Starting phenix.real_space_refine on Wed Feb 4 11:06:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b63_44244/02_2026/9b63_44244.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b63_44244/02_2026/9b63_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b63_44244/02_2026/9b63_44244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b63_44244/02_2026/9b63_44244.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b63_44244/02_2026/9b63_44244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b63_44244/02_2026/9b63_44244.map" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 3.19, per 1000 atoms: 0.30 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: 0.89 Conformation dependent library (CDL) restraints added in 601.9 milliseconds 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: 0.34 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: 1.82 Time building geometry restraints manager: 1.20 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: 3.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.100 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.400 ------------------------------------------------------------------------------- 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 : 4.91 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.41 (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 ARG 0.007 0.000 ARG B 594 TYR 0.010 0.001 TYR E 156 PHE 0.015 0.001 PHE G 97 TRP 0.008 0.001 TRP D 578 HIS 0.011 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00244 (10723) covalent geometry : angle 0.47419 (14527) SS BOND : bond 0.00137 ( 8) SS BOND : angle 0.72175 ( 16) hydrogen bonds : bond 0.14674 ( 842) hydrogen bonds : angle 4.24232 ( 2456) *********************** 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 : 0.396 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: 0.6742 (tm) outliers start: 24 outliers final: 25 residues processed: 156 average time/residue: 0.5109 time to fit residues: 86.5863 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 : 0.389 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.2980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.0070 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.4612 r_free = 0.4612 target = 0.246665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.186495 restraints weight = 23058.099| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 3.64 r_work: 0.3674 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.0809 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= 0.114 Angle : 0.443 7.368 14543 Z= 0.244 Chirality : 0.035 0.122 1646 Planarity : 0.003 0.033 1772 Dihedral : 5.621 59.824 1478 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.57 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.83 (0.23), residues: 1306 helix: 3.67 (0.15), residues: 952 sheet: -0.64 (1.77), residues: 10 loop : -0.93 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 594 TYR 0.009 0.001 TYR G 181 PHE 0.015 0.001 PHE D 584 TRP 0.009 0.001 TRP D 578 HIS 0.008 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00232 (10723) covalent geometry : angle 0.44242 (14527) SS BOND : bond 0.00091 ( 8) SS BOND : angle 0.75882 ( 16) hydrogen bonds : bond 0.04377 ( 842) hydrogen bonds : angle 3.23828 ( 2456) *********************** 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 : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 TYR cc_start: 0.7695 (m-10) cc_final: 0.7437 (m-10) REVERT: H 110 LEU cc_start: 0.7139 (tt) cc_final: 0.6665 (tm) REVERT: F 65 ARG cc_start: 0.6273 (OUTLIER) cc_final: 0.5600 (ppt-90) REVERT: C 594 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7580 (mtt-85) REVERT: E 21 PHE cc_start: 0.7085 (t80) cc_final: 0.6491 (t80) REVERT: E 185 LEU cc_start: 0.7094 (mt) cc_final: 0.6549 (mp) REVERT: G 55 GLU cc_start: 0.3205 (OUTLIER) cc_final: 0.2914 (tm-30) outliers start: 40 outliers final: 23 residues processed: 162 average time/residue: 0.5001 time to fit residues: 88.2849 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 : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 594 ARG Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 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 5 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4589 r_free = 0.4589 target = 0.243488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.180706 restraints weight = 20835.104| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 3.32 r_work: 0.3640 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10731 Z= 0.145 Angle : 0.483 7.300 14543 Z= 0.263 Chirality : 0.037 0.150 1646 Planarity : 0.003 0.035 1772 Dihedral : 4.583 56.666 1449 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.25 % Allowed : 22.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.57 (0.23), residues: 1306 helix: 3.46 (0.16), residues: 952 sheet: 0.05 (0.88), residues: 40 loop : -1.06 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 545 TYR 0.010 0.001 TYR B 523 PHE 0.017 0.002 PHE C 584 TRP 0.012 0.001 TRP D 578 HIS 0.019 0.002 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00323 (10723) covalent geometry : angle 0.48247 (14527) SS BOND : bond 0.00180 ( 8) SS BOND : angle 0.76073 ( 16) hydrogen bonds : bond 0.04700 ( 842) hydrogen bonds : angle 3.35821 ( 2456) *********************** 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 187 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7129 (tt) cc_final: 0.6680 (tm) REVERT: H 200 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6755 (mtt) REVERT: C 623 PHE cc_start: 0.8046 (m-10) cc_final: 0.7811 (m-10) REVERT: B 570 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6798 (mt-10) REVERT: G 55 GLU cc_start: 0.3102 (OUTLIER) cc_final: 0.2734 (tm-30) outliers start: 46 outliers final: 28 residues processed: 167 average time/residue: 0.4847 time to fit residues: 88.4832 Evaluate side-chains 164 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 78 LYS 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 8 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 114 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** ** 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 = 0.4587 r_free = 0.4587 target = 0.243194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.184494 restraints weight = 24882.627| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 3.79 r_work: 0.3586 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 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 = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10731 Z= 0.144 Angle : 0.470 6.821 14543 Z= 0.259 Chirality : 0.036 0.145 1646 Planarity : 0.003 0.037 1772 Dihedral : 4.147 57.596 1444 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.62 % Allowed : 21.70 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.23), residues: 1306 helix: 3.41 (0.16), residues: 948 sheet: 0.35 (1.80), residues: 10 loop : -0.98 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 545 TYR 0.012 0.001 TYR B 523 PHE 0.016 0.002 PHE D 584 TRP 0.012 0.001 TRP D 578 HIS 0.005 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00323 (10723) covalent geometry : angle 0.46974 (14527) SS BOND : bond 0.00264 ( 8) SS BOND : angle 0.74537 ( 16) hydrogen bonds : bond 0.04517 ( 842) hydrogen bonds : angle 3.34533 ( 2456) *********************** 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 185 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 135 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7184 (tt) cc_final: 0.6762 (tm) REVERT: H 200 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6766 (mtt) REVERT: B 570 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6845 (mt-10) REVERT: B 594 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7529 (mtt-85) REVERT: E 24 MET cc_start: 0.5037 (tpt) cc_final: 0.4814 (tpt) REVERT: G 55 GLU cc_start: 0.3143 (OUTLIER) cc_final: 0.2777 (tm-30) outliers start: 50 outliers final: 30 residues processed: 164 average time/residue: 0.4692 time to fit residues: 84.4439 Evaluate side-chains 162 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 200 MET Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 594 ARG 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 28 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 121 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4591 r_free = 0.4591 target = 0.243686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.183958 restraints weight = 22993.595| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 3.59 r_work: 0.3614 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1405 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= 0.135 Angle : 0.469 8.230 14543 Z= 0.256 Chirality : 0.036 0.150 1646 Planarity : 0.003 0.037 1772 Dihedral : 4.125 58.993 1444 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.34 % Allowed : 22.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.52 (0.23), residues: 1306 helix: 3.43 (0.16), residues: 948 sheet: 0.79 (1.72), residues: 10 loop : -1.01 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 545 TYR 0.017 0.001 TYR E 156 PHE 0.015 0.001 PHE D 584 TRP 0.011 0.001 TRP D 578 HIS 0.003 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00298 (10723) covalent geometry : angle 0.46815 (14527) SS BOND : bond 0.00221 ( 8) SS BOND : angle 0.83848 ( 16) hydrogen bonds : bond 0.04384 ( 842) hydrogen bonds : angle 3.30358 ( 2456) *********************** 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 178 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 131 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7132 (tt) cc_final: 0.6709 (tm) REVERT: H 200 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6763 (mtt) REVERT: F 58 MET cc_start: 0.5819 (OUTLIER) cc_final: 0.5618 (tpt) REVERT: B 570 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6868 (mt-10) REVERT: E 10 MET cc_start: 0.6686 (tpt) cc_final: 0.6148 (tpt) REVERT: E 208 LEU cc_start: 0.4214 (OUTLIER) cc_final: 0.3554 (pp) REVERT: G 55 GLU cc_start: 0.3070 (OUTLIER) cc_final: 0.2645 (tm-30) outliers start: 47 outliers final: 33 residues processed: 161 average time/residue: 0.4605 time to fit residues: 81.6403 Evaluate side-chains 166 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 58 MET 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 527 MET 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 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 195 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 48 optimal weight: 3.9990 chunk 118 optimal weight: 0.3980 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 0.2980 chunk 36 optimal weight: 0.4980 chunk 100 optimal weight: 10.0000 chunk 109 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4601 r_free = 0.4601 target = 0.244949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.182289 restraints weight = 22575.860| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 3.28 r_work: 0.3673 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10731 Z= 0.116 Angle : 0.442 7.112 14543 Z= 0.243 Chirality : 0.035 0.138 1646 Planarity : 0.003 0.036 1772 Dihedral : 4.038 59.718 1444 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.34 % Allowed : 22.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.70 (0.23), residues: 1306 helix: 3.59 (0.16), residues: 948 sheet: 0.89 (1.86), residues: 10 loop : -1.01 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 545 TYR 0.015 0.001 TYR B 523 PHE 0.013 0.001 PHE D 584 TRP 0.010 0.001 TRP D 578 HIS 0.003 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00248 (10723) covalent geometry : angle 0.44168 (14527) SS BOND : bond 0.00209 ( 8) SS BOND : angle 0.74385 ( 16) hydrogen bonds : bond 0.04053 ( 842) hydrogen bonds : angle 3.22581 ( 2456) *********************** 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 181 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7048 (tt) cc_final: 0.6634 (tm) REVERT: H 122 ILE cc_start: 0.6969 (mm) cc_final: 0.6432 (mm) REVERT: H 200 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6749 (mtt) REVERT: F 65 ARG cc_start: 0.6223 (OUTLIER) cc_final: 0.5674 (ppt-90) REVERT: B 570 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6807 (mt-10) REVERT: E 10 MET cc_start: 0.6724 (tpt) cc_final: 0.6201 (tpt) REVERT: E 24 MET cc_start: 0.4929 (tpt) cc_final: 0.4687 (tpt) REVERT: G 55 GLU cc_start: 0.3039 (OUTLIER) cc_final: 0.2617 (tm-30) outliers start: 47 outliers final: 32 residues processed: 163 average time/residue: 0.4442 time to fit residues: 79.5908 Evaluate side-chains 165 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 80 ILE 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 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 28 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 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 70 optimal weight: 0.5980 chunk 94 optimal weight: 0.1980 chunk 96 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.245656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.186764 restraints weight = 27852.501| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 3.92 r_work: 0.3618 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10731 Z= 0.107 Angle : 0.435 8.071 14543 Z= 0.236 Chirality : 0.035 0.136 1646 Planarity : 0.003 0.035 1772 Dihedral : 3.874 59.552 1443 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.25 % Allowed : 22.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.86 (0.23), residues: 1306 helix: 3.72 (0.16), residues: 948 sheet: 1.17 (1.85), residues: 10 loop : -1.01 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 545 TYR 0.016 0.001 TYR B 523 PHE 0.012 0.001 PHE D 584 TRP 0.008 0.001 TRP D 578 HIS 0.003 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00223 (10723) covalent geometry : angle 0.43475 (14527) SS BOND : bond 0.00160 ( 8) SS BOND : angle 0.81175 ( 16) hydrogen bonds : bond 0.03848 ( 842) hydrogen bonds : angle 3.15263 ( 2456) *********************** 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 176 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 130 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7076 (tt) cc_final: 0.6641 (tm) REVERT: H 122 ILE cc_start: 0.6949 (mm) cc_final: 0.6381 (mm) REVERT: H 200 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6744 (mtt) REVERT: F 10 MET cc_start: 0.6905 (tpp) cc_final: 0.6465 (tpp) REVERT: F 65 ARG cc_start: 0.6219 (OUTLIER) cc_final: 0.5690 (ppt-90) REVERT: B 570 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6783 (mt-10) REVERT: E 10 MET cc_start: 0.6695 (tpt) cc_final: 0.6179 (tpt) REVERT: E 58 MET cc_start: 0.6280 (tpp) cc_final: 0.5865 (mpt) REVERT: G 55 GLU cc_start: 0.2954 (OUTLIER) cc_final: 0.2551 (tm-30) outliers start: 46 outliers final: 33 residues processed: 158 average time/residue: 0.4335 time to fit residues: 75.1070 Evaluate side-chains 165 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain A residue 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 28 VAL 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 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 113 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** 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 = 0.244666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.179722 restraints weight = 27351.266| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 3.52 r_work: 0.3652 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 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 : 0.003 0.036 10731 Z= 0.120 Angle : 0.448 7.785 14543 Z= 0.244 Chirality : 0.035 0.134 1646 Planarity : 0.003 0.036 1772 Dihedral : 3.920 59.823 1443 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.34 % Allowed : 22.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.75 (0.23), residues: 1306 helix: 3.62 (0.16), residues: 948 sheet: 1.27 (1.85), residues: 10 loop : -0.99 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 545 TYR 0.014 0.001 TYR B 523 PHE 0.014 0.001 PHE C 584 TRP 0.010 0.001 TRP D 578 HIS 0.003 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00258 (10723) covalent geometry : angle 0.44761 (14527) SS BOND : bond 0.00152 ( 8) SS BOND : angle 0.74322 ( 16) hydrogen bonds : bond 0.04094 ( 842) hydrogen bonds : angle 3.21198 ( 2456) *********************** 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 177 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 110 LEU cc_start: 0.7038 (tt) cc_final: 0.6605 (tm) REVERT: H 122 ILE cc_start: 0.6951 (mm) cc_final: 0.6408 (mm) REVERT: H 200 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6778 (mtt) REVERT: F 10 MET cc_start: 0.6895 (tpp) cc_final: 0.6566 (tpp) REVERT: F 65 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.5634 (ppt-90) REVERT: B 570 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6757 (mt-10) REVERT: B 594 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7484 (mtt-85) REVERT: E 10 MET cc_start: 0.6652 (tpt) cc_final: 0.6129 (tpt) REVERT: E 58 MET cc_start: 0.6202 (tpp) cc_final: 0.5868 (mpt) REVERT: E 117 MET cc_start: 0.4010 (tpt) cc_final: 0.3643 (tpt) REVERT: E 208 LEU cc_start: 0.4030 (OUTLIER) cc_final: 0.3399 (pp) REVERT: G 55 GLU cc_start: 0.2933 (OUTLIER) cc_final: 0.2519 (tm-30) outliers start: 47 outliers final: 36 residues processed: 159 average time/residue: 0.4305 time to fit residues: 75.2723 Evaluate side-chains 169 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 135 ILE 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 594 ARG 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 28 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 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 15 optimal weight: 0.8980 chunk 126 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.243581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.181238 restraints weight = 19162.240| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 3.13 r_work: 0.3649 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1661 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= 0.138 Angle : 0.479 7.783 14543 Z= 0.259 Chirality : 0.036 0.132 1646 Planarity : 0.003 0.036 1772 Dihedral : 4.024 59.962 1443 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.16 % Allowed : 22.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.61 (0.23), residues: 1306 helix: 3.47 (0.16), residues: 948 sheet: 0.33 (0.94), residues: 40 loop : -0.97 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 545 TYR 0.014 0.001 TYR B 523 PHE 0.016 0.001 PHE C 584 TRP 0.011 0.001 TRP D 578 HIS 0.004 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00308 (10723) covalent geometry : angle 0.47724 (14527) SS BOND : bond 0.00177 ( 8) SS BOND : angle 1.19844 ( 16) hydrogen bonds : bond 0.04389 ( 842) hydrogen bonds : angle 3.31526 ( 2456) *********************** 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 171 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 115 LEU cc_start: 0.8216 (mp) cc_final: 0.8016 (mp) REVERT: H 200 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6905 (mtt) REVERT: F 10 MET cc_start: 0.6922 (tpp) cc_final: 0.6604 (tpp) REVERT: F 65 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.5634 (ppt-90) REVERT: B 570 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6809 (mt-10) REVERT: B 594 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7524 (mtt-85) REVERT: E 10 MET cc_start: 0.6679 (tpt) cc_final: 0.6137 (tpt) REVERT: E 58 MET cc_start: 0.6284 (tpp) cc_final: 0.5972 (mpt) REVERT: E 117 MET cc_start: 0.4157 (tpt) cc_final: 0.3885 (tpt) REVERT: E 208 LEU cc_start: 0.4146 (OUTLIER) cc_final: 0.3467 (pp) REVERT: G 55 GLU cc_start: 0.2948 (OUTLIER) cc_final: 0.2500 (tm-30) outliers start: 45 outliers final: 34 residues processed: 155 average time/residue: 0.4381 time to fit residues: 74.5919 Evaluate side-chains 166 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 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 594 ARG 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 28 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 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 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 68 optimal weight: 0.0170 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 chunk 32 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.246061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.183090 restraints weight = 24035.437| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 3.55 r_work: 0.3663 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1655 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= 0.105 Angle : 0.444 8.027 14543 Z= 0.240 Chirality : 0.035 0.133 1646 Planarity : 0.003 0.035 1772 Dihedral : 3.906 59.791 1443 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.05 % Allowed : 23.73 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.87 (0.23), residues: 1306 helix: 3.74 (0.16), residues: 948 sheet: 0.91 (1.78), residues: 10 loop : -1.04 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 545 TYR 0.015 0.001 TYR B 523 PHE 0.013 0.001 PHE D 584 TRP 0.009 0.001 TRP G 178 HIS 0.003 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00217 (10723) covalent geometry : angle 0.44211 (14527) SS BOND : bond 0.00219 ( 8) SS BOND : angle 1.23218 ( 16) hydrogen bonds : bond 0.03822 ( 842) hydrogen bonds : angle 3.19538 ( 2456) ********************** 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 161 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 122 ILE cc_start: 0.6916 (mm) cc_final: 0.6377 (mm) REVERT: H 200 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6713 (mtt) REVERT: F 10 MET cc_start: 0.6917 (tpp) cc_final: 0.6583 (tpp) REVERT: F 65 ARG cc_start: 0.6123 (OUTLIER) cc_final: 0.5587 (ppt-90) REVERT: B 570 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6770 (mt-10) REVERT: D 629 MET cc_start: 0.6285 (tpt) cc_final: 0.5862 (mmt) REVERT: E 10 MET cc_start: 0.6594 (tpt) cc_final: 0.6110 (tpt) REVERT: E 58 MET cc_start: 0.6192 (tpp) cc_final: 0.5854 (mpt) REVERT: E 117 MET cc_start: 0.4003 (tpt) cc_final: 0.3648 (tpt) REVERT: G 55 GLU cc_start: 0.2983 (OUTLIER) cc_final: 0.2569 (tm-30) outliers start: 33 outliers final: 30 residues processed: 149 average time/residue: 0.4460 time to fit residues: 72.7255 Evaluate side-chains 160 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 65 ARG 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 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 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 195 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 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 115 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 0.0050 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 7 optimal weight: 0.0970 chunk 42 optimal weight: 0.0020 chunk 125 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 116 optimal weight: 0.3980 chunk 71 optimal weight: 3.9990 overall best weight: 0.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.249361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.189993 restraints weight = 19580.396| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.90 r_work: 0.3749 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3735 r_free = 0.3735 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3735 r_free = 0.3735 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10731 Z= 0.093 Angle : 0.433 11.200 14543 Z= 0.229 Chirality : 0.034 0.174 1646 Planarity : 0.003 0.035 1772 Dihedral : 3.801 59.120 1443 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.12 % Allowed : 24.47 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.14 (0.23), residues: 1306 helix: 3.96 (0.16), residues: 948 sheet: 1.04 (1.79), residues: 10 loop : -1.04 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 545 TYR 0.016 0.001 TYR B 523 PHE 0.009 0.001 PHE D 584 TRP 0.010 0.001 TRP E 178 HIS 0.002 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00181 (10723) covalent geometry : angle 0.43126 (14527) SS BOND : bond 0.00219 ( 8) SS BOND : angle 1.16647 ( 16) hydrogen bonds : bond 0.03373 ( 842) hydrogen bonds : angle 3.08379 ( 2456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3972.34 seconds wall clock time: 68 minutes 27.38 seconds (4107.38 seconds total)