Starting phenix.real_space_refine on Sat Aug 23 00:29:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8z_36082/08_2025/8j8z_36082.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8z_36082/08_2025/8j8z_36082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j8z_36082/08_2025/8j8z_36082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8z_36082/08_2025/8j8z_36082.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j8z_36082/08_2025/8j8z_36082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8z_36082/08_2025/8j8z_36082.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 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 P 6 5.49 5 S 34 5.16 5 C 5564 2.51 5 N 1458 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8722 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2601 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 25, 'TRANS': 314} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 7, 'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 81 Chain: "H" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 898 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2607 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 314} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 6, 'GLU:plan': 7, 'ASP:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 80 Chain: "I" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 895 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "M" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 795 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 3} Unresolved non-hydrogen planarities: 12 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Time building chain proxies: 1.81, per 1000 atoms: 0.21 Number of scatterers: 8722 At special positions: 0 Unit cell: (81.9448, 144.867, 90.7246, 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) S 34 16.00 P 6 15.00 O 1660 8.00 N 1458 7.00 C 5564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 99 " distance=2.03 Simple disulfide: pdb=" SG CYS M 24 " - pdb=" SG CYS M 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 230.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 24 sheets defined 6.4% alpha, 47.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'I' and resid 31 through 33 No H-bonds generated for 'chain 'I' and resid 31 through 33' Processing helix chain 'I' and resid 65 through 68 Processing helix chain 'I' and resid 90 through 94 removed outlier: 3.739A pdb=" N THR I 94 " --> pdb=" O ALA I 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 84 removed outlier: 3.880A pdb=" N PHE M 84 " --> pdb=" O PRO M 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 117 removed outlier: 3.760A pdb=" N PHE A 115 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 39 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 19 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 22 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 10 " --> pdb=" O GLU V 349 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 29 removed outlier: 5.758A pdb=" N PHE A 27 " --> pdb=" O VAL A 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 85 removed outlier: 5.807A pdb=" N ARG A 76 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR A 63 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASP A 78 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE A 61 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 80 " --> pdb=" O CYS A 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 85 removed outlier: 5.807A pdb=" N ARG A 76 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR A 63 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASP A 78 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE A 61 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 80 " --> pdb=" O CYS A 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 190 removed outlier: 4.651A pdb=" N PHE A 190 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYS A 195 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 270 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 207 through 208 removed outlier: 4.228A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 207 through 208 removed outlier: 4.228A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 231 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU A 257 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 7 through 10 removed outlier: 3.639A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 13 through 14 Processing sheet with id=AB1, first strand: chain 'H' and resid 61 through 63 removed outlier: 5.333A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ARG H 103 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N LEU H 110 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.660A pdb=" N TYR L 87 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.660A pdb=" N TYR L 87 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 112 through 117 removed outlier: 3.791A pdb=" N PHE B 115 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 39 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 10 " --> pdb=" O GLU U 349 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 26 through 29 removed outlier: 5.943A pdb=" N PHE B 27 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.603A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE B 61 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 78 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 26 through 29 removed outlier: 5.943A pdb=" N PHE B 27 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.603A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 183 through 188 Processing sheet with id=AB9, first strand: chain 'B' and resid 207 through 208 removed outlier: 4.248A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE B 231 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU B 257 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE B 233 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N MET B 255 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B 235 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 7 through 10 Processing sheet with id=AC2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.841A pdb=" N GLY I 13 " --> pdb=" O THR I 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 60 through 63 removed outlier: 3.623A pdb=" N TYR I 60 " --> pdb=" O SER I 55 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N TRP I 50 " --> pdb=" O ARG I 41 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG I 41 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA I 52 " --> pdb=" O TRP I 39 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR I 112 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ARG I 103 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N LEU I 110 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 5 through 8 Processing sheet with id=AC5, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.934A pdb=" N LEU M 12 " --> pdb=" O GLU M 106 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR M 87 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR M 86 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR M 50 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.934A pdb=" N LEU M 12 " --> pdb=" O GLU M 106 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR M 87 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR M 98 " --> pdb=" O GLN M 91 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2099 1.33 - 1.45: 1728 1.45 - 1.57: 5030 1.57 - 1.69: 16 1.69 - 1.81: 44 Bond restraints: 8917 Sorted by residual: bond pdb=" O1P SEP V 348 " pdb=" P SEP V 348 " ideal model delta sigma weight residual 1.610 1.504 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" O3P SEP U 351 " pdb=" P SEP U 351 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" O3P SEP V 351 " pdb=" P SEP V 351 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" O1P SEP V 351 " pdb=" P SEP V 351 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" O2P SEP U 351 " pdb=" P SEP U 351 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.51e+01 ... (remaining 8912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 11729 1.74 - 3.48: 331 3.48 - 5.22: 73 5.22 - 6.95: 6 6.95 - 8.69: 7 Bond angle restraints: 12146 Sorted by residual: angle pdb=" CA PRO A 180 " pdb=" N PRO A 180 " pdb=" CD PRO A 180 " ideal model delta sigma weight residual 112.00 104.52 7.48 1.40e+00 5.10e-01 2.85e+01 angle pdb=" C GLN M 39 " pdb=" CA GLN M 39 " pdb=" CB GLN M 39 " ideal model delta sigma weight residual 111.77 103.75 8.02 1.52e+00 4.33e-01 2.78e+01 angle pdb=" C SER L 31 " pdb=" CA SER L 31 " pdb=" CB SER L 31 " ideal model delta sigma weight residual 116.34 110.85 5.49 1.40e+00 5.10e-01 1.54e+01 angle pdb=" CA GLN M 90 " pdb=" C GLN M 90 " pdb=" O GLN M 90 " ideal model delta sigma weight residual 120.32 116.33 3.99 1.11e+00 8.12e-01 1.30e+01 angle pdb=" CA TYR M 37 " pdb=" C TYR M 37 " pdb=" O TYR M 37 " ideal model delta sigma weight residual 120.66 116.72 3.94 1.15e+00 7.56e-01 1.18e+01 ... (remaining 12141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4905 17.85 - 35.70: 336 35.70 - 53.56: 87 53.56 - 71.41: 19 71.41 - 89.26: 11 Dihedral angle restraints: 5358 sinusoidal: 2023 harmonic: 3335 Sorted by residual: dihedral pdb=" CB CYS I 25 " pdb=" SG CYS I 25 " pdb=" SG CYS I 99 " pdb=" CB CYS I 99 " ideal model delta sinusoidal sigma weight residual 93.00 58.38 34.62 1 1.00e+01 1.00e-02 1.70e+01 dihedral pdb=" C TYR M 37 " pdb=" N TYR M 37 " pdb=" CA TYR M 37 " pdb=" CB TYR M 37 " ideal model delta harmonic sigma weight residual -122.60 -114.13 -8.47 0 2.50e+00 1.60e-01 1.15e+01 dihedral pdb=" CA LYS I 79 " pdb=" C LYS I 79 " pdb=" N ASN I 80 " pdb=" CA ASN I 80 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 5355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1227 0.066 - 0.132: 163 0.132 - 0.198: 4 0.198 - 0.264: 3 0.264 - 0.331: 2 Chirality restraints: 1399 Sorted by residual: chirality pdb=" CA ILE U 352 " pdb=" N ILE U 352 " pdb=" C ILE U 352 " pdb=" CB ILE U 352 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA TYR B 249 " pdb=" N TYR B 249 " pdb=" C TYR B 249 " pdb=" CB TYR B 249 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA TYR M 37 " pdb=" N TYR M 37 " pdb=" C TYR M 37 " pdb=" CB TYR M 37 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1396 not shown) Planarity restraints: 1538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS V 347 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C CYS V 347 " 0.036 2.00e-02 2.50e+03 pdb=" O CYS V 347 " -0.014 2.00e-02 2.50e+03 pdb=" N SEP V 348 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 251 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO B 252 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 252 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 252 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 179 " -0.031 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 180 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " -0.025 5.00e-02 4.00e+02 ... (remaining 1535 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 239 2.67 - 3.23: 8409 3.23 - 3.79: 12361 3.79 - 4.34: 17170 4.34 - 4.90: 29731 Nonbonded interactions: 67910 Sorted by model distance: nonbonded pdb=" N GLU B 50 " pdb=" OE1 GLU B 50 " model vdw 2.118 3.120 nonbonded pdb=" N GLU L 82 " pdb=" OE1 GLU L 82 " model vdw 2.239 3.120 nonbonded pdb=" N GLU M 82 " pdb=" OE1 GLU M 82 " model vdw 2.274 3.120 nonbonded pdb=" O LEU A 68 " pdb=" ND2 ASN B 245 " model vdw 2.299 3.120 nonbonded pdb=" O ASN H 87 " pdb=" OG SER H 88 " model vdw 2.302 3.040 ... (remaining 67905 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 6 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 66 or (resid 67 and (name N or name \ CA or name C or name O or name CB )) or resid 68 or (resid 69 and (name N or na \ me CA or name C or name O or name CB )) or resid 70 through 133 or (resid 134 th \ rough 135 and (name N or name CA or name C or name O or name CB )) or resid 136 \ through 159 or (resid 160 through 161 and (name N or name CA or name C or name O \ or name CB )) or resid 162 through 175 or (resid 176 through 177 and (name N or \ name CA or name C or name O or name CB )) or resid 178 through 357)) selection = (chain 'B' and (resid 6 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB )) or resid 72 through 76 or (resid 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 134 or (resid 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 through 156 or \ (resid 157 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 8 through 176 or (resid 177 and (name N or name CA or name C or name O or name C \ B )) or resid 178 through 214 or (resid 215 and (name N or name CA or name C or \ name O or name CB )) or resid 216 through 248 or (resid 249 and (name N or name \ CA or name C or name O or name CB )) or resid 250 through 284 or (resid 285 and \ (name N or name CA or name C or name O or name CB )) or resid 286 through 357)) } ncs_group { reference = (chain 'H' and (resid 5 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 through 121)) selection = chain 'I' } ncs_group { reference = (chain 'L' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 50 or (resid 51 through 52 and (name N \ or name CA or name C or name O or name CB )) or resid 53 through 89 or (resid 9 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 91 through 1 \ 07)) selection = chain 'M' } ncs_group { reference = chain 'U' selection = chain 'V' } 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=1.00 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.650 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.010 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.006 0.118 8921 Z= 0.267 Angle : 0.730 8.694 12154 Z= 0.399 Chirality : 0.047 0.331 1399 Planarity : 0.004 0.046 1538 Dihedral : 14.135 89.261 3202 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.86 % Allowed : 13.89 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.26), residues: 1112 helix: -1.05 (0.79), residues: 36 sheet: -0.30 (0.23), residues: 526 loop : -0.13 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 19 TYR 0.016 0.001 TYR L 94 PHE 0.012 0.001 PHE M 99 TRP 0.011 0.002 TRP I 50 HIS 0.006 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 8917) covalent geometry : angle 0.73047 (12146) SS BOND : bond 0.00382 ( 4) SS BOND : angle 0.42120 ( 8) hydrogen bonds : bond 0.22960 ( 315) hydrogen bonds : angle 8.89053 ( 915) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.241 Fit side-chains REVERT: H 33 TYR cc_start: 0.8669 (m-80) cc_final: 0.8367 (m-80) REVERT: H 49 GLU cc_start: 0.8121 (tt0) cc_final: 0.7819 (pt0) REVERT: L 106 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7067 (mt-10) REVERT: B 321 TYR cc_start: 0.8221 (m-80) cc_final: 0.7773 (m-80) REVERT: I 33 TYR cc_start: 0.8730 (m-80) cc_final: 0.8389 (m-80) REVERT: I 79 LYS cc_start: 0.8276 (ptpp) cc_final: 0.8070 (ptpp) REVERT: I 102 SER cc_start: 0.9151 (t) cc_final: 0.8880 (p) REVERT: M 28 GLN cc_start: 0.7027 (mp10) cc_final: 0.6653 (mp10) outliers start: 8 outliers final: 5 residues processed: 148 average time/residue: 0.0883 time to fit residues: 17.8817 Evaluate side-chains 128 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain U residue 347 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN L 28 GLN L 39 GLN B 219 HIS I 42 GLN M 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.141041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113604 restraints weight = 14685.898| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.01 r_work: 0.3346 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 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 : 0.004 0.055 8921 Z= 0.180 Angle : 0.656 6.320 12154 Z= 0.338 Chirality : 0.047 0.146 1399 Planarity : 0.004 0.036 1538 Dihedral : 6.248 55.108 1261 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.51 % Allowed : 14.75 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.26), residues: 1112 helix: -0.44 (0.86), residues: 36 sheet: -0.15 (0.22), residues: 554 loop : -0.00 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 22 TYR 0.013 0.002 TYR B 272 PHE 0.016 0.002 PHE A 268 TRP 0.014 0.002 TRP L 36 HIS 0.005 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8917) covalent geometry : angle 0.65608 (12146) SS BOND : bond 0.00555 ( 4) SS BOND : angle 0.68625 ( 8) hydrogen bonds : bond 0.04139 ( 315) hydrogen bonds : angle 5.61887 ( 915) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.207 Fit side-chains REVERT: A 144 TYR cc_start: 0.7822 (m-80) cc_final: 0.7116 (m-10) REVERT: A 208 TYR cc_start: 0.8608 (m-80) cc_final: 0.8380 (m-10) REVERT: A 255 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8164 (tmm) REVERT: A 321 TYR cc_start: 0.8483 (m-80) cc_final: 0.8179 (m-80) REVERT: H 33 TYR cc_start: 0.8761 (m-80) cc_final: 0.8409 (m-80) REVERT: H 49 GLU cc_start: 0.8246 (tt0) cc_final: 0.7797 (pt0) REVERT: L 5 MET cc_start: 0.9074 (mmt) cc_final: 0.8265 (mmt) REVERT: L 83 ASP cc_start: 0.6758 (m-30) cc_final: 0.6448 (m-30) REVERT: B 255 MET cc_start: 0.8203 (tmm) cc_final: 0.7961 (tmm) REVERT: B 321 TYR cc_start: 0.8495 (m-80) cc_final: 0.8183 (m-80) REVERT: I 33 TYR cc_start: 0.8707 (m-80) cc_final: 0.8341 (m-80) REVERT: M 28 GLN cc_start: 0.7351 (mp10) cc_final: 0.6971 (mp10) REVERT: M 56 TYR cc_start: 0.8492 (t80) cc_final: 0.8177 (t80) outliers start: 14 outliers final: 8 residues processed: 151 average time/residue: 0.0715 time to fit residues: 15.2282 Evaluate side-chains 125 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 0.4980 chunk 27 optimal weight: 0.0060 chunk 15 optimal weight: 0.0170 chunk 33 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.2632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN L 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.146369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120552 restraints weight = 13804.616| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.63 r_work: 0.3452 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8921 Z= 0.108 Angle : 0.570 5.349 12154 Z= 0.294 Chirality : 0.044 0.140 1399 Planarity : 0.004 0.036 1538 Dihedral : 5.822 59.393 1252 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.69 % Allowed : 14.53 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.26), residues: 1112 helix: -0.13 (0.90), residues: 36 sheet: 0.01 (0.22), residues: 568 loop : 0.06 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 22 TYR 0.011 0.001 TYR A 272 PHE 0.011 0.001 PHE A 268 TRP 0.011 0.001 TRP I 50 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8917) covalent geometry : angle 0.57015 (12146) SS BOND : bond 0.00542 ( 4) SS BOND : angle 0.61099 ( 8) hydrogen bonds : bond 0.03299 ( 315) hydrogen bonds : angle 5.05943 ( 915) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.222 Fit side-chains REVERT: A 21 TYR cc_start: 0.8213 (m-10) cc_final: 0.7915 (m-10) REVERT: A 144 TYR cc_start: 0.7707 (m-80) cc_final: 0.6955 (m-10) REVERT: A 255 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8179 (tmm) REVERT: A 321 TYR cc_start: 0.8557 (m-80) cc_final: 0.8187 (m-80) REVERT: H 22 ARG cc_start: 0.7628 (ttt90) cc_final: 0.7326 (ttm170) REVERT: H 41 ARG cc_start: 0.8583 (ptt180) cc_final: 0.7803 (ptm160) REVERT: L 5 MET cc_start: 0.8855 (mmt) cc_final: 0.8510 (mmt) REVERT: B 255 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7795 (tmm) REVERT: B 314 ILE cc_start: 0.7399 (mm) cc_final: 0.6924 (mp) REVERT: B 321 TYR cc_start: 0.8460 (m-80) cc_final: 0.8114 (m-80) REVERT: I 33 TYR cc_start: 0.8564 (m-80) cc_final: 0.8272 (m-80) REVERT: I 89 LEU cc_start: 0.7979 (mm) cc_final: 0.7704 (mm) REVERT: M 19 ARG cc_start: 0.8428 (ttt-90) cc_final: 0.8145 (ptm-80) REVERT: M 28 GLN cc_start: 0.7123 (mp10) cc_final: 0.6787 (mp10) outliers start: 25 outliers final: 14 residues processed: 158 average time/residue: 0.0668 time to fit residues: 15.0458 Evaluate side-chains 141 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain M residue 2 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 15 optimal weight: 0.0570 chunk 85 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.0570 chunk 77 optimal weight: 5.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN L 28 GLN I 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.145335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119107 restraints weight = 13974.374| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.70 r_work: 0.3425 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8921 Z= 0.130 Angle : 0.567 5.374 12154 Z= 0.292 Chirality : 0.044 0.139 1399 Planarity : 0.004 0.037 1538 Dihedral : 5.810 60.281 1252 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.34 % Allowed : 16.15 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.26), residues: 1112 helix: -0.04 (0.91), residues: 36 sheet: 0.00 (0.22), residues: 570 loop : 0.08 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 22 TYR 0.011 0.001 TYR A 208 PHE 0.015 0.002 PHE B 87 TRP 0.012 0.001 TRP H 50 HIS 0.003 0.001 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8917) covalent geometry : angle 0.56719 (12146) SS BOND : bond 0.00490 ( 4) SS BOND : angle 0.63135 ( 8) hydrogen bonds : bond 0.03204 ( 315) hydrogen bonds : angle 4.85917 ( 915) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.321 Fit side-chains REVERT: A 21 TYR cc_start: 0.8151 (m-10) cc_final: 0.7852 (m-10) REVERT: A 144 TYR cc_start: 0.7785 (m-80) cc_final: 0.7059 (m-10) REVERT: A 321 TYR cc_start: 0.8609 (m-80) cc_final: 0.8243 (m-80) REVERT: H 41 ARG cc_start: 0.8550 (ptt180) cc_final: 0.7907 (ptm160) REVERT: L 83 ASP cc_start: 0.6800 (m-30) cc_final: 0.6595 (m-30) REVERT: B 75 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7412 (p90) REVERT: B 255 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7831 (tmm) REVERT: B 314 ILE cc_start: 0.7660 (mm) cc_final: 0.7254 (mp) REVERT: B 321 TYR cc_start: 0.8484 (m-80) cc_final: 0.8091 (m-80) REVERT: I 33 TYR cc_start: 0.8636 (m-80) cc_final: 0.8374 (m-80) REVERT: I 41 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7982 (ptt180) REVERT: I 89 LEU cc_start: 0.7935 (mm) cc_final: 0.7645 (mm) REVERT: M 28 GLN cc_start: 0.7224 (mp10) cc_final: 0.6875 (mp10) outliers start: 31 outliers final: 18 residues processed: 150 average time/residue: 0.0801 time to fit residues: 16.6895 Evaluate side-chains 148 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain M residue 2 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 49 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 100 optimal weight: 0.0010 chunk 39 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 15 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN L 28 GLN I 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.146448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.120611 restraints weight = 13856.713| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.68 r_work: 0.3425 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8921 Z= 0.110 Angle : 0.547 5.079 12154 Z= 0.282 Chirality : 0.044 0.138 1399 Planarity : 0.004 0.037 1538 Dihedral : 5.646 62.012 1252 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.55 % Allowed : 16.58 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.26), residues: 1112 helix: 0.01 (0.91), residues: 36 sheet: 0.04 (0.22), residues: 572 loop : 0.18 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 103 TYR 0.012 0.001 TYR B 272 PHE 0.011 0.001 PHE A 277 TRP 0.009 0.001 TRP I 50 HIS 0.004 0.001 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8917) covalent geometry : angle 0.54664 (12146) SS BOND : bond 0.00493 ( 4) SS BOND : angle 0.61675 ( 8) hydrogen bonds : bond 0.02959 ( 315) hydrogen bonds : angle 4.71693 ( 915) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.255 Fit side-chains REVERT: A 21 TYR cc_start: 0.8133 (m-10) cc_final: 0.7765 (m-10) REVERT: A 321 TYR cc_start: 0.8551 (m-80) cc_final: 0.8174 (m-80) REVERT: H 41 ARG cc_start: 0.8502 (ptt180) cc_final: 0.7862 (ptm160) REVERT: B 75 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7088 (p90) REVERT: B 255 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7954 (tmm) REVERT: B 314 ILE cc_start: 0.7642 (mm) cc_final: 0.7265 (mp) REVERT: B 321 TYR cc_start: 0.8476 (m-80) cc_final: 0.8060 (m-80) REVERT: I 41 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7928 (ptt180) REVERT: I 89 LEU cc_start: 0.7840 (mm) cc_final: 0.7543 (mm) REVERT: M 28 GLN cc_start: 0.7217 (mp10) cc_final: 0.6910 (mp10) outliers start: 33 outliers final: 16 residues processed: 153 average time/residue: 0.0707 time to fit residues: 15.7816 Evaluate side-chains 144 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 0.0170 chunk 96 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 63 optimal weight: 0.0270 chunk 90 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN L 28 GLN I 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.145966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.119906 restraints weight = 13895.008| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.71 r_work: 0.3413 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8921 Z= 0.123 Angle : 0.557 7.084 12154 Z= 0.284 Chirality : 0.043 0.143 1399 Planarity : 0.004 0.038 1538 Dihedral : 5.618 62.260 1252 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.09 % Allowed : 16.36 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.26), residues: 1112 helix: 0.08 (0.92), residues: 36 sheet: 0.06 (0.22), residues: 574 loop : 0.12 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 22 TYR 0.011 0.001 TYR A 54 PHE 0.017 0.002 PHE B 87 TRP 0.010 0.001 TRP I 50 HIS 0.003 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8917) covalent geometry : angle 0.55739 (12146) SS BOND : bond 0.00415 ( 4) SS BOND : angle 0.69946 ( 8) hydrogen bonds : bond 0.02924 ( 315) hydrogen bonds : angle 4.68710 ( 915) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.344 Fit side-chains REVERT: A 185 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7548 (pm20) REVERT: A 283 GLU cc_start: 0.8254 (pm20) cc_final: 0.8021 (pp20) REVERT: A 321 TYR cc_start: 0.8578 (m-80) cc_final: 0.8199 (m-80) REVERT: H 41 ARG cc_start: 0.8530 (ptt180) cc_final: 0.7901 (ptm160) REVERT: B 75 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7189 (p90) REVERT: B 314 ILE cc_start: 0.7871 (mm) cc_final: 0.7513 (mp) REVERT: B 321 TYR cc_start: 0.8475 (m-80) cc_final: 0.8079 (m-80) REVERT: I 41 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7963 (ptt180) REVERT: M 28 GLN cc_start: 0.7240 (mp10) cc_final: 0.6886 (mp10) outliers start: 38 outliers final: 25 residues processed: 154 average time/residue: 0.0706 time to fit residues: 15.7999 Evaluate side-chains 150 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain V residue 353 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 52 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 109 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN L 38 GLN B 130 GLN I 80 ASN M 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.141467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.114361 restraints weight = 14633.952| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.98 r_work: 0.3366 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8921 Z= 0.177 Angle : 0.598 7.258 12154 Z= 0.304 Chirality : 0.045 0.142 1399 Planarity : 0.004 0.040 1538 Dihedral : 5.834 61.497 1252 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.98 % Allowed : 17.22 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.26), residues: 1112 helix: 0.07 (0.92), residues: 36 sheet: -0.05 (0.22), residues: 574 loop : 0.06 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 22 TYR 0.013 0.002 TYR A 238 PHE 0.017 0.002 PHE B 277 TRP 0.012 0.002 TRP H 50 HIS 0.005 0.001 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 8917) covalent geometry : angle 0.59775 (12146) SS BOND : bond 0.00543 ( 4) SS BOND : angle 0.71490 ( 8) hydrogen bonds : bond 0.03207 ( 315) hydrogen bonds : angle 4.82285 ( 915) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.291 Fit side-chains REVERT: A 283 GLU cc_start: 0.8413 (pm20) cc_final: 0.8121 (pp20) REVERT: A 321 TYR cc_start: 0.8667 (m-80) cc_final: 0.8367 (m-80) REVERT: H 41 ARG cc_start: 0.8660 (ptt180) cc_final: 0.7970 (ptm160) REVERT: B 75 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7677 (p90) REVERT: B 314 ILE cc_start: 0.7878 (mm) cc_final: 0.7432 (mp) REVERT: B 321 TYR cc_start: 0.8456 (m-80) cc_final: 0.8049 (m-80) REVERT: I 41 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8049 (ptt180) REVERT: M 28 GLN cc_start: 0.7191 (mp10) cc_final: 0.6838 (mp10) outliers start: 37 outliers final: 26 residues processed: 157 average time/residue: 0.0687 time to fit residues: 15.6811 Evaluate side-chains 154 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.4980 chunk 101 optimal weight: 0.0570 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 35 optimal weight: 0.0770 chunk 89 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN L 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.145167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119234 restraints weight = 13716.022| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.70 r_work: 0.3431 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8921 Z= 0.108 Angle : 0.554 6.509 12154 Z= 0.282 Chirality : 0.043 0.153 1399 Planarity : 0.004 0.039 1538 Dihedral : 5.553 63.899 1252 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.01 % Allowed : 18.41 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.26), residues: 1112 helix: 0.25 (0.94), residues: 36 sheet: 0.04 (0.22), residues: 576 loop : 0.16 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 22 TYR 0.012 0.001 TYR L 37 PHE 0.023 0.001 PHE B 87 TRP 0.010 0.001 TRP I 50 HIS 0.002 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8917) covalent geometry : angle 0.55448 (12146) SS BOND : bond 0.00428 ( 4) SS BOND : angle 0.52333 ( 8) hydrogen bonds : bond 0.02770 ( 315) hydrogen bonds : angle 4.61444 ( 915) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.203 Fit side-chains REVERT: A 185 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7564 (pm20) REVERT: A 321 TYR cc_start: 0.8578 (m-80) cc_final: 0.8233 (m-80) REVERT: H 41 ARG cc_start: 0.8543 (ptt180) cc_final: 0.7802 (ptm160) REVERT: H 87 ASN cc_start: 0.7745 (m-40) cc_final: 0.7517 (m-40) REVERT: H 93 ASP cc_start: 0.5768 (m-30) cc_final: 0.5415 (m-30) REVERT: H 98 TYR cc_start: 0.8518 (m-80) cc_final: 0.8088 (m-80) REVERT: L 19 ARG cc_start: 0.8227 (ttp80) cc_final: 0.7391 (ttt90) REVERT: B 75 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7306 (p90) REVERT: B 242 CYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7901 (p) REVERT: B 314 ILE cc_start: 0.7875 (mm) cc_final: 0.7470 (mp) REVERT: B 321 TYR cc_start: 0.8466 (m-80) cc_final: 0.8040 (m-80) REVERT: I 41 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7953 (ptt180) REVERT: M 28 GLN cc_start: 0.7369 (mp10) cc_final: 0.7050 (mp10) outliers start: 28 outliers final: 18 residues processed: 156 average time/residue: 0.0717 time to fit residues: 16.0309 Evaluate side-chains 149 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 0.0870 chunk 73 optimal weight: 3.9990 chunk 61 optimal weight: 0.0030 chunk 67 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.4568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN L 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.143881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.117029 restraints weight = 14422.232| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.95 r_work: 0.3426 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8921 Z= 0.127 Angle : 0.569 6.842 12154 Z= 0.290 Chirality : 0.044 0.149 1399 Planarity : 0.004 0.039 1538 Dihedral : 5.581 63.710 1252 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.69 % Allowed : 19.27 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.26), residues: 1112 helix: 0.29 (0.94), residues: 36 sheet: 0.11 (0.22), residues: 574 loop : 0.15 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 22 TYR 0.013 0.001 TYR L 37 PHE 0.013 0.001 PHE B 277 TRP 0.013 0.001 TRP H 39 HIS 0.003 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8917) covalent geometry : angle 0.56901 (12146) SS BOND : bond 0.00400 ( 4) SS BOND : angle 1.07654 ( 8) hydrogen bonds : bond 0.02816 ( 315) hydrogen bonds : angle 4.60583 ( 915) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.321 Fit side-chains REVERT: A 181 GLN cc_start: 0.8524 (tt0) cc_final: 0.8206 (tm-30) REVERT: A 320 SER cc_start: 0.7886 (m) cc_final: 0.7651 (p) REVERT: A 321 TYR cc_start: 0.8601 (m-80) cc_final: 0.8297 (m-80) REVERT: H 41 ARG cc_start: 0.8633 (ptt180) cc_final: 0.7875 (ptm160) REVERT: H 87 ASN cc_start: 0.7743 (m-40) cc_final: 0.7482 (m-40) REVERT: H 93 ASP cc_start: 0.5962 (m-30) cc_final: 0.5582 (m-30) REVERT: L 19 ARG cc_start: 0.8288 (ttp80) cc_final: 0.7411 (ttt90) REVERT: L 82 GLU cc_start: 0.7819 (pm20) cc_final: 0.7390 (pm20) REVERT: B 75 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7279 (p90) REVERT: B 242 CYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7934 (p) REVERT: B 314 ILE cc_start: 0.7911 (mm) cc_final: 0.7480 (mp) REVERT: B 321 TYR cc_start: 0.8402 (m-80) cc_final: 0.7973 (m-80) REVERT: I 41 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7956 (ptt180) REVERT: M 28 GLN cc_start: 0.7425 (mp10) cc_final: 0.7104 (mp10) outliers start: 25 outliers final: 20 residues processed: 144 average time/residue: 0.0687 time to fit residues: 14.2027 Evaluate side-chains 149 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain M residue 2 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 4 optimal weight: 0.0670 chunk 66 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 HIS L 28 GLN B 30 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.110176 restraints weight = 14770.507| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.00 r_work: 0.3315 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 8921 Z= 0.289 Angle : 0.693 7.975 12154 Z= 0.357 Chirality : 0.047 0.146 1399 Planarity : 0.004 0.039 1538 Dihedral : 6.139 60.515 1252 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.01 % Allowed : 18.84 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.26), residues: 1112 helix: 2.23 (1.03), residues: 24 sheet: -0.28 (0.22), residues: 580 loop : 0.07 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 22 TYR 0.022 0.002 TYR L 37 PHE 0.023 0.003 PHE B 87 TRP 0.017 0.002 TRP H 50 HIS 0.006 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00682 ( 8917) covalent geometry : angle 0.69303 (12146) SS BOND : bond 0.00602 ( 4) SS BOND : angle 1.11142 ( 8) hydrogen bonds : bond 0.03600 ( 315) hydrogen bonds : angle 5.13481 ( 915) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.357 Fit side-chains REVERT: A 181 GLN cc_start: 0.8612 (tt0) cc_final: 0.8149 (tm-30) REVERT: A 321 TYR cc_start: 0.8529 (m-80) cc_final: 0.8289 (m-80) REVERT: H 87 ASN cc_start: 0.8005 (m-40) cc_final: 0.7758 (m-40) REVERT: H 93 ASP cc_start: 0.6210 (m-30) cc_final: 0.5769 (m-30) REVERT: L 82 GLU cc_start: 0.7764 (pm20) cc_final: 0.7337 (pm20) REVERT: B 177 ARG cc_start: 0.7746 (tmm160) cc_final: 0.7403 (tmm160) REVERT: B 242 CYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7934 (p) REVERT: B 314 ILE cc_start: 0.7810 (mm) cc_final: 0.7420 (mp) REVERT: B 321 TYR cc_start: 0.8481 (m-80) cc_final: 0.8058 (m-80) REVERT: I 8 VAL cc_start: 0.8583 (t) cc_final: 0.8300 (m) REVERT: I 41 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8012 (ptt180) REVERT: M 28 GLN cc_start: 0.7210 (mp10) cc_final: 0.6820 (mp10) outliers start: 28 outliers final: 19 residues processed: 144 average time/residue: 0.0816 time to fit residues: 17.0458 Evaluate side-chains 141 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 chunk 107 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 24 optimal weight: 0.0030 chunk 56 optimal weight: 1.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.141115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.114271 restraints weight = 14325.071| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.95 r_work: 0.3374 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8921 Z= 0.140 Angle : 0.595 7.560 12154 Z= 0.304 Chirality : 0.044 0.148 1399 Planarity : 0.004 0.041 1538 Dihedral : 5.901 63.701 1252 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.15 % Allowed : 20.24 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.26), residues: 1112 helix: 2.56 (1.06), residues: 24 sheet: -0.17 (0.22), residues: 574 loop : 0.09 (0.30), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 22 TYR 0.015 0.001 TYR L 37 PHE 0.022 0.002 PHE B 87 TRP 0.012 0.001 TRP H 50 HIS 0.003 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8917) covalent geometry : angle 0.59492 (12146) SS BOND : bond 0.00378 ( 4) SS BOND : angle 1.13669 ( 8) hydrogen bonds : bond 0.02965 ( 315) hydrogen bonds : angle 4.87010 ( 915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1638.46 seconds wall clock time: 28 minutes 50.81 seconds (1730.81 seconds total)