Starting phenix.real_space_refine on Fri Jan 17 04:40:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b63_44244/01_2025/9b63_44244.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b63_44244/01_2025/9b63_44244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b63_44244/01_2025/9b63_44244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b63_44244/01_2025/9b63_44244.map" model { file = "/net/cci-nas-00/data/ceres_data/9b63_44244/01_2025/9b63_44244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b63_44244/01_2025/9b63_44244.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6909 2.51 5 N 1655 2.21 5 O 1825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10461 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1146 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1154 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 149, 1154 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 1172 Chain: "A" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1141 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 1161 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1150 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 149, 1150 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 1168 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N APHE B 623 " occ=0.44 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.56 residue: pdb=" N APHE D 623 " occ=0.40 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.60 Time building chain proxies: 7.96, per 1000 atoms: 0.76 Number of scatterers: 10461 At special positions: 0 Unit cell: (109.88, 111.52, 97.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1825 8.00 N 1655 7.00 C 6909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 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 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 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 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: 2.95 Conformation dependent library (CDL) restraints added in 1.7 seconds 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 4 sheets defined 74.2% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'H' and resid 5 through 30 Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.724A pdb=" N TYR H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 124 Processing helix chain 'H' and resid 125 through 127 No H-bonds generated for 'chain 'H' and resid 125 through 127' Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.789A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 214 removed outlier: 3.536A pdb=" N PHE H 201 " --> pdb=" O ALA H 197 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.644A pdb=" N TYR F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER F 105 " --> pdb=" O VAL F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 126 removed outlier: 4.051A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.675A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 214 removed outlier: 3.515A pdb=" N ALA F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.675A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 629 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 825 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.915A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) 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 626 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 825 removed outlier: 3.594A pdb=" N MET B 825 " --> pdb=" O GLU B 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.784A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 removed outlier: 3.594A pdb=" N TRP A 551 " --> pdb=" O PRO A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 629 Processing helix chain 'A' and resid 788 through 825 removed outlier: 3.946A pdb=" N VAL A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLY A 794 " --> pdb=" O SER A 790 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.583A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) 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 626 Processing helix chain 'D' and resid 788 through 825 removed outlier: 3.697A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 125 Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.715A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.509A pdb=" N ILE E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG E 213 " --> pdb=" O ARG E 209 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 125 Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.926A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 removed outlier: 3.826A pdb=" N ALA G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 77 through 79 removed outlier: 3.828A pdb=" N VAL H 57 " --> pdb=" O GLY H 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AA3, first strand: chain 'E' and resid 78 through 79 removed outlier: 3.709A pdb=" N HIS E 60 " --> pdb=" O CYS E 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 79 842 hydrogen bonds defined for protein. 2456 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: 3.22 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3151 1.35 - 1.46: 3016 1.46 - 1.58: 4444 1.58 - 1.70: 0 1.70 - 1.82: 112 Bond restraints: 10723 Sorted by residual: bond pdb=" CG PRO B 512 " pdb=" CD PRO B 512 " ideal model delta sigma weight residual 1.503 1.377 0.126 3.40e-02 8.65e+02 1.38e+01 bond pdb=" CG1 ILE H 150 " pdb=" CD1 ILE H 150 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.46e-01 bond pdb=" CA PHE G 73 " pdb=" CB PHE G 73 " ideal model delta sigma weight residual 1.531 1.555 -0.024 3.28e-02 9.30e+02 5.30e-01 bond pdb=" N LYS F 41 " pdb=" CA LYS F 41 " ideal model delta sigma weight residual 1.460 1.470 -0.010 1.42e-02 4.96e+03 5.18e-01 bond pdb=" CA GLU F 70 " pdb=" CB GLU F 70 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.69e-02 3.50e+03 5.04e-01 ... (remaining 10718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 14463 2.56 - 5.13: 54 5.13 - 7.69: 5 7.69 - 10.25: 2 10.25 - 12.81: 3 Bond angle restraints: 14527 Sorted by residual: angle pdb=" N PRO B 512 " pdb=" CD PRO B 512 " pdb=" CG PRO B 512 " ideal model delta sigma weight residual 103.20 90.39 12.81 1.50e+00 4.44e-01 7.30e+01 angle pdb=" CA PRO B 512 " pdb=" CB PRO B 512 " pdb=" CG PRO B 512 " ideal model delta sigma weight residual 104.50 92.66 11.84 1.90e+00 2.77e-01 3.88e+01 angle pdb=" CA PRO B 512 " pdb=" N PRO B 512 " pdb=" CD PRO B 512 " ideal model delta sigma weight residual 112.00 103.66 8.34 1.40e+00 5.10e-01 3.55e+01 angle pdb=" CB PRO B 512 " pdb=" CG PRO B 512 " pdb=" CD PRO B 512 " ideal model delta sigma weight residual 106.10 94.16 11.94 3.20e+00 9.77e-02 1.39e+01 angle pdb=" N PRO B 512 " pdb=" CA PRO B 512 " pdb=" CB PRO B 512 " ideal model delta sigma weight residual 103.31 100.40 2.91 8.90e-01 1.26e+00 1.07e+01 ... (remaining 14522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 5192 17.61 - 35.23: 658 35.23 - 52.84: 190 52.84 - 70.46: 37 70.46 - 88.07: 10 Dihedral angle restraints: 6087 sinusoidal: 2223 harmonic: 3864 Sorted by residual: dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual 93.00 175.72 -82.72 1 1.00e+01 1.00e-02 8.38e+01 dihedral pdb=" CB CYS G 67 " pdb=" SG CYS G 67 " pdb=" SG CYS G 77 " pdb=" CB CYS G 77 " ideal model delta sinusoidal sigma weight residual -86.00 -123.66 37.66 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" N PRO B 512 " pdb=" CG PRO B 512 " pdb=" CD PRO B 512 " pdb=" CB PRO B 512 " ideal model delta sinusoidal sigma weight residual -30.00 -72.35 42.35 1 1.50e+01 4.44e-03 1.11e+01 ... (remaining 6084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1046 0.025 - 0.051: 363 0.051 - 0.076: 170 0.076 - 0.101: 54 0.101 - 0.127: 13 Chirality restraints: 1646 Sorted by residual: chirality pdb=" CA PHE E 107 " pdb=" N PHE E 107 " pdb=" C PHE E 107 " pdb=" CB PHE E 107 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA LYS H 41 " pdb=" N LYS H 41 " pdb=" C LYS H 41 " pdb=" CB LYS H 41 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.27e-01 chirality pdb=" CA PHE G 107 " pdb=" N PHE G 107 " pdb=" C PHE G 107 " pdb=" CB PHE G 107 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.14e-01 ... (remaining 1643 not shown) Planarity restraints: 1772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 511 " 0.022 5.00e-02 4.00e+02 3.07e-02 1.50e+00 pdb=" N PRO B 512 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 512 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 512 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 107 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO G 108 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO G 108 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 108 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 60 " -0.007 2.00e-02 2.50e+03 8.59e-03 1.11e+00 pdb=" CG HIS H 60 " 0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS H 60 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS H 60 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS H 60 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS H 60 " -0.002 2.00e-02 2.50e+03 ... (remaining 1769 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2063 2.77 - 3.30: 10166 3.30 - 3.84: 18583 3.84 - 4.37: 19973 4.37 - 4.90: 35422 Nonbonded interactions: 86207 Sorted by model distance: nonbonded pdb=" OG1 THR H 30 " pdb=" OG SER H 179 " model vdw 2.238 3.040 nonbonded pdb=" O GLU B 550 " pdb=" OG1 THR B 568 " model vdw 2.281 3.040 nonbonded pdb=" O PRO A 520 " pdb=" ND2 ASN A 619 " model vdw 2.292 3.120 nonbonded pdb=" O GLU D 550 " pdb=" OG1 THR D 568 " model vdw 2.302 3.040 nonbonded pdb=" NH2 ARG C 545 " pdb=" O ASN C 569 " model vdw 2.310 3.120 ... (remaining 86202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 511 through 575 or (resid 576 and (name N or name CA or na \ me C or name O or name CB )) or resid 577 through 622 or resid 624 through 626 o \ r (resid 627 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 28 through 629 or resid 784 through 812 or (resid 813 and (name N or name CA or \ name C or name O or name CB )) or resid 814 through 818 or (resid 819 through 82 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 821 through \ 825)) selection = (chain 'B' and ((resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 575 or (resid 576 and (name N or name CA or name C or n \ ame O or name CB )) or resid 577 through 593 or (resid 594 and (name N or name C \ A or name C or name O or name CB )) or resid 595 through 622 or resid 624 throug \ h 626 or (resid 627 and (name N or name CA or name C or name O or name CB )) or \ resid 628 through 629 or (resid 784 and (name N or name CA or name C or name O o \ r name CB )) or resid 785 through 825)) selection = (chain 'C' and (resid 511 through 593 or (resid 594 and (name N or name CA or na \ me C or name O or name CB )) or resid 595 through 622 or resid 624 through 626 o \ r (resid 627 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 28 through 629 or resid 784 through 812 or (resid 813 and (name N or name CA or \ name C or name O or name CB )) or resid 814 through 818 or (resid 819 through 82 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 821 through \ 825)) selection = (chain 'D' and ((resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 575 or (resid 576 and (name N or name CA or name C or n \ ame O or name CB )) or resid 577 through 593 or (resid 594 and (name N or name C \ A or name C or name O or name CB )) or resid 595 through 622 or resid 624 throug \ h 629 or (resid 784 and (name N or name CA or name C or name O or name CB )) or \ resid 785 through 825)) } ncs_group { reference = (chain 'E' and resid 5 through 214) selection = (chain 'F' and (resid 5 through 41 or resid 55 through 214)) selection = (chain 'G' and resid 5 through 214) selection = (chain 'H' and (resid 5 through 41 or resid 55 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=0.40 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.820 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 0.126 10723 Z= 0.155 Angle : 0.474 12.813 14527 Z= 0.256 Chirality : 0.034 0.127 1646 Planarity : 0.003 0.031 1772 Dihedral : 17.288 88.074 3587 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.22 % Allowed : 25.12 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.23), residues: 1306 helix: 3.34 (0.16), residues: 948 sheet: -1.66 (1.87), residues: 10 loop : -0.90 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 578 HIS 0.011 0.001 HIS H 60 PHE 0.015 0.001 PHE G 97 TYR 0.010 0.001 TYR E 156 ARG 0.007 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7153 (tt) cc_final: 0.6741 (tm) outliers start: 24 outliers final: 25 residues processed: 156 average time/residue: 1.0403 time to fit residues: 177.1829 Evaluate side-chains 154 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 173 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 192 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.246196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.185800 restraints weight = 26111.254| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 3.73 r_work: 0.3647 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10723 Z= 0.156 Angle : 0.449 7.465 14527 Z= 0.247 Chirality : 0.035 0.124 1646 Planarity : 0.003 0.033 1772 Dihedral : 5.645 58.623 1478 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.88 % Allowed : 22.25 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.23), residues: 1306 helix: 3.63 (0.15), residues: 952 sheet: -0.67 (1.77), residues: 10 loop : -0.94 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 578 HIS 0.008 0.001 HIS H 60 PHE 0.016 0.001 PHE D 584 TYR 0.010 0.001 TYR G 181 ARG 0.005 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 TYR cc_start: 0.7717 (m-10) cc_final: 0.7476 (m-10) REVERT: H 110 LEU cc_start: 0.7137 (tt) cc_final: 0.6670 (tm) REVERT: F 65 ARG cc_start: 0.6158 (OUTLIER) cc_final: 0.5492 (ppt-90) REVERT: C 594 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7586 (mtt-85) REVERT: E 21 PHE cc_start: 0.7054 (t80) cc_final: 0.6520 (t80) REVERT: E 185 LEU cc_start: 0.7020 (mt) cc_final: 0.6459 (mp) REVERT: G 55 GLU cc_start: 0.3211 (OUTLIER) cc_final: 0.2903 (tm-30) outliers start: 42 outliers final: 25 residues processed: 165 average time/residue: 1.0045 time to fit residues: 181.6102 Evaluate side-chains 161 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 594 ARG Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 84 optimal weight: 0.0670 chunk 112 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 57 optimal weight: 0.0270 chunk 99 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.247685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.184587 restraints weight = 22288.689| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 3.28 r_work: 0.3712 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10723 Z= 0.131 Angle : 0.429 7.502 14527 Z= 0.232 Chirality : 0.035 0.149 1646 Planarity : 0.003 0.032 1772 Dihedral : 4.396 56.154 1449 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.23 % Allowed : 23.18 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.02 (0.23), residues: 1306 helix: 3.83 (0.15), residues: 952 sheet: -0.15 (1.69), residues: 10 loop : -0.93 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 578 HIS 0.019 0.001 HIS E 60 PHE 0.012 0.001 PHE D 584 TYR 0.012 0.001 TYR B 523 ARG 0.005 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.6881 (tt) cc_final: 0.6424 (tm) REVERT: H 200 MET cc_start: 0.7130 (mmm) cc_final: 0.6572 (mtt) REVERT: F 65 ARG cc_start: 0.6219 (OUTLIER) cc_final: 0.5620 (ppt-90) REVERT: C 594 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7334 (mtt-85) REVERT: B 511 LYS cc_start: 0.6134 (tmtm) cc_final: 0.5868 (mttt) REVERT: B 570 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6871 (mt-10) REVERT: G 55 GLU cc_start: 0.3144 (OUTLIER) cc_final: 0.2826 (tm-30) outliers start: 35 outliers final: 18 residues processed: 157 average time/residue: 1.0504 time to fit residues: 180.3930 Evaluate side-chains 155 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 594 ARG Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 70 optimal weight: 0.9990 chunk 103 optimal weight: 0.3980 chunk 29 optimal weight: 0.0670 chunk 75 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 chunk 43 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.247740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.189150 restraints weight = 25089.122| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 3.84 r_work: 0.3638 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10723 Z= 0.126 Angle : 0.408 4.932 14527 Z= 0.227 Chirality : 0.034 0.142 1646 Planarity : 0.003 0.032 1772 Dihedral : 3.775 55.375 1441 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.97 % Allowed : 22.44 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.12 (0.23), residues: 1306 helix: 3.92 (0.15), residues: 948 sheet: 0.17 (1.71), residues: 10 loop : -0.92 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 578 HIS 0.004 0.001 HIS G 205 PHE 0.012 0.001 PHE D 584 TYR 0.013 0.001 TYR B 523 ARG 0.004 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.6818 (tt) cc_final: 0.6367 (tm) REVERT: H 200 MET cc_start: 0.7136 (mmm) cc_final: 0.6725 (mtt) REVERT: F 65 ARG cc_start: 0.6132 (OUTLIER) cc_final: 0.5541 (ppt-90) REVERT: F 135 ILE cc_start: 0.7553 (mm) cc_final: 0.7256 (tt) REVERT: C 594 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7471 (mtt-85) REVERT: B 511 LYS cc_start: 0.6093 (tmtm) cc_final: 0.5872 (mttt) REVERT: B 527 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7529 (ptm) REVERT: B 570 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6917 (mt-10) REVERT: E 113 ILE cc_start: 0.6530 (mt) cc_final: 0.6311 (mm) REVERT: G 55 GLU cc_start: 0.3097 (OUTLIER) cc_final: 0.2762 (tm-30) outliers start: 43 outliers final: 27 residues processed: 165 average time/residue: 0.9882 time to fit residues: 178.8440 Evaluate side-chains 162 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 594 ARG Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 107 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.243326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.184559 restraints weight = 24994.959| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 3.78 r_work: 0.3587 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10723 Z= 0.232 Angle : 0.487 7.562 14527 Z= 0.266 Chirality : 0.037 0.150 1646 Planarity : 0.003 0.043 1772 Dihedral : 4.027 55.631 1441 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.06 % Allowed : 22.53 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.23), residues: 1306 helix: 3.49 (0.16), residues: 948 sheet: 0.16 (0.89), residues: 40 loop : -0.98 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 578 HIS 0.004 0.001 HIS G 60 PHE 0.019 0.002 PHE C 584 TYR 0.011 0.001 TYR B 523 ARG 0.004 0.000 ARG C 545 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7165 (tt) cc_final: 0.6735 (tm) REVERT: H 200 MET cc_start: 0.7308 (mmm) cc_final: 0.7015 (mtm) REVERT: B 570 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: G 55 GLU cc_start: 0.3112 (OUTLIER) cc_final: 0.2770 (tm-30) outliers start: 44 outliers final: 26 residues processed: 163 average time/residue: 0.9813 time to fit residues: 175.6962 Evaluate side-chains 159 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 13 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 60 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 = 0.4608 r_free = 0.4608 target = 0.245554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.185881 restraints weight = 27875.192| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 3.97 r_work: 0.3613 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10723 Z= 0.155 Angle : 0.439 7.236 14527 Z= 0.241 Chirality : 0.035 0.137 1646 Planarity : 0.003 0.034 1772 Dihedral : 3.911 56.106 1441 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.79 % Allowed : 23.18 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.23), residues: 1306 helix: 3.65 (0.16), residues: 948 sheet: 0.87 (1.74), residues: 10 loop : -0.95 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 578 HIS 0.003 0.001 HIS E 60 PHE 0.012 0.001 PHE D 584 TYR 0.014 0.001 TYR B 523 ARG 0.003 0.000 ARG C 545 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7045 (tt) cc_final: 0.6622 (tm) REVERT: H 122 ILE cc_start: 0.6879 (mm) cc_final: 0.6313 (mm) REVERT: H 200 MET cc_start: 0.7253 (mmm) cc_final: 0.6949 (mtm) REVERT: F 10 MET cc_start: 0.6806 (tpp) cc_final: 0.6314 (tpp) REVERT: F 65 ARG cc_start: 0.6139 (OUTLIER) cc_final: 0.5579 (ppt-90) REVERT: F 135 ILE cc_start: 0.7662 (mm) cc_final: 0.7379 (tt) REVERT: B 570 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6999 (mt-10) REVERT: G 55 GLU cc_start: 0.3126 (OUTLIER) cc_final: 0.2737 (tm-30) outliers start: 41 outliers final: 29 residues processed: 162 average time/residue: 0.9790 time to fit residues: 174.1872 Evaluate side-chains 162 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 95 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 50 optimal weight: 0.0670 chunk 19 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 60 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 = 0.4607 r_free = 0.4607 target = 0.245466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.182216 restraints weight = 24472.678| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 3.38 r_work: 0.3668 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10723 Z= 0.155 Angle : 0.434 5.603 14527 Z= 0.239 Chirality : 0.035 0.135 1646 Planarity : 0.003 0.034 1772 Dihedral : 3.874 56.049 1441 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.60 % Allowed : 23.27 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.23), residues: 1306 helix: 3.68 (0.16), residues: 948 sheet: 1.05 (1.87), residues: 10 loop : -0.94 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 578 HIS 0.003 0.001 HIS E 60 PHE 0.013 0.001 PHE D 584 TYR 0.014 0.001 TYR B 523 ARG 0.003 0.000 ARG C 545 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7064 (tt) cc_final: 0.6624 (tm) REVERT: H 122 ILE cc_start: 0.6900 (mm) cc_final: 0.6345 (mm) REVERT: H 200 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.7083 (mtm) REVERT: F 65 ARG cc_start: 0.6189 (OUTLIER) cc_final: 0.5649 (ppt-90) REVERT: F 135 ILE cc_start: 0.7681 (mm) cc_final: 0.7407 (tt) REVERT: B 570 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6936 (mt-10) REVERT: G 55 GLU cc_start: 0.2981 (OUTLIER) cc_final: 0.2612 (tm-30) outliers start: 39 outliers final: 29 residues processed: 158 average time/residue: 0.9520 time to fit residues: 165.6281 Evaluate side-chains 163 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 107 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 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 = 0.4603 r_free = 0.4603 target = 0.245116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.184374 restraints weight = 17523.704| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.51 r_work: 0.3707 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10723 Z= 0.163 Angle : 0.453 8.226 14527 Z= 0.244 Chirality : 0.035 0.133 1646 Planarity : 0.003 0.034 1772 Dihedral : 3.884 56.006 1441 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.79 % Allowed : 23.45 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.23), residues: 1306 helix: 3.64 (0.16), residues: 948 sheet: 1.23 (1.94), residues: 10 loop : -0.95 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 578 HIS 0.004 0.001 HIS E 60 PHE 0.013 0.001 PHE D 584 TYR 0.014 0.001 TYR B 523 ARG 0.003 0.000 ARG C 545 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7035 (tt) cc_final: 0.6610 (tm) REVERT: H 122 ILE cc_start: 0.6978 (mm) cc_final: 0.6405 (mm) REVERT: H 200 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7145 (mtm) REVERT: F 65 ARG cc_start: 0.6227 (OUTLIER) cc_final: 0.5692 (ppt-90) REVERT: F 135 ILE cc_start: 0.7722 (mm) cc_final: 0.7448 (tt) REVERT: B 570 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6671 (mt-10) REVERT: D 629 MET cc_start: 0.6206 (tpt) cc_final: 0.5729 (mmt) REVERT: E 58 MET cc_start: 0.6187 (tpp) cc_final: 0.5921 (mpt) REVERT: G 55 GLU cc_start: 0.2974 (OUTLIER) cc_final: 0.2588 (tm-30) outliers start: 41 outliers final: 30 residues processed: 157 average time/residue: 0.9647 time to fit residues: 166.7683 Evaluate side-chains 160 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 99 optimal weight: 0.0980 chunk 115 optimal weight: 10.0000 chunk 98 optimal weight: 0.3980 chunk 101 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 96 optimal weight: 0.0470 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.248045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.188902 restraints weight = 26204.825| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 3.74 r_work: 0.3662 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10723 Z= 0.125 Angle : 0.423 8.009 14527 Z= 0.229 Chirality : 0.034 0.128 1646 Planarity : 0.003 0.035 1772 Dihedral : 3.767 55.761 1441 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.14 % Allowed : 23.92 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.07 (0.23), residues: 1306 helix: 3.88 (0.15), residues: 950 sheet: 1.04 (1.82), residues: 10 loop : -0.99 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 178 HIS 0.002 0.001 HIS E 60 PHE 0.011 0.001 PHE D 584 TYR 0.015 0.001 TYR B 523 ARG 0.002 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.6822 (tt) cc_final: 0.6383 (tm) REVERT: H 122 ILE cc_start: 0.6869 (mm) cc_final: 0.6322 (mm) REVERT: H 200 MET cc_start: 0.7206 (mmm) cc_final: 0.6986 (mtm) REVERT: F 65 ARG cc_start: 0.6115 (OUTLIER) cc_final: 0.5736 (ppt-90) REVERT: B 527 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7495 (ptm) REVERT: B 570 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6940 (mt-10) REVERT: D 629 MET cc_start: 0.6257 (tpt) cc_final: 0.5756 (mmt) REVERT: E 117 MET cc_start: 0.3884 (tpt) cc_final: 0.3587 (tpt) REVERT: E 208 LEU cc_start: 0.3893 (OUTLIER) cc_final: 0.3327 (pp) REVERT: G 55 GLU cc_start: 0.2983 (OUTLIER) cc_final: 0.2596 (tm-30) outliers start: 34 outliers final: 25 residues processed: 150 average time/residue: 1.0109 time to fit residues: 165.9800 Evaluate side-chains 156 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 12 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 82 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.246792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.188319 restraints weight = 21612.749| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 3.60 r_work: 0.3654 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10723 Z= 0.144 Angle : 0.453 8.475 14527 Z= 0.240 Chirality : 0.035 0.130 1646 Planarity : 0.003 0.035 1772 Dihedral : 3.790 54.824 1441 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.05 % Allowed : 24.10 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.97 (0.23), residues: 1306 helix: 3.80 (0.15), residues: 950 sheet: 0.85 (1.82), residues: 10 loop : -0.99 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 578 HIS 0.005 0.001 HIS F 205 PHE 0.012 0.001 PHE D 584 TYR 0.015 0.001 TYR B 523 ARG 0.006 0.000 ARG C 545 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.6878 (tt) cc_final: 0.6449 (tm) REVERT: H 122 ILE cc_start: 0.6967 (mm) cc_final: 0.6405 (mm) REVERT: F 65 ARG cc_start: 0.6129 (OUTLIER) cc_final: 0.5622 (ppt-90) REVERT: B 527 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7517 (ptm) REVERT: B 570 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6912 (mt-10) REVERT: D 629 MET cc_start: 0.6300 (tpt) cc_final: 0.5778 (mmt) REVERT: E 117 MET cc_start: 0.4025 (tpt) cc_final: 0.3730 (tpt) REVERT: E 208 LEU cc_start: 0.4020 (OUTLIER) cc_final: 0.3419 (pp) REVERT: G 55 GLU cc_start: 0.3020 (OUTLIER) cc_final: 0.2634 (tm-30) outliers start: 33 outliers final: 28 residues processed: 149 average time/residue: 0.9957 time to fit residues: 162.6114 Evaluate side-chains 158 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 22 optimal weight: 0.0000 chunk 107 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.245861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.185791 restraints weight = 17173.844| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 2.32 r_work: 0.3729 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10723 Z= 0.158 Angle : 0.451 8.659 14527 Z= 0.243 Chirality : 0.035 0.129 1646 Planarity : 0.003 0.036 1772 Dihedral : 3.860 54.410 1441 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.14 % Allowed : 23.92 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.88 (0.23), residues: 1306 helix: 3.74 (0.15), residues: 948 sheet: 0.96 (1.84), residues: 10 loop : -0.99 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 578 HIS 0.005 0.001 HIS F 205 PHE 0.013 0.001 PHE D 584 TYR 0.015 0.001 TYR B 523 ARG 0.006 0.000 ARG C 545 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7736.49 seconds wall clock time: 137 minutes 12.54 seconds (8232.54 seconds total)