Starting phenix.real_space_refine on Tue May 13 13:06:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fpg_29363/05_2025/8fpg_29363.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fpg_29363/05_2025/8fpg_29363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fpg_29363/05_2025/8fpg_29363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fpg_29363/05_2025/8fpg_29363.map" model { file = "/net/cci-nas-00/data/ceres_data/8fpg_29363/05_2025/8fpg_29363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fpg_29363/05_2025/8fpg_29363.cif" } resolution = 2.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 72 5.16 5 Cl 4 4.86 5 C 6927 2.51 5 N 1657 2.21 5 O 2014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10674 Number of models: 1 Model: "" Number of chains: 20 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: 1157 Number of conformers: 2 Conformer: "A" 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 1164 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: 1152 Number of conformers: 2 Conformer: "A" 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 1159 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 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N APHE C 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 623 " occ=0.50 residue: pdb=" N APHE B 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.50 residue: pdb=" N APHE A 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 623 " occ=0.50 residue: pdb=" N APHE D 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.50 Time building chain proxies: 9.19, per 1000 atoms: 0.86 Number of scatterers: 10674 At special positions: 0 Unit cell: (108.994, 105.716, 92.6035, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 72 16.00 O 2014 8.00 N 1657 7.00 C 6927 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.8 seconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 74.5% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'H' and resid 5 through 30 Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.989A pdb=" N TYR H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 128 removed outlier: 4.146A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR H 128 " --> pdb=" O ALA H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.737A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 214 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.925A pdb=" N TYR F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 128 removed outlier: 4.019A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR F 128 " --> pdb=" O ALA F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.769A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 214 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.709A 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 586 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 removed outlier: 3.619A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.572A 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 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.711A 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 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 791 Processing helix chain 'A' and resid 792 through 825 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.574A 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 791 Processing helix chain 'D' and resid 792 through 825 removed outlier: 3.660A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (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: 3.596A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 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: 3.587A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 Processing sheet with id=AA1, first strand: chain 'H' and resid 77 through 79 removed outlier: 3.895A 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 removed outlier: 3.947A pdb=" N VAL F 57 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 34 through 38 Processing sheet with id=AA4, first strand: chain 'G' and resid 34 through 38 854 hydrogen bonds defined for protein. 2494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3155 1.34 - 1.46: 2703 1.46 - 1.58: 4779 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 10749 Sorted by residual: bond pdb=" CB MET E 200 " pdb=" CG MET E 200 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.40e+00 bond pdb=" CB MET G 200 " pdb=" CG MET G 200 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CB MET H 200 " pdb=" CG MET H 200 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.95e-01 bond pdb=" CB MET F 200 " pdb=" CG MET F 200 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.41e-01 bond pdb=" CG MET G 200 " pdb=" SD MET G 200 " ideal model delta sigma weight residual 1.803 1.781 0.022 2.50e-02 1.60e+03 7.74e-01 ... (remaining 10744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 14387 1.83 - 3.66: 158 3.66 - 5.48: 17 5.48 - 7.31: 0 7.31 - 9.14: 3 Bond angle restraints: 14565 Sorted by residual: angle pdb=" C CYS H 40 " pdb=" N LYS H 41 " pdb=" CA LYS H 41 " ideal model delta sigma weight residual 121.54 126.54 -5.00 1.91e+00 2.74e-01 6.87e+00 angle pdb=" CA LEU A 542 " pdb=" CB LEU A 542 " pdb=" CG LEU A 542 " ideal model delta sigma weight residual 116.30 125.44 -9.14 3.50e+00 8.16e-02 6.82e+00 angle pdb=" CA LEU C 542 " pdb=" CB LEU C 542 " pdb=" CG LEU C 542 " ideal model delta sigma weight residual 116.30 125.36 -9.06 3.50e+00 8.16e-02 6.71e+00 angle pdb=" CA LEU E 98 " pdb=" CB LEU E 98 " pdb=" CG LEU E 98 " ideal model delta sigma weight residual 116.30 124.89 -8.59 3.50e+00 8.16e-02 6.02e+00 angle pdb=" C CYS F 40 " pdb=" N LYS F 41 " pdb=" CA LYS F 41 " ideal model delta sigma weight residual 121.54 125.50 -3.96 1.91e+00 2.74e-01 4.29e+00 ... (remaining 14560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 5329 17.15 - 34.30: 559 34.30 - 51.45: 164 51.45 - 68.59: 39 68.59 - 85.74: 8 Dihedral angle restraints: 6099 sinusoidal: 2227 harmonic: 3872 Sorted by residual: dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual 93.00 121.57 -28.57 1 1.00e+01 1.00e-02 1.17e+01 dihedral pdb=" CA ASP A 590 " pdb=" CB ASP A 590 " pdb=" CG ASP A 590 " pdb=" OD1 ASP A 590 " ideal model delta sinusoidal sigma weight residual -30.00 -88.27 58.27 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP C 590 " pdb=" CB ASP C 590 " pdb=" CG ASP C 590 " pdb=" OD1 ASP C 590 " ideal model delta sinusoidal sigma weight residual -30.00 -87.82 57.82 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 6096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1152 0.035 - 0.071: 393 0.071 - 0.106: 89 0.106 - 0.142: 13 0.142 - 0.177: 1 Chirality restraints: 1648 Sorted by residual: chirality pdb=" CB ILE E 106 " pdb=" CA ILE E 106 " pdb=" CG1 ILE E 106 " pdb=" CG2 ILE E 106 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CA PHE H 107 " pdb=" N PHE H 107 " pdb=" C PHE H 107 " pdb=" CB PHE H 107 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-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 2.38 0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 1645 not shown) Planarity restraints: 1778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 32 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C TYR E 32 " -0.029 2.00e-02 2.50e+03 pdb=" O TYR E 32 " 0.011 2.00e-02 2.50e+03 pdb=" N TRP E 33 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR G 32 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C TYR G 32 " 0.028 2.00e-02 2.50e+03 pdb=" O TYR G 32 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP G 33 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 107 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO E 108 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 108 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 108 " 0.018 5.00e-02 4.00e+02 ... (remaining 1775 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 370 2.71 - 3.26: 10886 3.26 - 3.81: 18809 3.81 - 4.35: 22219 4.35 - 4.90: 37551 Nonbonded interactions: 89835 Sorted by model distance: nonbonded pdb=" OD1 ASN G 160 " pdb=" O HOH G 501 " model vdw 2.165 3.040 nonbonded pdb=" OD1 ASN E 160 " pdb=" O HOH E 501 " model vdw 2.167 3.040 nonbonded pdb=" O PHE A 579 " pdb=" O HOH A 901 " model vdw 2.169 3.040 nonbonded pdb=" O HOH D 911 " pdb=" O HOH D 920 " model vdw 2.172 3.040 nonbonded pdb=" O HOH C 923 " pdb=" O HOH B1001 " model vdw 2.174 3.040 ... (remaining 89830 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 or resid 401)) selection = (chain 'F' and (resid 5 through 41 or resid 55 through 214 or resid 401)) selection = (chain 'G' and (resid 5 through 214 or resid 401)) selection = (chain 'H' and (resid 5 through 41 or resid 55 through 214 or resid 401)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 28.260 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.003 0.035 10757 Z= 0.143 Angle : 0.490 9.141 14581 Z= 0.263 Chirality : 0.037 0.177 1648 Planarity : 0.003 0.031 1778 Dihedral : 16.030 85.743 3595 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.84 % Allowed : 17.42 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.23), residues: 1312 helix: 3.19 (0.16), residues: 948 sheet: 0.46 (0.78), residues: 48 loop : -0.87 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 64 HIS 0.006 0.001 HIS E 132 PHE 0.017 0.002 PHE C 584 TYR 0.015 0.002 TYR C 523 ARG 0.003 0.000 ARG C 545 Details of bonding type rmsd hydrogen bonds : bond 0.14449 ( 854) hydrogen bonds : angle 4.32247 ( 2494) SS BOND : bond 0.00257 ( 8) SS BOND : angle 0.73457 ( 16) covalent geometry : bond 0.00308 (10749) covalent geometry : angle 0.48968 (14565) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: E 11 LEU cc_start: 0.7721 (tp) cc_final: 0.7037 (tp) outliers start: 20 outliers final: 14 residues processed: 171 average time/residue: 1.1126 time to fit residues: 207.1169 Evaluate side-chains 168 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 150 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS C 791 ASN E 79 GLN G 9 GLN G 79 GLN G 132 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.191836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.135101 restraints weight = 23908.681| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.08 r_work: 0.3103 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10757 Z= 0.117 Angle : 0.445 8.302 14581 Z= 0.246 Chirality : 0.035 0.138 1648 Planarity : 0.003 0.034 1778 Dihedral : 4.115 42.513 1462 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.04 % Allowed : 16.50 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.23 (0.23), residues: 1312 helix: 3.93 (0.15), residues: 950 sheet: 1.01 (1.30), residues: 10 loop : -0.61 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 33 HIS 0.003 0.001 HIS E 132 PHE 0.014 0.001 PHE G 107 TYR 0.013 0.001 TYR H 181 ARG 0.002 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.04983 ( 854) hydrogen bonds : angle 3.17924 ( 2494) SS BOND : bond 0.00143 ( 8) SS BOND : angle 0.52393 ( 16) covalent geometry : bond 0.00219 (10749) covalent geometry : angle 0.44454 (14565) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 1.114 Fit side-chains REVERT: H 113 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7650 (mt) REVERT: F 113 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7634 (mt) outliers start: 33 outliers final: 6 residues processed: 176 average time/residue: 0.9519 time to fit residues: 183.9241 Evaluate side-chains 156 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 117 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 30 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 HIS H 199 HIS F 60 HIS F 199 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.187769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.132115 restraints weight = 24390.847| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.10 r_work: 0.3021 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10757 Z= 0.177 Angle : 0.533 7.013 14581 Z= 0.297 Chirality : 0.039 0.150 1648 Planarity : 0.004 0.036 1778 Dihedral : 3.707 20.112 1444 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.59 % Allowed : 14.84 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.23), residues: 1312 helix: 3.63 (0.15), residues: 948 sheet: 1.77 (1.32), residues: 10 loop : -0.59 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 33 HIS 0.005 0.001 HIS E 60 PHE 0.018 0.002 PHE A 584 TYR 0.016 0.002 TYR D 549 ARG 0.003 0.000 ARG C 545 Details of bonding type rmsd hydrogen bonds : bond 0.06194 ( 854) hydrogen bonds : angle 3.42070 ( 2494) SS BOND : bond 0.00306 ( 8) SS BOND : angle 0.85016 ( 16) covalent geometry : bond 0.00383 (10749) covalent geometry : angle 0.53205 (14565) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 1.025 Fit side-chains REVERT: H 78 LYS cc_start: 0.6822 (OUTLIER) cc_final: 0.6595 (tmmt) REVERT: H 113 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7700 (mt) REVERT: F 78 LYS cc_start: 0.6724 (OUTLIER) cc_final: 0.6482 (tmmt) REVERT: F 113 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7682 (mt) outliers start: 39 outliers final: 14 residues processed: 183 average time/residue: 1.0354 time to fit residues: 206.1122 Evaluate side-chains 168 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 25 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS E 132 HIS G 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.189783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132309 restraints weight = 23697.515| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.26 r_work: 0.3061 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10757 Z= 0.125 Angle : 0.454 6.608 14581 Z= 0.256 Chirality : 0.036 0.131 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.469 17.441 1444 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.95 % Allowed : 15.76 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.19 (0.23), residues: 1312 helix: 3.90 (0.16), residues: 950 sheet: 0.73 (1.14), residues: 10 loop : -0.64 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 33 HIS 0.003 0.001 HIS G 205 PHE 0.012 0.001 PHE C 584 TYR 0.014 0.001 TYR H 181 ARG 0.001 0.000 ARG G 102 Details of bonding type rmsd hydrogen bonds : bond 0.05106 ( 854) hydrogen bonds : angle 3.20665 ( 2494) SS BOND : bond 0.00256 ( 8) SS BOND : angle 0.48981 ( 16) covalent geometry : bond 0.00246 (10749) covalent geometry : angle 0.45390 (14565) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.173 Fit side-chains REVERT: H 78 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6557 (tmmt) REVERT: H 113 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7588 (mt) REVERT: F 113 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7581 (mt) REVERT: E 120 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6397 (tp) outliers start: 32 outliers final: 11 residues processed: 176 average time/residue: 1.0521 time to fit residues: 201.6612 Evaluate side-chains 169 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 75 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 101 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS E 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.190639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133027 restraints weight = 23786.202| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.28 r_work: 0.3074 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10757 Z= 0.114 Angle : 0.434 7.268 14581 Z= 0.243 Chirality : 0.035 0.125 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.353 17.210 1444 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.86 % Allowed : 15.76 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.36 (0.23), residues: 1312 helix: 4.04 (0.16), residues: 950 sheet: 0.74 (1.14), residues: 10 loop : -0.60 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 33 HIS 0.003 0.001 HIS G 205 PHE 0.011 0.001 PHE C 584 TYR 0.013 0.001 TYR F 181 ARG 0.001 0.000 ARG G 102 Details of bonding type rmsd hydrogen bonds : bond 0.04770 ( 854) hydrogen bonds : angle 3.10707 ( 2494) SS BOND : bond 0.00259 ( 8) SS BOND : angle 0.29943 ( 16) covalent geometry : bond 0.00218 (10749) covalent geometry : angle 0.43401 (14565) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 1.051 Fit side-chains REVERT: H 78 LYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6636 (tmmt) REVERT: H 113 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7601 (mt) REVERT: F 113 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7595 (mt) REVERT: G 149 ASN cc_start: 0.8034 (t0) cc_final: 0.7756 (t0) REVERT: G 209 ARG cc_start: 0.5257 (OUTLIER) cc_final: 0.5013 (mtp85) outliers start: 31 outliers final: 14 residues processed: 181 average time/residue: 0.9904 time to fit residues: 195.5832 Evaluate side-chains 170 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 209 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 50 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS E 60 HIS E 132 HIS G 60 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.190398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.134039 restraints weight = 29572.494| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.51 r_work: 0.3046 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10757 Z= 0.119 Angle : 0.447 7.575 14581 Z= 0.249 Chirality : 0.036 0.122 1648 Planarity : 0.003 0.036 1778 Dihedral : 3.377 17.376 1444 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.95 % Allowed : 16.13 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.31 (0.23), residues: 1312 helix: 3.99 (0.16), residues: 950 sheet: 0.85 (1.15), residues: 10 loop : -0.59 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 33 HIS 0.017 0.002 HIS E 60 PHE 0.012 0.001 PHE A 584 TYR 0.014 0.001 TYR H 181 ARG 0.001 0.000 ARG G 102 Details of bonding type rmsd hydrogen bonds : bond 0.04896 ( 854) hydrogen bonds : angle 3.13780 ( 2494) SS BOND : bond 0.00226 ( 8) SS BOND : angle 0.33871 ( 16) covalent geometry : bond 0.00230 (10749) covalent geometry : angle 0.44699 (14565) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 1.096 Fit side-chains REVERT: H 78 LYS cc_start: 0.6852 (OUTLIER) cc_final: 0.6618 (tmmt) REVERT: H 113 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7604 (mt) REVERT: F 113 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7615 (mt) REVERT: C 589 CYS cc_start: 0.5746 (p) cc_final: 0.4557 (m) REVERT: A 589 CYS cc_start: 0.5774 (p) cc_final: 0.4572 (m) REVERT: E 11 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6516 (tp) REVERT: G 56 GLU cc_start: 0.5386 (OUTLIER) cc_final: 0.4497 (mm-30) REVERT: G 209 ARG cc_start: 0.5270 (OUTLIER) cc_final: 0.5011 (mtp85) outliers start: 32 outliers final: 16 residues processed: 179 average time/residue: 1.0978 time to fit residues: 214.0394 Evaluate side-chains 170 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 209 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 57 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS E 132 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.189465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134463 restraints weight = 29052.680| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.21 r_work: 0.3035 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10757 Z= 0.132 Angle : 0.471 7.729 14581 Z= 0.262 Chirality : 0.036 0.128 1648 Planarity : 0.003 0.036 1778 Dihedral : 3.470 17.838 1444 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.32 % Allowed : 15.76 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.18 (0.23), residues: 1312 helix: 3.88 (0.16), residues: 950 sheet: 0.93 (1.16), residues: 10 loop : -0.58 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 33 HIS 0.005 0.001 HIS E 132 PHE 0.013 0.001 PHE C 584 TYR 0.015 0.001 TYR F 181 ARG 0.001 0.000 ARG G 102 Details of bonding type rmsd hydrogen bonds : bond 0.05239 ( 854) hydrogen bonds : angle 3.21082 ( 2494) SS BOND : bond 0.00244 ( 8) SS BOND : angle 0.35984 ( 16) covalent geometry : bond 0.00264 (10749) covalent geometry : angle 0.47120 (14565) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 1.078 Fit side-chains REVERT: H 78 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6633 (tmmt) REVERT: H 113 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7588 (mt) REVERT: F 113 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7595 (mt) REVERT: E 11 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6536 (tp) REVERT: E 95 GLU cc_start: 0.5388 (tt0) cc_final: 0.4936 (mp0) REVERT: G 11 LEU cc_start: 0.7105 (tp) cc_final: 0.6363 (tp) REVERT: G 56 GLU cc_start: 0.5388 (OUTLIER) cc_final: 0.4624 (mm-30) REVERT: G 120 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6498 (tp) REVERT: G 209 ARG cc_start: 0.5278 (OUTLIER) cc_final: 0.5005 (mtp85) outliers start: 36 outliers final: 16 residues processed: 181 average time/residue: 1.0748 time to fit residues: 211.4011 Evaluate side-chains 174 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 209 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 52 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS E 132 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.190911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133299 restraints weight = 21974.564| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.22 r_work: 0.3079 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10757 Z= 0.115 Angle : 0.443 8.127 14581 Z= 0.246 Chirality : 0.036 0.123 1648 Planarity : 0.003 0.036 1778 Dihedral : 3.361 19.087 1444 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.49 % Allowed : 16.77 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.34 (0.23), residues: 1312 helix: 4.01 (0.16), residues: 952 sheet: 0.70 (1.13), residues: 10 loop : -0.59 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 33 HIS 0.004 0.001 HIS G 132 PHE 0.011 0.001 PHE A 584 TYR 0.014 0.001 TYR F 181 ARG 0.001 0.000 ARG G 102 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 854) hydrogen bonds : angle 3.10759 ( 2494) SS BOND : bond 0.00183 ( 8) SS BOND : angle 0.30966 ( 16) covalent geometry : bond 0.00221 (10749) covalent geometry : angle 0.44280 (14565) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.103 Fit side-chains REVERT: H 78 LYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6667 (tmmt) REVERT: H 113 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7570 (mt) REVERT: F 113 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7589 (mt) REVERT: C 589 CYS cc_start: 0.5755 (p) cc_final: 0.4555 (m) REVERT: A 589 CYS cc_start: 0.5787 (p) cc_final: 0.4590 (m) REVERT: E 11 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6473 (tp) REVERT: E 95 GLU cc_start: 0.5214 (tt0) cc_final: 0.4830 (mp0) REVERT: G 11 LEU cc_start: 0.7004 (tp) cc_final: 0.6434 (tp) REVERT: G 120 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6491 (tp) outliers start: 27 outliers final: 15 residues processed: 173 average time/residue: 1.0829 time to fit residues: 203.8455 Evaluate side-chains 172 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 54 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS ** G 149 ASN ** 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 = 0.4130 r_free = 0.4130 target = 0.189070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.133937 restraints weight = 29494.567| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.28 r_work: 0.3027 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10757 Z= 0.143 Angle : 0.495 8.471 14581 Z= 0.274 Chirality : 0.037 0.130 1648 Planarity : 0.003 0.036 1778 Dihedral : 3.516 20.729 1442 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.76 % Allowed : 16.41 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.07 (0.23), residues: 1312 helix: 3.78 (0.16), residues: 950 sheet: 0.96 (1.15), residues: 10 loop : -0.57 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 33 HIS 0.005 0.001 HIS E 132 PHE 0.016 0.002 PHE C 531 TYR 0.016 0.002 TYR F 181 ARG 0.002 0.000 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.05479 ( 854) hydrogen bonds : angle 3.26449 ( 2494) SS BOND : bond 0.00239 ( 8) SS BOND : angle 0.40864 ( 16) covalent geometry : bond 0.00297 (10749) covalent geometry : angle 0.49482 (14565) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.224 Fit side-chains REVERT: H 78 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6757 (tmmt) REVERT: H 113 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7674 (mt) REVERT: F 113 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7672 (mt) REVERT: E 11 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6580 (tp) REVERT: G 11 LEU cc_start: 0.7189 (tp) cc_final: 0.6617 (tp) REVERT: G 56 GLU cc_start: 0.5420 (OUTLIER) cc_final: 0.4691 (mm-30) REVERT: G 120 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6565 (tp) outliers start: 30 outliers final: 19 residues processed: 170 average time/residue: 1.0388 time to fit residues: 193.0122 Evaluate side-chains 173 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 38 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 29 optimal weight: 0.0870 chunk 49 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS ** G 149 ASN ** 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 = 0.4146 r_free = 0.4146 target = 0.190553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.136069 restraints weight = 28768.632| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.30 r_work: 0.3048 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10757 Z= 0.122 Angle : 0.462 8.699 14581 Z= 0.255 Chirality : 0.036 0.130 1648 Planarity : 0.003 0.036 1778 Dihedral : 3.396 19.633 1442 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.49 % Allowed : 16.59 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.24 (0.23), residues: 1312 helix: 3.94 (0.16), residues: 950 sheet: 0.83 (1.10), residues: 10 loop : -0.61 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 33 HIS 0.004 0.001 HIS E 132 PHE 0.020 0.001 PHE A 531 TYR 0.015 0.001 TYR F 181 ARG 0.001 0.000 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.04906 ( 854) hydrogen bonds : angle 3.15348 ( 2494) SS BOND : bond 0.00195 ( 8) SS BOND : angle 0.30542 ( 16) covalent geometry : bond 0.00239 (10749) covalent geometry : angle 0.46206 (14565) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 1.035 Fit side-chains REVERT: H 78 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6708 (tmmt) REVERT: H 113 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7664 (mt) REVERT: F 113 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7660 (mt) REVERT: C 589 CYS cc_start: 0.5908 (p) cc_final: 0.4655 (m) REVERT: A 589 CYS cc_start: 0.5861 (p) cc_final: 0.4629 (m) REVERT: E 11 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6550 (tp) REVERT: G 11 LEU cc_start: 0.7048 (tp) cc_final: 0.6517 (tp) REVERT: G 120 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6527 (tp) outliers start: 27 outliers final: 18 residues processed: 167 average time/residue: 0.9920 time to fit residues: 181.1714 Evaluate side-chains 169 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 10 MET Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 5 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 chunk 111 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS ** G 149 ASN ** 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 = 0.4162 r_free = 0.4162 target = 0.191989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.137107 restraints weight = 26098.586| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.20 r_work: 0.3085 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10757 Z= 0.108 Angle : 0.435 8.729 14581 Z= 0.240 Chirality : 0.035 0.133 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.272 18.382 1442 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.30 % Allowed : 16.96 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.42 (0.23), residues: 1312 helix: 4.08 (0.16), residues: 952 sheet: 0.71 (1.11), residues: 10 loop : -0.60 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 178 HIS 0.004 0.001 HIS E 132 PHE 0.012 0.001 PHE E 141 TYR 0.012 0.001 TYR H 181 ARG 0.001 0.000 ARG F 6 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 854) hydrogen bonds : angle 3.04909 ( 2494) SS BOND : bond 0.00154 ( 8) SS BOND : angle 0.25935 ( 16) covalent geometry : bond 0.00201 (10749) covalent geometry : angle 0.43485 (14565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9118.29 seconds wall clock time: 157 minutes 14.85 seconds (9434.85 seconds total)