136 1674 Planarity : 0.003 0.036 1808 Dihedral : 3.652 17.618 1468 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.07 % Allowed : 18.43 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.08 (0.24), residues: 1336 helix: 3.67 (0.16), residues: 956 sheet: -0.58 (1.02), residues: 30 loop : 0.08 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 204 TYR 0.011 0.001 TYR G 181 PHE 0.015 0.001 PHE E 127 TRP 0.007 0.001 TRP F 178 HIS 0.003 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00241 (10924) covalent geometry : angle 0.42074 (14798) SS BOND : bond 0.00216 ( 8) SS BOND : angle 0.68081 ( 16) hydrogen bonds : bond 0.04500 ( 860) hydrogen bonds : angle 3.36668 ( 2498) *********************** 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 171 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.389 Fit side-chains REVERT: A 514 VAL cc_start: 0.7395 (m) cc_final: 0.7108 (p) REVERT: B 619 ASN cc_start: 0.7444 (m-40) cc_final: 0.7172 (m-40) REVERT: B 825 MET cc_start: 0.5476 (ppp) cc_final: 0.5118 (pp-130) REVERT: C 514 VAL cc_start: 0.7343 (m) cc_final: 0.7088 (p) REVERT: D 825 MET cc_start: 0.5256 (ppp) cc_final: 0.5018 (pp-130) REVERT: H 191 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8552 (mm-30) outliers start: 12 outliers final: 11 residues processed: 168 average time/residue: 0.5297 time to fit residues: 96.2089 Evaluate side-chains 166 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 514 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain H residue 203 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 0.8980 chunk 87 optimal weight: 0.0470 chunk 105 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 33 optimal weight: 0.0070 chunk 120 optimal weight: 0.0270 chunk 4 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS F 205 HIS H 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.169476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.127622 restraints weight = 30698.548| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 4.77 r_work: 0.2799 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 10932 Z= 0.096 Angle : 0.385 5.054 14814 Z= 0.216 Chirality : 0.035 0.135 1674 Planarity : 0.003 0.037 1808 Dihedral : 3.424 16.032 1468 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.98 % Allowed : 18.96 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.33 (0.23), residues: 1336 helix: 3.88 (0.16), residues: 956 sheet: 0.26 (1.41), residues: 20 loop : 0.02 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 204 TYR 0.009 0.001 TYR D 523 PHE 0.014 0.001 PHE E 127 TRP 0.009 0.001 TRP G 178 HIS 0.003 0.000 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00176 (10924) covalent geometry : angle 0.38482 (14798) SS BOND : bond 0.00138 ( 8) SS BOND : angle 0.56221 ( 16) hydrogen bonds : bond 0.03862 ( 860) hydrogen bonds : angle 3.22137 ( 2498) *********************** 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 180 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 514 VAL cc_start: 0.7308 (m) cc_final: 0.7082 (p) REVERT: B 619 ASN cc_start: 0.7374 (m-40) cc_final: 0.7124 (m-40) REVERT: B 825 MET cc_start: 0.5369 (ppp) cc_final: 0.4912 (pp-130) REVERT: D 619 ASN cc_start: 0.7323 (m-40) cc_final: 0.7065 (m-40) REVERT: F 191 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8574 (mm-30) REVERT: H 191 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8567 (mm-30) outliers start: 11 outliers final: 8 residues processed: 178 average time/residue: 0.5416 time to fit residues: 104.0509 Evaluate side-chains 171 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 77 CYS Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 209 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 129 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 78 optimal weight: 0.0670 chunk 97 optimal weight: 0.0010 chunk 80 optimal weight: 6.9990 chunk 101 optimal weight: 0.0980 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 0.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS H 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.169884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127946 restraints weight = 29941.761| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 4.75 r_work: 0.2813 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 10932 Z= 0.095 Angle : 0.384 5.030 14814 Z= 0.214 Chirality : 0.035 0.134 1674 Planarity : 0.003 0.041 1808 Dihedral : 3.369 15.684 1468 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.89 % Allowed : 18.96 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.38 (0.23), residues: 1336 helix: 3.92 (0.16), residues: 956 sheet: 0.24 (1.42), residues: 20 loop : 0.01 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 204 TYR 0.008 0.001 TYR E 89 PHE 0.015 0.001 PHE E 127 TRP 0.010 0.001 TRP G 178 HIS 0.001 0.000 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00173 (10924) covalent geometry : angle 0.38367 (14798) SS BOND : bond 0.00136 ( 8) SS BOND : angle 0.53402 ( 16) hydrogen bonds : bond 0.03829 ( 860) hydrogen bonds : angle 3.20201 ( 2498) ********************** 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 177 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 619 ASN cc_start: 0.7368 (m-40) cc_final: 0.7123 (m-40) REVERT: B 825 MET cc_start: 0.5347 (ppp) cc_final: 0.4942 (pp-130) REVERT: D 619 ASN cc_start: 0.7347 (m-40) cc_final: 0.7098 (m-40) REVERT: F 191 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8572 (mm-30) REVERT: H 191 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8547 (mm-30) outliers start: 10 outliers final: 6 residues processed: 175 average time/residue: 0.5288 time to fit residues: 100.3665 Evaluate side-chains 171 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 165 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 175 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.165912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.112159 restraints weight = 35258.023| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.33 r_work: 0.2736 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10932 Z= 0.143 Angle : 0.454 5.186 14814 Z= 0.254 Chirality : 0.037 0.136 1674 Planarity : 0.003 0.040 1808 Dihedral : 3.696 17.892 1468 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.07 % Allowed : 18.43 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.09 (0.24), residues: 1336 helix: 3.68 (0.16), residues: 955 sheet: -0.53 (1.02), residues: 30 loop : 0.07 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 204 TYR 0.014 0.002 TYR G 181 PHE 0.016 0.002 PHE E 127 TRP 0.007 0.001 TRP D 606 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00302 (10924) covalent geometry : angle 0.45362 (14798) SS BOND : bond 0.00271 ( 8) SS BOND : angle 0.77830 ( 16) hydrogen bonds : bond 0.04862 ( 860) hydrogen bonds : angle 3.42776 ( 2498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4707.47 seconds wall clock time: 80 minutes 39.09 seconds (4839.09 seconds total)