Starting phenix.real_space_refine on Mon Jul 28 13:06:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b63_44244/07_2025/9b63_44244.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b63_44244/07_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_44244/07_2025/9b63_44244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b63_44244/07_2025/9b63_44244.map" model { file = "/net/cci-nas-00/data/ceres_data/9b63_44244/07_2025/9b63_44244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b63_44244/07_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.90, 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: 2.82 Conformation dependent library (CDL) restraints added in 1.6 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: 0.89 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: 3.20 Time building geometry restraints manager: 3.30 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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.270 Find NCS groups from input model: 0.490 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:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.970 ------------------------------------------------------------------------------- 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 10731 Z= 0.107 Angle : 0.475 12.813 14543 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 Details of bonding type rmsd hydrogen bonds : bond 0.14674 ( 842) hydrogen bonds : angle 4.24232 ( 2456) SS BOND : bond 0.00137 ( 8) SS BOND : angle 0.72175 ( 16) covalent geometry : bond 0.00244 (10723) covalent geometry : angle 0.47419 (14527) *********************** 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 : 1.091 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: 1.0758 time to fit residues: 183.4509 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 : 1.171 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.6982 ------------------------------------------------------------------------------- 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 = 0.246272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.186907 restraints weight = 26270.017| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 3.66 r_work: 0.3644 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 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 = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10731 Z= 0.118 Angle : 0.447 7.266 14543 Z= 0.246 Chirality : 0.035 0.124 1646 Planarity : 0.003 0.033 1772 Dihedral : 5.653 59.941 1478 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.69 % Allowed : 22.44 % 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: 3.79 (0.23), residues: 1306 helix: 3.64 (0.15), residues: 952 sheet: -0.63 (1.78), residues: 10 loop : -0.93 (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 0.015 0.001 PHE D 584 TYR 0.009 0.001 TYR G 181 ARG 0.005 0.000 ARG B 594 Details of bonding type rmsd hydrogen bonds : bond 0.04472 ( 842) hydrogen bonds : angle 3.25501 ( 2456) SS BOND : bond 0.00099 ( 8) SS BOND : angle 0.74775 ( 16) covalent geometry : bond 0.00242 (10723) covalent geometry : angle 0.44680 (14527) *********************** 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 181 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 TYR cc_start: 0.7680 (m-10) cc_final: 0.7428 (m-10) REVERT: H 110 LEU cc_start: 0.7129 (tt) cc_final: 0.6646 (tm) REVERT: F 65 ARG cc_start: 0.6178 (OUTLIER) cc_final: 0.5506 (ppt-90) REVERT: C 594 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7596 (mtt-85) REVERT: E 21 PHE cc_start: 0.7072 (t80) cc_final: 0.6471 (t80) REVERT: E 185 LEU cc_start: 0.7016 (mt) cc_final: 0.6456 (mp) REVERT: G 55 GLU cc_start: 0.3202 (OUTLIER) cc_final: 0.2906 (tm-30) outliers start: 40 outliers final: 23 residues processed: 162 average time/residue: 1.1962 time to fit residues: 211.9311 Evaluate side-chains 159 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU 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 78 LYS 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 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: 0.2980 chunk 112 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 chunk 25 optimal weight: 0.0770 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- 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 = 0.4611 r_free = 0.4611 target = 0.246327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.182743 restraints weight = 22239.683| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 3.31 r_work: 0.3691 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10731 Z= 0.112 Angle : 0.441 7.591 14543 Z= 0.239 Chirality : 0.035 0.150 1646 Planarity : 0.003 0.033 1772 Dihedral : 4.459 56.104 1449 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.88 % Allowed : 22.53 % 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: 3.90 (0.23), residues: 1306 helix: 3.73 (0.15), residues: 952 sheet: -0.04 (1.70), residues: 10 loop : -0.95 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 578 HIS 0.018 0.002 HIS E 60 PHE 0.013 0.001 PHE D 584 TYR 0.011 0.001 TYR B 523 ARG 0.005 0.000 ARG B 594 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 842) hydrogen bonds : angle 3.19849 ( 2456) SS BOND : bond 0.00111 ( 8) SS BOND : angle 0.67893 ( 16) covalent geometry : bond 0.00232 (10723) covalent geometry : angle 0.44108 (14527) *********************** 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 178 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 TYR cc_start: 0.7518 (m-10) cc_final: 0.7294 (m-10) REVERT: H 110 LEU cc_start: 0.6973 (tt) cc_final: 0.6515 (tm) REVERT: H 200 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6586 (mtt) REVERT: F 65 ARG cc_start: 0.6232 (OUTLIER) cc_final: 0.5610 (ppt-90) REVERT: C 594 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7552 (mtt-85) REVERT: B 511 LYS cc_start: 0.6060 (tmtm) cc_final: 0.5856 (mttt) REVERT: B 570 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6894 (mt-10) REVERT: G 55 GLU cc_start: 0.3102 (OUTLIER) cc_final: 0.2773 (tm-30) outliers start: 42 outliers final: 26 residues processed: 162 average time/residue: 1.1521 time to fit residues: 204.1223 Evaluate side-chains 162 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 70 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 75 optimal weight: 0.0980 chunk 107 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.245920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.187820 restraints weight = 24854.735| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 3.83 r_work: 0.3633 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10731 Z= 0.110 Angle : 0.424 4.947 14543 Z= 0.235 Chirality : 0.035 0.142 1646 Planarity : 0.003 0.033 1772 Dihedral : 4.171 55.559 1446 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.88 % Allowed : 22.62 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.79 (0.15), residues: 948 sheet: 0.17 (1.72), residues: 10 loop : -0.92 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 578 HIS 0.004 0.001 HIS G 205 PHE 0.013 0.001 PHE D 584 TYR 0.012 0.001 TYR B 523 ARG 0.006 0.000 ARG B 594 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 842) hydrogen bonds : angle 3.16155 ( 2456) SS BOND : bond 0.00152 ( 8) SS BOND : angle 0.67787 ( 16) covalent geometry : bond 0.00229 (10723) covalent geometry : angle 0.42352 (14527) *********************** 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 182 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 TYR cc_start: 0.7565 (m-80) cc_final: 0.7359 (m-10) REVERT: H 110 LEU cc_start: 0.6894 (tt) cc_final: 0.6448 (tm) REVERT: H 200 MET cc_start: 0.7168 (mmm) cc_final: 0.6723 (mtt) REVERT: F 65 ARG cc_start: 0.6154 (OUTLIER) cc_final: 0.5506 (ppt-90) REVERT: B 570 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6990 (mt-10) REVERT: E 113 ILE cc_start: 0.6595 (mt) cc_final: 0.6349 (mm) REVERT: G 55 GLU cc_start: 0.3120 (OUTLIER) cc_final: 0.2769 (tm-30) outliers start: 42 outliers final: 26 residues processed: 163 average time/residue: 1.0549 time to fit residues: 188.6290 Evaluate side-chains 162 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 65 ARG Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain C residue 524 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 107 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 106 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 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 = 0.4581 r_free = 0.4581 target = 0.242120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.182961 restraints weight = 24220.147| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 3.71 r_work: 0.3581 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10731 Z= 0.173 Angle : 0.511 7.733 14543 Z= 0.279 Chirality : 0.038 0.161 1646 Planarity : 0.004 0.048 1772 Dihedral : 4.170 56.828 1443 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.80 % Allowed : 21.61 % 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: 3.38 (0.23), residues: 1306 helix: 3.29 (0.16), residues: 952 sheet: 0.13 (0.88), residues: 40 loop : -1.05 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 578 HIS 0.003 0.001 HIS F 205 PHE 0.020 0.002 PHE C 584 TYR 0.012 0.002 TYR A 523 ARG 0.005 0.000 ARG C 545 Details of bonding type rmsd hydrogen bonds : bond 0.04921 ( 842) hydrogen bonds : angle 3.42223 ( 2456) SS BOND : bond 0.00250 ( 8) SS BOND : angle 0.79336 ( 16) covalent geometry : bond 0.00401 (10723) covalent geometry : angle 0.51078 (14527) *********************** 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 186 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 134 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 200 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6812 (mtt) REVERT: B 570 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6888 (mt-10) REVERT: E 199 HIS cc_start: 0.4658 (OUTLIER) cc_final: 0.4449 (t70) REVERT: G 55 GLU cc_start: 0.3075 (OUTLIER) cc_final: 0.2664 (tm-30) outliers start: 52 outliers final: 33 residues processed: 167 average time/residue: 1.1911 time to fit residues: 219.6011 Evaluate side-chains 167 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 66 THR 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 591 ILE 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 527 MET Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 13 THR 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 E residue 199 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 13 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 57 optimal weight: 0.0870 chunk 99 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 71 optimal weight: 0.2980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.4614 r_free = 0.4614 target = 0.246559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.184772 restraints weight = 27853.116| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 3.86 r_work: 0.3638 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10731 Z= 0.103 Angle : 0.427 7.135 14543 Z= 0.234 Chirality : 0.035 0.136 1646 Planarity : 0.003 0.035 1772 Dihedral : 3.902 58.106 1443 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.69 % Allowed : 23.27 % 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: 3.88 (0.23), residues: 1306 helix: 3.73 (0.16), residues: 948 sheet: 0.92 (1.74), residues: 10 loop : -0.95 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 178 HIS 0.002 0.001 HIS F 205 PHE 0.013 0.001 PHE D 584 TYR 0.016 0.001 TYR B 523 ARG 0.002 0.000 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 842) hydrogen bonds : angle 3.16240 ( 2456) SS BOND : bond 0.00187 ( 8) SS BOND : angle 0.83024 ( 16) covalent geometry : bond 0.00209 (10723) covalent geometry : angle 0.42585 (14527) *********************** 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: 40 poor density : 136 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.6909 (tt) cc_final: 0.6373 (tm) REVERT: H 122 ILE cc_start: 0.6917 (mm) cc_final: 0.6346 (mm) REVERT: H 200 MET cc_start: 0.7115 (mmm) cc_final: 0.6695 (mtt) REVERT: F 10 MET cc_start: 0.6933 (tpp) cc_final: 0.6522 (tpp) REVERT: F 65 ARG cc_start: 0.6110 (OUTLIER) cc_final: 0.5553 (ppt-90) REVERT: B 570 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6806 (mt-10) REVERT: E 58 MET cc_start: 0.6205 (tpp) cc_final: 0.5860 (mpt) REVERT: G 55 GLU cc_start: 0.3037 (OUTLIER) cc_final: 0.2641 (tm-30) outliers start: 40 outliers final: 30 residues processed: 162 average time/residue: 0.9713 time to fit residues: 172.8595 Evaluate side-chains 164 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 80 ILE 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 570 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 807 MET 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 E residue 67 CYS 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 67 CYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 192 MET 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: 0.8980 chunk 92 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4593 r_free = 0.4593 target = 0.243722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.182753 restraints weight = 24457.377| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 3.63 r_work: 0.3620 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10731 Z= 0.136 Angle : 0.467 7.407 14543 Z= 0.254 Chirality : 0.036 0.136 1646 Planarity : 0.003 0.036 1772 Dihedral : 3.974 57.401 1441 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.79 % Allowed : 23.36 % 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: 3.66 (0.23), residues: 1306 helix: 3.53 (0.16), residues: 948 sheet: 1.07 (1.89), residues: 10 loop : -0.94 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 578 HIS 0.003 0.001 HIS E 60 PHE 0.017 0.001 PHE C 584 TYR 0.014 0.001 TYR B 523 ARG 0.007 0.000 ARG C 545 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 842) hydrogen bonds : angle 3.27497 ( 2456) SS BOND : bond 0.00182 ( 8) SS BOND : angle 0.91127 ( 16) covalent geometry : bond 0.00305 (10723) covalent geometry : angle 0.46617 (14527) *********************** 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 174 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7119 (tt) cc_final: 0.6574 (tm) REVERT: H 122 ILE cc_start: 0.6942 (mm) cc_final: 0.6364 (mm) REVERT: H 200 MET cc_start: 0.7304 (mmm) cc_final: 0.6971 (mtt) REVERT: F 10 MET cc_start: 0.7025 (tpp) cc_final: 0.6583 (tpp) REVERT: F 65 ARG cc_start: 0.6280 (OUTLIER) cc_final: 0.5742 (ppt-90) REVERT: B 570 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6771 (mt-10) REVERT: E 58 MET cc_start: 0.6274 (tpp) cc_final: 0.5977 (mpt) REVERT: E 208 LEU cc_start: 0.4185 (OUTLIER) cc_final: 0.3500 (pp) REVERT: G 55 GLU cc_start: 0.3023 (OUTLIER) cc_final: 0.2647 (tm-30) outliers start: 41 outliers final: 31 residues processed: 159 average time/residue: 0.9269 time to fit residues: 163.0337 Evaluate side-chains 164 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 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 807 MET 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 67 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 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 192 MET 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: 3.9990 chunk 1 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 89 optimal weight: 0.0170 chunk 9 optimal weight: 0.3980 chunk 82 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- 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 = 0.4598 r_free = 0.4598 target = 0.244358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.183712 restraints weight = 17430.235| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.33 r_work: 0.3712 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10731 Z= 0.122 Angle : 0.465 11.476 14543 Z= 0.250 Chirality : 0.036 0.208 1646 Planarity : 0.003 0.035 1772 Dihedral : 3.937 57.804 1441 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.69 % Allowed : 23.18 % 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: 3.69 (0.23), residues: 1306 helix: 3.56 (0.16), residues: 948 sheet: 1.06 (1.85), residues: 10 loop : -0.95 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 578 HIS 0.004 0.001 HIS E 60 PHE 0.014 0.001 PHE D 584 TYR 0.015 0.001 TYR B 523 ARG 0.005 0.000 ARG C 545 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 842) hydrogen bonds : angle 3.24479 ( 2456) SS BOND : bond 0.00164 ( 8) SS BOND : angle 0.89482 ( 16) covalent geometry : bond 0.00267 (10723) covalent geometry : angle 0.46465 (14527) *********************** 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 170 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.6913 (tt) cc_final: 0.6400 (tm) REVERT: H 122 ILE cc_start: 0.7014 (mm) cc_final: 0.6473 (mm) REVERT: H 200 MET cc_start: 0.7381 (mmm) cc_final: 0.7024 (mtt) REVERT: F 10 MET cc_start: 0.7044 (tpp) cc_final: 0.6536 (tpp) REVERT: F 65 ARG cc_start: 0.6332 (OUTLIER) cc_final: 0.5793 (ppt-90) REVERT: B 570 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6745 (mt-10) REVERT: D 629 MET cc_start: 0.6207 (tpt) cc_final: 0.5745 (mmt) REVERT: E 58 MET cc_start: 0.6284 (tpp) cc_final: 0.6040 (mpt) REVERT: E 208 LEU cc_start: 0.4099 (OUTLIER) cc_final: 0.3413 (pp) REVERT: G 55 GLU cc_start: 0.3059 (OUTLIER) cc_final: 0.2697 (tm-30) outliers start: 40 outliers final: 32 residues processed: 155 average time/residue: 0.9780 time to fit residues: 166.9347 Evaluate side-chains 162 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 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 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 591 ILE Chi-restraints excluded: chain B residue 807 MET 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 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 E residue 67 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 208 LEU 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 192 MET 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: 0.0570 chunk 115 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.4610 r_free = 0.4610 target = 0.245969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.186236 restraints weight = 25771.470| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 3.66 r_work: 0.3637 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10731 Z= 0.106 Angle : 0.439 11.044 14543 Z= 0.238 Chirality : 0.035 0.175 1646 Planarity : 0.003 0.035 1772 Dihedral : 3.830 57.590 1441 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.88 % Allowed : 22.99 % 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: 3.89 (0.23), residues: 1306 helix: 3.73 (0.16), residues: 948 sheet: 1.28 (1.90), residues: 10 loop : -0.95 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 578 HIS 0.003 0.001 HIS E 60 PHE 0.012 0.001 PHE D 584 TYR 0.017 0.001 TYR B 523 ARG 0.003 0.000 ARG C 545 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 842) hydrogen bonds : angle 3.15787 ( 2456) SS BOND : bond 0.00131 ( 8) SS BOND : angle 0.77999 ( 16) covalent geometry : bond 0.00222 (10723) covalent geometry : angle 0.43885 (14527) *********************** 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 170 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.6877 (tt) cc_final: 0.6333 (tm) REVERT: H 122 ILE cc_start: 0.6921 (mm) cc_final: 0.6360 (mm) REVERT: H 200 MET cc_start: 0.7248 (mmm) cc_final: 0.6907 (mtt) REVERT: F 10 MET cc_start: 0.6805 (tpp) cc_final: 0.6310 (tpp) REVERT: F 65 ARG cc_start: 0.6128 (OUTLIER) cc_final: 0.5609 (ppt-90) REVERT: B 570 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6787 (mt-10) REVERT: D 629 MET cc_start: 0.6176 (tpt) cc_final: 0.5681 (mmt) REVERT: E 58 MET cc_start: 0.6173 (tpp) cc_final: 0.5863 (mpt) REVERT: E 208 LEU cc_start: 0.4013 (OUTLIER) cc_final: 0.3400 (pp) REVERT: G 55 GLU cc_start: 0.3055 (OUTLIER) cc_final: 0.2673 (tm-30) outliers start: 42 outliers final: 28 residues processed: 157 average time/residue: 0.8860 time to fit residues: 153.8676 Evaluate side-chains 159 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 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 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 630 VAL 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 E residue 67 CYS Chi-restraints excluded: chain E residue 68 CYS 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 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 192 MET 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: 3.9990 chunk 56 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4602 r_free = 0.4602 target = 0.244928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.182893 restraints weight = 20952.842| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 3.30 r_work: 0.3664 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10731 Z= 0.119 Angle : 0.467 10.595 14543 Z= 0.249 Chirality : 0.036 0.175 1646 Planarity : 0.003 0.035 1772 Dihedral : 3.864 56.731 1441 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.05 % Allowed : 23.82 % 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: 3.74 (0.23), residues: 1306 helix: 3.61 (0.16), residues: 948 sheet: 1.14 (1.86), residues: 10 loop : -0.97 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 578 HIS 0.003 0.001 HIS E 60 PHE 0.013 0.001 PHE D 584 TYR 0.016 0.001 TYR B 523 ARG 0.004 0.000 ARG C 545 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 842) hydrogen bonds : angle 3.21781 ( 2456) SS BOND : bond 0.00146 ( 8) SS BOND : angle 1.24412 ( 16) covalent geometry : bond 0.00259 (10723) covalent geometry : angle 0.46534 (14527) ********************** 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 163 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.6894 (tt) cc_final: 0.6363 (tm) REVERT: H 122 ILE cc_start: 0.6950 (mm) cc_final: 0.6406 (mm) REVERT: H 200 MET cc_start: 0.7326 (mmm) cc_final: 0.7020 (mtm) REVERT: F 10 MET cc_start: 0.6826 (tpp) cc_final: 0.6340 (tpp) REVERT: F 65 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.5681 (ppt-90) REVERT: B 570 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6734 (mt-10) REVERT: A 629 MET cc_start: 0.7744 (ptm) cc_final: 0.7460 (ptp) REVERT: D 629 MET cc_start: 0.6185 (tpt) cc_final: 0.5705 (mmt) REVERT: E 58 MET cc_start: 0.6213 (tpp) cc_final: 0.5928 (mpt) REVERT: E 208 LEU cc_start: 0.4036 (OUTLIER) cc_final: 0.3405 (pp) REVERT: G 55 GLU cc_start: 0.3055 (OUTLIER) cc_final: 0.2670 (tm-30) outliers start: 33 outliers final: 27 residues processed: 153 average time/residue: 0.9303 time to fit residues: 156.4309 Evaluate side-chains 157 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 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 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 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 E residue 67 CYS Chi-restraints excluded: chain E residue 68 CYS 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 155 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 192 MET 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: 0.8980 chunk 37 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4606 r_free = 0.4606 target = 0.245511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.185340 restraints weight = 17200.381| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.40 r_work: 0.3733 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10731 Z= 0.115 Angle : 0.459 10.395 14543 Z= 0.247 Chirality : 0.035 0.170 1646 Planarity : 0.003 0.035 1772 Dihedral : 3.865 56.600 1441 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.95 % Allowed : 24.10 % 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: 3.77 (0.23), residues: 1306 helix: 3.64 (0.16), residues: 948 sheet: 0.77 (1.80), residues: 10 loop : -1.01 (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 0.013 0.001 PHE H 142 TYR 0.016 0.001 TYR B 523 ARG 0.004 0.000 ARG C 545 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 842) hydrogen bonds : angle 3.22590 ( 2456) SS BOND : bond 0.00220 ( 8) SS BOND : angle 1.32938 ( 16) covalent geometry : bond 0.00246 (10723) covalent geometry : angle 0.45682 (14527) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8426.39 seconds wall clock time: 148 minutes 45.84 seconds (8925.84 seconds total)