Starting phenix.real_space_refine on Thu Jul 2 23:00:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fp4_29359/07_2026/8fp4_29359.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fp4_29359/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fp4_29359/07_2026/8fp4_29359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fp4_29359/07_2026/8fp4_29359.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fp4_29359/07_2026/8fp4_29359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fp4_29359/07_2026/8fp4_29359.map" } 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-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 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: 3.35, per 1000 atoms: 0.31 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: 0.70 Conformation dependent library (CDL) restraints added in 683.6 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: 0.27 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: 1.59 Time building geometry restraints manager: 0.91 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: 0.02 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: 3.790 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.020 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: 0.000 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 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/Z covalent geometry : bond 0.00235 / 0.12 (10924) covalent geometry : angle 0.42220 / 0.24 (14798) SS BOND : bond 0.00221 / 0.12 ( 8) SS BOND : angle 0.53663 / 0.28 ( 16) hydrogen bonds : bond 0.09919 / 6.78 ( 860) hydrogen bonds : angle 3.95304 / 2.88 ( 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 : 0.328 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: 0.4785 time to fit residues: 90.3235 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 : 0.352 ------------------------------------------------------------------------------- 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: 2.9990 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... 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 = 0.165556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.109962 restraints weight = 32906.613| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.54 r_work: 0.2722 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 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 = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.0657 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 : 0.474 7.195 14814 Z= 0.267 Chirality : 0.038 0.131 1674 Planarity : 0.004 0.038 1808 Dihedral : 4.565 51.625 1482 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.29 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: 3.99 (0.24), residues: 1336 helix: 3.61 (0.16), residues: 954 sheet: 0.03 (1.07), residues: 28 loop : -0.02 (0.35), residues: 354 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/Z covalent geometry : bond 0.00338 / 0.16 (10924) covalent geometry : angle 0.47311 / 0.27 (14798) SS BOND : bond 0.00370 / 0.20 ( 8) SS BOND : angle 0.78935 / 0.40 ( 16) hydrogen bonds : bond 0.05198 / 3.37 ( 860) hydrogen bonds : angle 3.59474 / 2.59 ( 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 : 0.428 Fit side-chains REVERT: F 99 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6583 (tpp-160) REVERT: H 122 ILE cc_start: 0.7255 (OUTLIER) cc_final: 0.7013 (mm) REVERT: H 191 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8606 (mm-30) outliers start: 19 outliers final: 11 residues processed: 175 average time/residue: 0.4605 time to fit residues: 87.8401 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 : 0.282 ------------------------------------------------------------------------------- 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: 0.9990 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3862 r_free = 0.3862 target = 0.167110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123861 restraints weight = 28821.278| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 4.69 r_work: 0.2737 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 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 = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.0686 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= 0.119 Angle : 0.422 7.088 14814 Z= 0.237 Chirality : 0.036 0.132 1674 Planarity : 0.003 0.035 1808 Dihedral : 3.864 40.530 1476 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.97 % Allowed : 18.25 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.09 (0.24), residues: 1336 helix: 3.69 (0.16), residues: 956 sheet: -0.52 (1.05), residues: 30 loop : 0.03 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 204 TYR 0.010 0.001 TYR G 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/Z covalent geometry : bond 0.00239 / 0.12 (10924) covalent geometry : angle 0.42180 / 0.24 (14798) SS BOND : bond 0.00228 / 0.13 ( 8) SS BOND : angle 0.61689 / 0.31 ( 16) hydrogen bonds : bond 0.04497 / 2.90 ( 860) hydrogen bonds : angle 3.39940 / 2.45 ( 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 191 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 514 VAL cc_start: 0.7418 (m) cc_final: 0.7086 (p) REVERT: B 619 ASN cc_start: 0.7516 (m-40) cc_final: 0.7266 (m-40) REVERT: C 514 VAL cc_start: 0.7402 (m) cc_final: 0.7094 (p) REVERT: E 9 GLN cc_start: 0.6870 (OUTLIER) cc_final: 0.6622 (tt0) REVERT: G 9 GLN cc_start: 0.6908 (OUTLIER) cc_final: 0.6661 (tt0) REVERT: F 99 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6684 (tpp-160) REVERT: F 191 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8642 (mm-30) REVERT: H 122 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6989 (mm) outliers start: 22 outliers final: 9 residues processed: 182 average time/residue: 0.4349 time to fit residues: 85.8354 Evaluate side-chains 175 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 9 GLN Chi-restraints excluded: chain G residue 173 SER 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: 0.7980 chunk 68 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3849 r_free = 0.3849 target = 0.165978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.112639 restraints weight = 32005.568| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.28 r_work: 0.2756 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 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 = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10932 Z= 0.135 Angle : 0.447 7.960 14814 Z= 0.249 Chirality : 0.037 0.132 1674 Planarity : 0.003 0.036 1808 Dihedral : 3.800 30.756 1469 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.15 % Allowed : 18.16 % 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 are not related in a simple way. whole: 4.05 (0.24), residues: 1336 helix: 3.64 (0.16), residues: 954 sheet: -0.42 (1.09), residues: 30 loop : 0.07 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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/Z covalent geometry : bond 0.00281 / 0.13 (10924) covalent geometry : angle 0.44629 / 0.25 (14798) SS BOND : bond 0.00261 / 0.14 ( 8) SS BOND : angle 0.72075 / 0.38 ( 16) hydrogen bonds : bond 0.04799 / 3.10 ( 860) hydrogen bonds : angle 3.44973 / 2.48 ( 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 187 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.423 Fit side-chains REVERT: A 514 VAL cc_start: 0.7414 (m) cc_final: 0.7137 (p) REVERT: B 619 ASN cc_start: 0.7492 (m-40) cc_final: 0.7244 (m-40) REVERT: C 514 VAL cc_start: 0.7378 (m) cc_final: 0.7128 (p) REVERT: D 825 MET cc_start: 0.5365 (ppp) cc_final: 0.4985 (pp-130) REVERT: E 9 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6523 (tt0) REVERT: G 9 GLN cc_start: 0.6781 (OUTLIER) cc_final: 0.6529 (tt0) REVERT: F 99 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6556 (tpp-160) outliers start: 24 outliers final: 14 residues processed: 181 average time/residue: 0.4916 time to fit residues: 96.6680 Evaluate side-chains 174 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 E residue 175 SER Chi-restraints excluded: chain G residue 9 GLN 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=3.50 ------------------------------------------------------------------------------- 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: 2.9990 chunk 69 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3840 r_free = 0.3840 target = 0.165280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.111482 restraints weight = 33576.024| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.33 r_work: 0.2742 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- 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 = 0.36 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 = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.0840 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= 0.150 Angle : 0.466 7.480 14814 Z= 0.260 Chirality : 0.037 0.134 1674 Planarity : 0.003 0.036 1808 Dihedral : 3.881 25.127 1469 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.97 % Allowed : 17.71 % Favored : 80.32 % 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: 3.94 (0.24), residues: 1336 helix: 3.55 (0.16), residues: 954 sheet: -0.35 (1.06), residues: 30 loop : 0.05 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 204 TYR 0.015 0.002 TYR G 181 PHE 0.014 0.002 PHE E 127 TRP 0.008 0.001 TRP D 606 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (10924) covalent geometry : angle 0.46603 / 0.26 (14798) SS BOND : bond 0.00286 / 0.16 ( 8) SS BOND : angle 0.75445 / 0.38 ( 16) hydrogen bonds : bond 0.05017 / 3.24 ( 860) hydrogen bonds : angle 3.49546 / 2.51 ( 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 : 0.277 Fit side-chains REVERT: A 514 VAL cc_start: 0.7391 (m) cc_final: 0.7103 (p) REVERT: B 619 ASN cc_start: 0.7501 (m-40) cc_final: 0.7242 (m-40) REVERT: C 514 VAL cc_start: 0.7406 (m) cc_final: 0.7128 (p) REVERT: D 825 MET cc_start: 0.5441 (ppp) cc_final: 0.5118 (pp-130) REVERT: E 9 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.6546 (tt0) REVERT: G 9 GLN cc_start: 0.6820 (OUTLIER) cc_final: 0.6576 (tt0) REVERT: F 99 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6555 (tpp-160) outliers start: 22 outliers final: 16 residues processed: 177 average time/residue: 0.4278 time to fit residues: 82.3204 Evaluate side-chains 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 E residue 175 SER Chi-restraints excluded: chain G residue 9 GLN 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: 3.9990 chunk 84 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3862 r_free = 0.3862 target = 0.167120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.113353 restraints weight = 34717.284| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.40 r_work: 0.2780 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10932 Z= 0.113 Angle : 0.417 7.265 14814 Z= 0.233 Chirality : 0.036 0.136 1674 Planarity : 0.003 0.036 1808 Dihedral : 3.640 18.383 1469 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.70 % Allowed : 17.89 % Favored : 80.41 % 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: 4.14 (0.24), residues: 1336 helix: 3.71 (0.16), residues: 956 sheet: -0.43 (1.05), residues: 30 loop : 0.09 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 204 TYR 0.010 0.001 TYR G 181 PHE 0.015 0.001 PHE E 127 TRP 0.007 0.001 TRP H 178 HIS 0.003 0.001 HIS H 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (10924) covalent geometry : angle 0.41649 / 0.23 (14798) SS BOND : bond 0.00191 / 0.10 ( 8) SS BOND : angle 0.63926 / 0.33 ( 16) hydrogen bonds : bond 0.04368 / 2.82 ( 860) hydrogen bonds : angle 3.34500 / 2.41 ( 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 182 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.468 Fit side-chains REVERT: A 514 VAL cc_start: 0.7373 (m) cc_final: 0.7094 (p) REVERT: B 515 PHE cc_start: 0.8660 (m-80) cc_final: 0.8430 (m-80) REVERT: B 619 ASN cc_start: 0.7453 (m-40) cc_final: 0.7192 (m-40) REVERT: C 514 VAL cc_start: 0.7360 (m) cc_final: 0.7105 (p) REVERT: D 825 MET cc_start: 0.5406 (ppp) cc_final: 0.5123 (pp-130) REVERT: F 191 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8552 (mm-30) REVERT: H 191 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8558 (mm-30) outliers start: 19 outliers final: 12 residues processed: 177 average time/residue: 0.5039 time to fit residues: 96.8878 Evaluate side-chains 169 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 175 SER 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 209 ARG Chi-restraints excluded: chain F residue 31 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: 3.9990 chunk 130 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 chunk 78 optimal weight: 0.3980 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: 1.9990 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN 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 = 0.3842 r_free = 0.3842 target = 0.165370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110719 restraints weight = 35418.604| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.44 r_work: 0.2753 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.0903 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= 0.148 Angle : 0.458 5.628 14814 Z= 0.257 Chirality : 0.037 0.135 1674 Planarity : 0.003 0.036 1808 Dihedral : 3.806 18.387 1468 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.61 % Allowed : 18.16 % Favored : 80.23 % 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: 3.59 (0.16), residues: 954 sheet: -0.50 (1.01), residues: 30 loop : 0.04 (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 B 606 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (10924) covalent geometry : angle 0.45786 / 0.26 (14798) SS BOND : bond 0.00275 / 0.15 ( 8) SS BOND : angle 0.77277 / 0.40 ( 16) hydrogen bonds : bond 0.04976 / 3.21 ( 860) hydrogen bonds : angle 3.47165 / 2.49 ( 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 180 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.430 Fit side-chains REVERT: A 514 VAL cc_start: 0.7418 (m) cc_final: 0.7129 (p) REVERT: B 619 ASN cc_start: 0.7525 (m-40) cc_final: 0.7251 (m-40) REVERT: B 825 MET cc_start: 0.5345 (ppp) cc_final: 0.4975 (pp-130) REVERT: C 514 VAL cc_start: 0.7422 (m) cc_final: 0.7148 (p) REVERT: D 825 MET cc_start: 0.5340 (ppp) cc_final: 0.5079 (pp-130) outliers start: 18 outliers final: 14 residues processed: 173 average time/residue: 0.4951 time to fit residues: 93.1412 Evaluate side-chains 172 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 E residue 175 SER 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 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: 0.9990 chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 127 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3861 r_free = 0.3861 target = 0.167026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113662 restraints weight = 34113.799| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.35 r_work: 0.2756 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 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 = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10932 Z= 0.115 Angle : 0.417 5.321 14814 Z= 0.234 Chirality : 0.036 0.136 1674 Planarity : 0.003 0.036 1808 Dihedral : 3.624 17.442 1468 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.34 % Allowed : 18.34 % Favored : 80.32 % 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: 3.70 (0.16), residues: 956 sheet: -0.51 (1.03), residues: 30 loop : 0.07 (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 H 178 HIS 0.003 0.001 HIS H 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 (10924) covalent geometry : angle 0.41634 / 0.23 (14798) SS BOND : bond 0.00205 / 0.11 ( 8) SS BOND : angle 0.65450 / 0.33 ( 16) hydrogen bonds : bond 0.04417 / 2.85 ( 860) hydrogen bonds : angle 3.35199 / 2.41 ( 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 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.333 Fit side-chains REVERT: A 514 VAL cc_start: 0.7369 (m) cc_final: 0.7104 (p) REVERT: B 619 ASN cc_start: 0.7435 (m-40) cc_final: 0.7163 (m-40) REVERT: B 825 MET cc_start: 0.5477 (ppp) cc_final: 0.5106 (pp-130) REVERT: C 514 VAL cc_start: 0.7367 (m) cc_final: 0.7118 (p) REVERT: D 825 MET cc_start: 0.5232 (ppp) cc_final: 0.4899 (pp-130) outliers start: 15 outliers final: 15 residues processed: 173 average time/residue: 0.4705 time to fit residues: 88.6379 Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 E residue 175 SER Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 89 TYR 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 H residue 31 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: 0.9980 chunk 87 optimal weight: 0.0170 chunk 105 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 65 optimal weight: 0.0670 chunk 68 optimal weight: 0.9990 chunk 33 optimal weight: 0.0040 chunk 120 optimal weight: 0.0870 chunk 4 optimal weight: 7.9990 chunk 35 optimal weight: 0.0870 overall best weight: 0.0524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3943 r_free = 0.3943 target = 0.174396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.133329 restraints weight = 32791.171| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 4.98 r_work: 0.2902 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1470 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= 0.088 Angle : 0.373 4.793 14814 Z= 0.208 Chirality : 0.034 0.133 1674 Planarity : 0.003 0.036 1808 Dihedral : 3.266 14.499 1468 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.72 % Allowed : 19.05 % Favored : 80.23 % 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: 4.47 (0.23), residues: 1336 helix: 3.99 (0.16), residues: 958 sheet: 0.31 (1.43), residues: 20 loop : 0.00 (0.34), residues: 358 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 0.013 0.001 PHE E 127 TRP 0.012 0.001 TRP G 178 HIS 0.002 0.000 HIS H 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00160 / 0.09 (10924) covalent geometry : angle 0.37285 / 0.21 (14798) SS BOND : bond 0.00162 / 0.08 ( 8) SS BOND : angle 0.52607 / 0.29 ( 16) hydrogen bonds : bond 0.03367 / 2.17 ( 860) hydrogen bonds : angle 3.11567 / 2.27 ( 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 186 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 178 time to evaluate : 0.424 Fit side-chains REVERT: A 594 ARG cc_start: 0.8782 (mtt-85) cc_final: 0.8532 (mmt180) REVERT: B 515 PHE cc_start: 0.8684 (m-80) cc_final: 0.8395 (m-80) REVERT: B 825 MET cc_start: 0.5516 (ppp) cc_final: 0.5184 (pp-130) REVERT: D 619 ASN cc_start: 0.7214 (m-40) cc_final: 0.6976 (m-40) outliers start: 8 outliers final: 3 residues processed: 186 average time/residue: 0.4963 time to fit residues: 99.9808 Evaluate side-chains 168 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 165 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 129 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 101 optimal weight: 0.0570 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.169972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.127785 restraints weight = 29328.598| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 4.73 r_work: 0.2809 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1354 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= 0.101 Angle : 0.402 7.353 14814 Z= 0.222 Chirality : 0.035 0.136 1674 Planarity : 0.003 0.042 1808 Dihedral : 3.352 15.853 1468 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.54 % Allowed : 19.32 % 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: 4.43 (0.23), residues: 1336 helix: 3.97 (0.16), residues: 956 sheet: -0.55 (1.05), residues: 30 loop : 0.08 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 204 TYR 0.011 0.001 TYR D 523 PHE 0.015 0.001 PHE E 127 TRP 0.007 0.001 TRP G 178 HIS 0.002 0.000 HIS G 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.10 (10924) covalent geometry : angle 0.40136 / 0.22 (14798) SS BOND : bond 0.00147 / 0.08 ( 8) SS BOND : angle 0.59699 / 0.31 ( 16) hydrogen bonds : bond 0.03921 / 2.52 ( 860) hydrogen bonds : angle 3.20534 / 2.31 ( 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 175 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 169 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 515 PHE cc_start: 0.8693 (m-80) cc_final: 0.8395 (m-80) REVERT: B 825 MET cc_start: 0.5323 (ppp) cc_final: 0.4963 (pp-130) REVERT: D 619 ASN cc_start: 0.7277 (m-40) cc_final: 0.7038 (m-40) REVERT: D 825 MET cc_start: 0.5219 (mmp) cc_final: 0.4676 (pp-130) outliers start: 6 outliers final: 5 residues processed: 173 average time/residue: 0.4713 time to fit residues: 88.8037 Evaluate side-chains 173 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 168 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain H residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3856 r_free = 0.3856 target = 0.166555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.111743 restraints weight = 35499.519| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.52 r_work: 0.2745 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1073 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= 0.129 Angle : 0.445 7.565 14814 Z= 0.247 Chirality : 0.036 0.135 1674 Planarity : 0.003 0.039 1808 Dihedral : 3.599 17.448 1468 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.72 % Allowed : 19.32 % Favored : 79.96 % 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: 4.19 (0.23), residues: 1336 helix: 3.77 (0.16), residues: 955 sheet: -0.57 (1.03), 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 0.013 0.001 TYR E 35 PHE 0.015 0.002 PHE E 127 TRP 0.006 0.001 TRP D 606 HIS 0.003 0.001 HIS E 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (10924) covalent geometry : angle 0.44503 / 0.25 (14798) SS BOND : bond 0.00224 / 0.12 ( 8) SS BOND : angle 0.73011 / 0.38 ( 16) hydrogen bonds : bond 0.04629 / 2.98 ( 860) hydrogen bonds : angle 3.37928 / 2.42 ( 2498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4305.95 seconds wall clock time: 73 minutes 55.94 seconds (4435.94 seconds total)