Starting phenix.real_space_refine on Mon May 12 06:18:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8z_36082/05_2025/8j8z_36082.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8z_36082/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j8z_36082/05_2025/8j8z_36082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8z_36082/05_2025/8j8z_36082.map" model { file = "/net/cci-nas-00/data/ceres_data/8j8z_36082/05_2025/8j8z_36082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8z_36082/05_2025/8j8z_36082.cif" } resolution = 3.4 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= 0.025 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 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: {'GLU:plan': 1, 'ARG: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, 'GLU:plan': 7, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 3} 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: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG: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: 5.38, per 1000 atoms: 0.62 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: 2.10 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.25 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: 2.52 Time building geometry restraints manager: 2.45 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: 1.290 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 22.100 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.810 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.011 0.002 TRP I 50 HIS 0.006 0.001 HIS A 159 PHE 0.012 0.001 PHE M 99 TYR 0.016 0.001 TYR L 94 ARG 0.005 0.001 ARG M 19 Details of bonding type rmsd hydrogen bonds : bond 0.22960 ( 315) hydrogen bonds : angle 8.89053 ( 915) SS BOND : bond 0.00382 ( 4) SS BOND : angle 0.42120 ( 8) covalent geometry : bond 0.00553 ( 8917) covalent geometry : angle 0.73047 (12146) *********************** 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 : 1.062 Fit side-chains REVERT: H 33 TYR cc_start: 0.8669 (m-80) cc_final: 0.8368 (m-80) REVERT: H 49 GLU cc_start: 0.8121 (tt0) cc_final: 0.7808 (pt0) REVERT: L 106 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7067 (mt-10) REVERT: B 272 TYR cc_start: 0.7460 (m-80) cc_final: 0.7086 (m-10) REVERT: B 321 TYR cc_start: 0.8221 (m-80) cc_final: 0.7774 (m-80) REVERT: I 33 TYR cc_start: 0.8730 (m-80) cc_final: 0.8390 (m-80) REVERT: I 79 LYS cc_start: 0.8276 (ptpp) cc_final: 0.8071 (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: 0.2188 time to fit residues: 44.4525 Evaluate side-chains 129 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.139939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112598 restraints weight = 14480.480| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.97 r_work: 0.3335 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8921 Z= 0.200 Angle : 0.672 6.433 12154 Z= 0.346 Chirality : 0.047 0.149 1399 Planarity : 0.004 0.037 1538 Dihedral : 6.338 54.885 1261 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.72 % Allowed : 14.75 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.33 (0.26), residues: 1112 helix: -0.52 (0.86), residues: 36 sheet: -0.18 (0.22), residues: 554 loop : -0.05 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 50 HIS 0.005 0.001 HIS A 159 PHE 0.016 0.002 PHE A 268 TYR 0.014 0.002 TYR A 238 ARG 0.007 0.001 ARG H 22 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 315) hydrogen bonds : angle 5.64723 ( 915) SS BOND : bond 0.00558 ( 4) SS BOND : angle 0.71121 ( 8) covalent geometry : bond 0.00473 ( 8917) covalent geometry : angle 0.67226 (12146) *********************** 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: 16 poor density : 142 time to evaluate : 1.057 Fit side-chains REVERT: A 144 TYR cc_start: 0.7843 (m-80) cc_final: 0.7195 (m-10) REVERT: A 255 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8190 (tmm) REVERT: A 321 TYR cc_start: 0.8499 (m-80) cc_final: 0.8194 (m-80) REVERT: H 33 TYR cc_start: 0.8765 (m-80) cc_final: 0.8416 (m-80) REVERT: H 49 GLU cc_start: 0.8244 (tt0) cc_final: 0.7792 (pt0) REVERT: L 5 MET cc_start: 0.9074 (mmt) cc_final: 0.8265 (mmt) REVERT: L 83 ASP cc_start: 0.6863 (m-30) cc_final: 0.6570 (m-30) REVERT: L 106 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7049 (mt-10) REVERT: B 255 MET cc_start: 0.8221 (tmm) cc_final: 0.7974 (tmm) REVERT: B 321 TYR cc_start: 0.8509 (m-80) cc_final: 0.8188 (m-80) REVERT: I 33 TYR cc_start: 0.8720 (m-80) cc_final: 0.8338 (m-80) REVERT: I 87 ASN cc_start: 0.7970 (m-40) cc_final: 0.7744 (m-40) REVERT: M 28 GLN cc_start: 0.7375 (mp10) cc_final: 0.6997 (mp10) REVERT: M 56 TYR cc_start: 0.8483 (t80) cc_final: 0.8189 (t80) outliers start: 16 outliers final: 10 residues processed: 151 average time/residue: 0.2072 time to fit residues: 43.5278 Evaluate side-chains 127 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLU 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 73 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU 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 51 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 59 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 38 GLN M 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.140715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113457 restraints weight = 14661.244| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.99 r_work: 0.3353 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8921 Z= 0.164 Angle : 0.617 5.331 12154 Z= 0.318 Chirality : 0.046 0.154 1399 Planarity : 0.004 0.036 1538 Dihedral : 6.071 57.803 1252 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.23 % Allowed : 14.85 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.34 (0.26), residues: 1112 helix: -0.29 (0.89), residues: 36 sheet: -0.23 (0.22), residues: 572 loop : -0.01 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 50 HIS 0.004 0.001 HIS B 353 PHE 0.014 0.002 PHE A 268 TYR 0.015 0.001 TYR B 272 ARG 0.008 0.000 ARG H 22 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 315) hydrogen bonds : angle 5.24692 ( 915) SS BOND : bond 0.00542 ( 4) SS BOND : angle 0.69288 ( 8) covalent geometry : bond 0.00387 ( 8917) covalent geometry : angle 0.61718 (12146) *********************** 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: 30 poor density : 140 time to evaluate : 0.967 Fit side-chains REVERT: A 62 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6780 (ptp90) REVERT: A 321 TYR cc_start: 0.8590 (m-80) cc_final: 0.8196 (m-80) REVERT: H 22 ARG cc_start: 0.8014 (ttt90) cc_final: 0.7715 (ttt90) REVERT: H 33 TYR cc_start: 0.8519 (m-80) cc_final: 0.8290 (m-80) REVERT: H 41 ARG cc_start: 0.8659 (ptt180) cc_final: 0.7990 (ptm160) REVERT: H 87 ASN cc_start: 0.7801 (m-40) cc_final: 0.7552 (m-40) REVERT: B 75 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7637 (p90) REVERT: B 255 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7893 (tmm) REVERT: B 314 ILE cc_start: 0.7755 (mm) cc_final: 0.7325 (mp) REVERT: B 321 TYR cc_start: 0.8449 (m-80) cc_final: 0.8142 (m-80) REVERT: I 33 TYR cc_start: 0.8684 (m-80) cc_final: 0.8306 (m-80) REVERT: I 41 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8030 (ptt180) REVERT: I 89 LEU cc_start: 0.8035 (mm) cc_final: 0.7703 (mm) REVERT: I 93 ASP cc_start: 0.7443 (p0) cc_final: 0.7240 (p0) REVERT: M 28 GLN cc_start: 0.7131 (mp10) cc_final: 0.6767 (mp10) outliers start: 30 outliers final: 17 residues processed: 159 average time/residue: 0.2013 time to fit residues: 44.4973 Evaluate side-chains 145 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 185 GLU 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 20 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 251 CYS 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 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 107 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 0.0670 chunk 67 optimal weight: 0.0770 chunk 7 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 0.1980 chunk 86 optimal weight: 2.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.145148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.118827 restraints weight = 13770.706| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.72 r_work: 0.3425 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2061 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= 0.117 Angle : 0.561 5.290 12154 Z= 0.289 Chirality : 0.044 0.139 1399 Planarity : 0.004 0.038 1538 Dihedral : 5.849 60.498 1252 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.69 % Allowed : 16.90 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.22 (0.26), residues: 1112 helix: -0.17 (0.90), residues: 36 sheet: -0.09 (0.22), residues: 568 loop : -0.02 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 50 HIS 0.003 0.001 HIS B 353 PHE 0.015 0.001 PHE B 87 TYR 0.010 0.001 TYR I 83 ARG 0.005 0.000 ARG H 22 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 315) hydrogen bonds : angle 4.92192 ( 915) SS BOND : bond 0.00497 ( 4) SS BOND : angle 0.62222 ( 8) covalent geometry : bond 0.00273 ( 8917) covalent geometry : angle 0.56054 (12146) *********************** 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 168 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.043 Fit side-chains REVERT: A 321 TYR cc_start: 0.8623 (m-80) cc_final: 0.8275 (m-80) REVERT: H 22 ARG cc_start: 0.7838 (ttt90) cc_final: 0.7560 (ttt90) REVERT: H 33 TYR cc_start: 0.8516 (m-80) cc_final: 0.8285 (m-80) REVERT: H 41 ARG cc_start: 0.8498 (ptt180) cc_final: 0.7891 (ptm160) REVERT: H 87 ASN cc_start: 0.7785 (m-40) cc_final: 0.7531 (m-40) REVERT: B 75 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7341 (p90) REVERT: B 255 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.8014 (tmm) REVERT: B 314 ILE cc_start: 0.7889 (mm) cc_final: 0.7511 (mp) REVERT: B 321 TYR cc_start: 0.8486 (m-80) cc_final: 0.8085 (m-80) REVERT: I 33 TYR cc_start: 0.8600 (m-80) cc_final: 0.8320 (m-80) REVERT: I 41 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8061 (ptt180) REVERT: I 89 LEU cc_start: 0.7928 (mm) cc_final: 0.7612 (mm) REVERT: I 93 ASP cc_start: 0.7411 (p0) cc_final: 0.7197 (p0) REVERT: M 28 GLN cc_start: 0.7089 (mp10) cc_final: 0.6718 (mp10) outliers start: 25 outliers final: 11 residues processed: 158 average time/residue: 0.2000 time to fit residues: 44.1834 Evaluate side-chains 137 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain B residue 41 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 255 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 62 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 B 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.140081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112938 restraints weight = 14541.836| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.96 r_work: 0.3360 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8921 Z= 0.198 Angle : 0.629 8.704 12154 Z= 0.322 Chirality : 0.045 0.139 1399 Planarity : 0.004 0.039 1538 Dihedral : 6.043 59.523 1252 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.20 % Allowed : 17.22 % 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 (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: -0.40 (0.26), residues: 1112 helix: -0.28 (0.88), residues: 36 sheet: -0.32 (0.21), residues: 580 loop : 0.03 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 50 HIS 0.004 0.001 HIS B 353 PHE 0.013 0.002 PHE L 99 TYR 0.014 0.002 TYR A 238 ARG 0.005 0.000 ARG H 22 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 315) hydrogen bonds : angle 5.01999 ( 915) SS BOND : bond 0.00603 ( 4) SS BOND : angle 0.76889 ( 8) covalent geometry : bond 0.00467 ( 8917) covalent geometry : angle 0.62887 (12146) *********************** 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: 39 poor density : 128 time to evaluate : 0.935 Fit side-chains REVERT: A 62 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6788 (ptp90) REVERT: A 321 TYR cc_start: 0.8590 (m-80) cc_final: 0.8264 (m-80) REVERT: H 33 TYR cc_start: 0.8530 (m-80) cc_final: 0.8176 (m-80) REVERT: H 87 ASN cc_start: 0.7870 (m-40) cc_final: 0.7629 (m-40) REVERT: H 93 ASP cc_start: 0.6320 (m-30) cc_final: 0.5879 (m-30) REVERT: B 75 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.7929 (p90) REVERT: B 314 ILE cc_start: 0.7960 (mm) cc_final: 0.7611 (mp) REVERT: B 321 TYR cc_start: 0.8431 (m-80) cc_final: 0.8071 (m-80) REVERT: I 33 TYR cc_start: 0.8686 (m-80) cc_final: 0.8348 (m-80) REVERT: I 41 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8066 (ptt180) REVERT: I 89 LEU cc_start: 0.7850 (mm) cc_final: 0.7583 (mm) REVERT: I 93 ASP cc_start: 0.7495 (p0) cc_final: 0.7284 (p0) REVERT: M 28 GLN cc_start: 0.7226 (mp10) cc_final: 0.6839 (mp10) outliers start: 39 outliers final: 20 residues processed: 156 average time/residue: 0.1909 time to fit residues: 42.1232 Evaluate side-chains 146 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL 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 111 HIS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU 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 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 38 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.140694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.113675 restraints weight = 14419.873| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.94 r_work: 0.3361 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8921 Z= 0.168 Angle : 0.607 7.654 12154 Z= 0.308 Chirality : 0.045 0.147 1399 Planarity : 0.004 0.039 1538 Dihedral : 5.988 61.084 1252 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.66 % Allowed : 17.98 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.26 (0.26), residues: 1112 helix: 2.02 (1.01), residues: 24 sheet: -0.28 (0.21), residues: 574 loop : 0.05 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 50 HIS 0.004 0.001 HIS B 353 PHE 0.016 0.002 PHE B 87 TYR 0.013 0.001 TYR B 272 ARG 0.010 0.000 ARG H 22 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 315) hydrogen bonds : angle 4.96770 ( 915) SS BOND : bond 0.00522 ( 4) SS BOND : angle 0.66023 ( 8) covalent geometry : bond 0.00395 ( 8917) covalent geometry : angle 0.60663 (12146) *********************** 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 167 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 1.071 Fit side-chains REVERT: A 62 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6778 (ptp90) REVERT: A 321 TYR cc_start: 0.8584 (m-80) cc_final: 0.8300 (m-80) REVERT: H 33 TYR cc_start: 0.8735 (m-80) cc_final: 0.8456 (m-80) REVERT: H 87 ASN cc_start: 0.7854 (m-40) cc_final: 0.7574 (m-40) REVERT: H 93 ASP cc_start: 0.6200 (m-30) cc_final: 0.5929 (m-30) REVERT: H 101 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8497 (tmm-80) REVERT: B 75 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7713 (p90) REVERT: B 177 ARG cc_start: 0.7850 (tmm160) cc_final: 0.7605 (tmm160) REVERT: B 242 CYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7858 (p) REVERT: B 314 ILE cc_start: 0.7820 (mm) cc_final: 0.7397 (mp) REVERT: B 321 TYR cc_start: 0.8431 (m-80) cc_final: 0.8031 (m-80) REVERT: I 33 TYR cc_start: 0.8671 (m-80) cc_final: 0.8363 (m-80) REVERT: I 41 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8012 (ptt180) REVERT: I 89 LEU cc_start: 0.7806 (mm) cc_final: 0.7524 (mm) REVERT: I 93 ASP cc_start: 0.7493 (p0) cc_final: 0.7282 (p0) REVERT: M 28 GLN cc_start: 0.7276 (mp10) cc_final: 0.6925 (mp10) outliers start: 34 outliers final: 24 residues processed: 157 average time/residue: 0.1994 time to fit residues: 43.8047 Evaluate side-chains 155 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 62 ARG 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 83 TYR Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 5 MET 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 42 LEU 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 242 CYS 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 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 34 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 43 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 85 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 = 0.3870 r_free = 0.3870 target = 0.141526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114574 restraints weight = 14486.818| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.95 r_work: 0.3376 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8921 Z= 0.143 Angle : 0.585 6.998 12154 Z= 0.298 Chirality : 0.044 0.144 1399 Planarity : 0.004 0.040 1538 Dihedral : 5.892 61.855 1252 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.34 % Allowed : 18.62 % 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 (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: -0.21 (0.26), residues: 1112 helix: 2.16 (1.02), residues: 24 sheet: -0.25 (0.22), residues: 574 loop : 0.08 (0.30), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 50 HIS 0.004 0.001 HIS B 353 PHE 0.011 0.001 PHE A 268 TYR 0.012 0.001 TYR A 272 ARG 0.008 0.000 ARG H 22 Details of bonding type rmsd hydrogen bonds : bond 0.03048 ( 315) hydrogen bonds : angle 4.87875 ( 915) SS BOND : bond 0.00446 ( 4) SS BOND : angle 0.81700 ( 8) covalent geometry : bond 0.00337 ( 8917) covalent geometry : angle 0.58472 (12146) *********************** 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 160 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.962 Fit side-chains REVERT: A 181 GLN cc_start: 0.8662 (tt0) cc_final: 0.8313 (tm-30) REVERT: A 229 LYS cc_start: 0.6712 (mttt) cc_final: 0.6486 (mmtp) REVERT: A 321 TYR cc_start: 0.8598 (m-80) cc_final: 0.8300 (m-80) REVERT: H 22 ARG cc_start: 0.7741 (ttt90) cc_final: 0.7469 (ttt90) REVERT: H 33 TYR cc_start: 0.8499 (m-80) cc_final: 0.8136 (m-80) REVERT: H 87 ASN cc_start: 0.7834 (m-40) cc_final: 0.7593 (m-40) REVERT: H 93 ASP cc_start: 0.6075 (m-30) cc_final: 0.5825 (m-30) REVERT: H 101 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8527 (tmm-80) REVERT: B 75 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7715 (p90) REVERT: B 314 ILE cc_start: 0.7795 (mm) cc_final: 0.7458 (mp) REVERT: B 321 TYR cc_start: 0.8455 (m-80) cc_final: 0.8035 (m-80) REVERT: I 33 TYR cc_start: 0.8646 (m-80) cc_final: 0.8325 (m-80) REVERT: I 41 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7974 (ptt180) REVERT: I 89 LEU cc_start: 0.7665 (mm) cc_final: 0.7382 (mm) REVERT: M 28 GLN cc_start: 0.7309 (mp10) cc_final: 0.6910 (mp10) outliers start: 31 outliers final: 23 residues processed: 147 average time/residue: 0.2100 time to fit residues: 42.1729 Evaluate side-chains 152 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 5 MET 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 42 LEU 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 120 THR Chi-restraints excluded: chain I residue 121 VAL 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 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 22 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 85 GLN L 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.140754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.113611 restraints weight = 14728.764| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.99 r_work: 0.3370 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8921 Z= 0.168 Angle : 0.603 7.025 12154 Z= 0.308 Chirality : 0.045 0.149 1399 Planarity : 0.004 0.039 1538 Dihedral : 5.890 61.711 1252 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.34 % Allowed : 18.62 % 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 (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: -0.25 (0.26), residues: 1112 helix: 2.23 (1.03), residues: 24 sheet: -0.28 (0.22), residues: 574 loop : 0.06 (0.30), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 50 HIS 0.004 0.001 HIS B 353 PHE 0.017 0.002 PHE B 87 TYR 0.016 0.001 TYR B 54 ARG 0.009 0.000 ARG H 22 Details of bonding type rmsd hydrogen bonds : bond 0.03132 ( 315) hydrogen bonds : angle 4.88399 ( 915) SS BOND : bond 0.00520 ( 4) SS BOND : angle 0.47297 ( 8) covalent geometry : bond 0.00397 ( 8917) covalent geometry : angle 0.60263 (12146) *********************** 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 157 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.188 Fit side-chains REVERT: A 181 GLN cc_start: 0.8668 (tt0) cc_final: 0.8194 (tm-30) REVERT: A 229 LYS cc_start: 0.6684 (mttt) cc_final: 0.6473 (mmtp) REVERT: A 321 TYR cc_start: 0.8620 (m-80) cc_final: 0.8332 (m-80) REVERT: H 22 ARG cc_start: 0.7803 (ttt90) cc_final: 0.7543 (ttt90) REVERT: H 33 TYR cc_start: 0.8562 (m-80) cc_final: 0.8187 (m-80) REVERT: H 87 ASN cc_start: 0.7837 (m-40) cc_final: 0.7608 (m-40) REVERT: H 93 ASP cc_start: 0.6213 (m-30) cc_final: 0.5826 (m-30) REVERT: H 101 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8538 (tmm-80) REVERT: L 83 ASP cc_start: 0.7462 (m-30) cc_final: 0.7232 (m-30) REVERT: B 75 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.7771 (p90) REVERT: B 314 ILE cc_start: 0.7804 (mm) cc_final: 0.7400 (mp) REVERT: B 321 TYR cc_start: 0.8440 (m-80) cc_final: 0.8041 (m-80) REVERT: I 33 TYR cc_start: 0.8658 (m-80) cc_final: 0.8357 (m-80) REVERT: I 41 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7972 (ptt180) REVERT: I 89 LEU cc_start: 0.7422 (mm) cc_final: 0.7176 (mm) REVERT: M 28 GLN cc_start: 0.7218 (mp10) cc_final: 0.6865 (mp10) outliers start: 31 outliers final: 23 residues processed: 147 average time/residue: 0.1874 time to fit residues: 38.9258 Evaluate side-chains 151 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 5 MET 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 42 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 B 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.140265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.112361 restraints weight = 14682.227| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.02 r_work: 0.3345 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8921 Z= 0.178 Angle : 0.609 7.357 12154 Z= 0.311 Chirality : 0.045 0.146 1399 Planarity : 0.004 0.041 1538 Dihedral : 5.918 61.501 1252 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % 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 (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: -0.26 (0.26), residues: 1112 helix: 2.30 (1.04), residues: 24 sheet: -0.31 (0.22), residues: 574 loop : 0.07 (0.30), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.004 0.001 HIS B 353 PHE 0.012 0.002 PHE L 99 TYR 0.014 0.002 TYR B 54 ARG 0.008 0.000 ARG H 22 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 315) hydrogen bonds : angle 4.92992 ( 915) SS BOND : bond 0.00578 ( 4) SS BOND : angle 0.52923 ( 8) covalent geometry : bond 0.00419 ( 8917) covalent geometry : angle 0.60933 (12146) *********************** 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 159 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 181 GLN cc_start: 0.8666 (tt0) cc_final: 0.8172 (tm-30) REVERT: A 229 LYS cc_start: 0.6688 (mttt) cc_final: 0.6478 (mmtp) REVERT: A 321 TYR cc_start: 0.8626 (m-80) cc_final: 0.8337 (m-80) REVERT: H 33 TYR cc_start: 0.8561 (m-80) cc_final: 0.8238 (m-80) REVERT: H 87 ASN cc_start: 0.7887 (m-40) cc_final: 0.7637 (m-40) REVERT: H 93 ASP cc_start: 0.6212 (m-30) cc_final: 0.5817 (m-30) REVERT: H 101 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8542 (tmm-80) REVERT: L 82 GLU cc_start: 0.7633 (pm20) cc_final: 0.7282 (pm20) REVERT: B 75 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7956 (p90) REVERT: B 314 ILE cc_start: 0.7959 (mm) cc_final: 0.7673 (mp) REVERT: B 321 TYR cc_start: 0.8440 (m-80) cc_final: 0.8041 (m-80) REVERT: I 33 TYR cc_start: 0.8671 (m-80) cc_final: 0.8379 (m-80) REVERT: I 41 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7986 (ptt180) REVERT: I 89 LEU cc_start: 0.7345 (mm) cc_final: 0.7041 (mm) REVERT: M 28 GLN cc_start: 0.7222 (mp10) cc_final: 0.6826 (mp10) outliers start: 28 outliers final: 21 residues processed: 150 average time/residue: 0.1911 time to fit residues: 40.2313 Evaluate side-chains 152 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 5 MET 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 42 LEU 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 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 17 optimal weight: 0.0470 chunk 7 optimal weight: 1.9990 chunk 93 optimal weight: 0.0770 chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.142143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.115169 restraints weight = 14426.079| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.95 r_work: 0.3395 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8921 Z= 0.116 Angle : 0.580 8.237 12154 Z= 0.292 Chirality : 0.044 0.148 1399 Planarity : 0.004 0.040 1538 Dihedral : 5.750 63.498 1252 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.69 % Allowed : 19.16 % 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 (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: -0.13 (0.26), residues: 1112 helix: 2.45 (1.05), residues: 24 sheet: -0.19 (0.22), residues: 574 loop : 0.11 (0.30), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 50 HIS 0.003 0.001 HIS B 353 PHE 0.009 0.001 PHE A 268 TYR 0.013 0.001 TYR B 54 ARG 0.003 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.02857 ( 315) hydrogen bonds : angle 4.74566 ( 915) SS BOND : bond 0.00513 ( 4) SS BOND : angle 0.62705 ( 8) covalent geometry : bond 0.00273 ( 8917) covalent geometry : angle 0.57950 (12146) ********************** 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 156 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 1.073 Fit side-chains REVERT: A 181 GLN cc_start: 0.8556 (tt0) cc_final: 0.8063 (tm-30) REVERT: A 321 TYR cc_start: 0.8646 (m-80) cc_final: 0.8378 (m-80) REVERT: H 33 TYR cc_start: 0.8525 (m-80) cc_final: 0.8171 (m-80) REVERT: H 41 ARG cc_start: 0.8762 (ptt-90) cc_final: 0.7908 (ptm160) REVERT: H 87 ASN cc_start: 0.7867 (m-40) cc_final: 0.7628 (m-40) REVERT: H 93 ASP cc_start: 0.6051 (m-30) cc_final: 0.5656 (m-30) REVERT: L 82 GLU cc_start: 0.7640 (pm20) cc_final: 0.7278 (pm20) REVERT: B 75 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.7564 (p90) REVERT: B 177 ARG cc_start: 0.7434 (tmm160) cc_final: 0.7212 (tmm160) REVERT: B 314 ILE cc_start: 0.7714 (mm) cc_final: 0.7460 (mp) REVERT: B 321 TYR cc_start: 0.8441 (m-80) cc_final: 0.7997 (m-80) REVERT: I 33 TYR cc_start: 0.8685 (m-80) cc_final: 0.8425 (m-80) REVERT: I 41 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7977 (ptt180) REVERT: I 89 LEU cc_start: 0.7325 (mm) cc_final: 0.7051 (mm) REVERT: M 28 GLN cc_start: 0.7382 (mp10) cc_final: 0.7041 (mp10) outliers start: 25 outliers final: 19 residues processed: 148 average time/residue: 0.2045 time to fit residues: 42.2182 Evaluate side-chains 146 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 5 MET 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 42 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 109 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 85 GLN L 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.140828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113126 restraints weight = 14620.765| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.99 r_work: 0.3363 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8921 Z= 0.162 Angle : 0.605 7.900 12154 Z= 0.306 Chirality : 0.045 0.147 1399 Planarity : 0.004 0.040 1538 Dihedral : 5.818 62.898 1252 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.58 % Allowed : 19.70 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.19 (0.26), residues: 1112 helix: 2.43 (1.05), residues: 24 sheet: -0.22 (0.22), residues: 574 loop : 0.06 (0.30), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.004 0.001 HIS B 353 PHE 0.023 0.002 PHE B 87 TYR 0.014 0.001 TYR B 54 ARG 0.004 0.000 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.03057 ( 315) hydrogen bonds : angle 4.81035 ( 915) SS BOND : bond 0.00554 ( 4) SS BOND : angle 0.49397 ( 8) covalent geometry : bond 0.00384 ( 8917) covalent geometry : angle 0.60477 (12146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3794.50 seconds wall clock time: 66 minutes 48.59 seconds (4008.59 seconds total)