Starting phenix.real_space_refine on Fri Jul 25 06:54:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ja3_36124/07_2025/8ja3_36124.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ja3_36124/07_2025/8ja3_36124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ja3_36124/07_2025/8ja3_36124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ja3_36124/07_2025/8ja3_36124.map" model { file = "/net/cci-nas-00/data/ceres_data/8ja3_36124/07_2025/8ja3_36124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ja3_36124/07_2025/8ja3_36124.cif" } resolution = 3.94 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= 0.013 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 8 5.49 5 S 23 5.16 5 C 4537 2.51 5 N 1222 2.21 5 O 1340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7130 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2118 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 291} Chain breaks: 4 Unresolved non-hydrogen bonds: 409 Unresolved non-hydrogen angles: 501 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 12, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 5, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 233 Chain: "U" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 81 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'TPO:plan-1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 756 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 104} Chain breaks: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "M" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 680 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 52 Chain: "A" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2070 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 285} Chain breaks: 6 Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 494 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 5, 'HIS:plan': 4, 'PHE:plan': 3, 'GLU:plan': 16, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 224 Chain: "V" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 81 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'TPO:plan-1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 684 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 60 Chain: "L" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 660 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 94} Chain breaks: 2 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'PHE:plan': 1, 'ARG:plan': 2, 'TYR:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 55 Time building chain proxies: 5.20, per 1000 atoms: 0.73 Number of scatterers: 7130 At special positions: 0 Unit cell: (87.0348, 168.362, 79.9008, 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 23 16.00 P 8 15.00 O 1340 8.00 N 1222 7.00 C 4537 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 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=2.03 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 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: 2.08 Conformation dependent library (CDL) restraints added in 1.1 seconds 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1994 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 20 sheets defined 6.4% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.551A pdb=" N LYS B 94 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.587A pdb=" N LYS B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.880A pdb=" N ASN B 280 " --> pdb=" O PHE B 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 68 Processing helix chain 'I' and resid 77 through 79 No H-bonds generated for 'chain 'I' and resid 77 through 79' Processing helix chain 'I' and resid 90 through 94 removed outlier: 3.866A pdb=" N THR I 94 " --> pdb=" O ALA I 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.561A pdb=" N ARG A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.506A pdb=" N ARG A 282 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 35 Processing helix chain 'H' and resid 65 through 68 removed outlier: 3.503A pdb=" N LYS H 68 " --> pdb=" O ASP H 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 65 through 68' Processing helix chain 'H' and resid 77 through 79 No H-bonds generated for 'chain 'H' and resid 77 through 79' Processing sheet with id=AA1, first strand: chain 'B' and resid 9 through 12 removed outlier: 3.522A pdb=" N VAL B 41 " --> pdb=" O TYR B 113 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR B 113 " --> pdb=" O VAL B 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.890A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR B 58 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE B 80 " --> pdb=" O CYS B 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 187 removed outlier: 3.818A pdb=" N SER B 202 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B 218 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS B 270 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 207 through 208 removed outlier: 7.472A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY B 316 " --> pdb=" O CYS B 242 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 254 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN B 237 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ALA B 239 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LYS B 250 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE B 241 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLN B 248 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 7 through 10 removed outlier: 3.931A pdb=" N LEU I 23 " --> pdb=" O LEU I 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 61 through 63 removed outlier: 6.070A pdb=" N TRP I 50 " --> pdb=" O ARG I 41 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG I 41 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA I 52 " --> pdb=" O TRP I 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 5 through 8 removed outlier: 4.054A pdb=" N SER M 8 " --> pdb=" O THR M 23 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N THR M 23 " --> pdb=" O SER M 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.557A pdb=" N LEU M 12 " --> pdb=" O LYS M 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'M' and resid 54 through 55 removed outlier: 6.704A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TYR M 50 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN M 91 " --> pdb=" O THR M 98 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR M 98 " --> pdb=" O GLN M 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 113 through 117 removed outlier: 4.099A pdb=" N TYR A 113 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 41 " --> pdb=" O TYR A 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 26 through 28 removed outlier: 5.962A pdb=" N PHE A 27 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 80 " --> pdb=" O CYS A 59 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AB5, first strand: chain 'A' and resid 184 through 186 removed outlier: 3.964A pdb=" N GLU A 200 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL A 218 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS A 270 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.785A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS A 322 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 236 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 231 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLU A 257 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AB8, first strand: chain 'H' and resid 61 through 63 removed outlier: 5.722A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 6 through 8 removed outlier: 3.569A pdb=" N PHE L 72 " --> pdb=" O CYS L 24 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.779A pdb=" N LEU L 12 " --> pdb=" O LYS L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.424A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 627 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: 2.20 Time building geometry restraints manager: 2.23 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: 2126 1.33 - 1.46: 1243 1.46 - 1.58: 3860 1.58 - 1.70: 17 1.70 - 1.82: 28 Bond restraints: 7274 Sorted by residual: bond pdb=" C LEU A 33 " pdb=" N VAL A 34 " ideal model delta sigma weight residual 1.330 1.470 -0.140 1.97e-02 2.58e+03 5.04e+01 bond pdb=" OG1 TPO V 463 " pdb=" P TPO V 463 " ideal model delta sigma weight residual 1.717 1.598 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" OG1 TPO V 466 " pdb=" P TPO V 466 " ideal model delta sigma weight residual 1.717 1.602 0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" OG1 TPO U 463 " pdb=" P TPO U 463 " ideal model delta sigma weight residual 1.717 1.602 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" OG1 TPO U 466 " pdb=" P TPO U 466 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.01e+01 ... (remaining 7269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 9854 3.20 - 6.40: 144 6.40 - 9.60: 5 9.60 - 12.80: 3 12.80 - 16.00: 2 Bond angle restraints: 10008 Sorted by residual: angle pdb=" C LEU A 33 " pdb=" N VAL A 34 " pdb=" CA VAL A 34 " ideal model delta sigma weight residual 122.91 133.35 -10.44 1.43e+00 4.89e-01 5.33e+01 angle pdb=" N SEP U 465 " pdb=" CA SEP U 465 " pdb=" C SEP U 465 " ideal model delta sigma weight residual 111.20 127.20 -16.00 2.80e+00 1.28e-01 3.27e+01 angle pdb=" O LEU A 33 " pdb=" C LEU A 33 " pdb=" N VAL A 34 " ideal model delta sigma weight residual 123.17 117.27 5.90 1.21e+00 6.83e-01 2.37e+01 angle pdb=" N ARG U 464 " pdb=" CA ARG U 464 " pdb=" C ARG U 464 " ideal model delta sigma weight residual 111.00 124.31 -13.31 2.80e+00 1.28e-01 2.26e+01 angle pdb=" C SER L 31 " pdb=" CA SER L 31 " pdb=" CB SER L 31 " ideal model delta sigma weight residual 116.54 111.36 5.18 1.15e+00 7.56e-01 2.03e+01 ... (remaining 10003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 3891 17.26 - 34.53: 300 34.53 - 51.79: 53 51.79 - 69.05: 14 69.05 - 86.31: 4 Dihedral angle restraints: 4262 sinusoidal: 1196 harmonic: 3066 Sorted by residual: dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 39.38 53.62 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CA ARG B 169 " pdb=" C ARG B 169 " pdb=" N LYS B 170 " pdb=" CA LYS B 170 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA LEU I 110 " pdb=" C LEU I 110 " pdb=" N ASP I 111 " pdb=" CA ASP I 111 " ideal model delta harmonic sigma weight residual 180.00 -155.39 -24.61 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 4259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1036 0.069 - 0.137: 166 0.137 - 0.206: 11 0.206 - 0.275: 3 0.275 - 0.344: 1 Chirality restraints: 1217 Sorted by residual: chirality pdb=" CA SEP U 465 " pdb=" N SEP U 465 " pdb=" C SEP U 465 " pdb=" CB SEP U 465 " both_signs ideal model delta sigma weight residual False 2.50 2.16 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA ARG U 464 " pdb=" N ARG U 464 " pdb=" C ARG U 464 " pdb=" CB ARG U 464 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB TPO U 463 " pdb=" CA TPO U 463 " pdb=" OG1 TPO U 463 " pdb=" CG2 TPO U 463 " both_signs ideal model delta sigma weight residual False 2.48 2.72 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1214 not shown) Planarity restraints: 1284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER I 102 " -0.024 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" C SER I 102 " 0.082 2.00e-02 2.50e+03 pdb=" O SER I 102 " -0.030 2.00e-02 2.50e+03 pdb=" N ARG I 103 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU U 462 " -0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C LEU U 462 " 0.081 2.00e-02 2.50e+03 pdb=" O LEU U 462 " -0.031 2.00e-02 2.50e+03 pdb=" N TPO U 463 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SEP U 459 " 0.019 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C SEP U 459 " -0.064 2.00e-02 2.50e+03 pdb=" O SEP U 459 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU U 460 " 0.021 2.00e-02 2.50e+03 ... (remaining 1281 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1427 2.77 - 3.30: 6975 3.30 - 3.84: 11066 3.84 - 4.37: 12499 4.37 - 4.90: 21638 Nonbonded interactions: 53605 Sorted by model distance: nonbonded pdb=" N GLY L 17 " pdb=" O LEU L 79 " model vdw 2.242 3.120 nonbonded pdb=" O ASN H 80 " pdb=" OD1 ASN H 80 " model vdw 2.255 3.040 nonbonded pdb=" OE1 GLN B 172 " pdb=" OG1 THR B 304 " model vdw 2.260 3.040 nonbonded pdb=" O PHE H 30 " pdb=" ND2 ASN H 80 " model vdw 2.271 3.120 nonbonded pdb=" O THR A 221 " pdb=" OG1 THR A 221 " model vdw 2.289 3.040 ... (remaining 53600 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 7 through 45 or (resid 46 through 51 and (name N or name C \ A or name C or name O or name CB )) or resid 52 through 100 or (resid 101 throug \ h 102 and (name N or name CA or name C or name O or name CB )) or resid 103 thro \ ugh 122 or (resid 123 and (name N or name CA or name C or name O or name CB )) o \ r resid 124 through 184 or (resid 185 and (name N or name CA or name C or name O \ or name CB )) or resid 186 through 193 or (resid 194 through 195 and (name N or \ name CA or name C or name O or name CB )) or resid 196 through 209 or (resid 21 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 211 or (resi \ d 212 and (name N or name CA or name C or name O or name CB )) or resid 213 thro \ ugh 220 or (resid 221 through 222 and (name N or name CA or name C or name O or \ name CB )) or resid 223 through 227 or (resid 228 and (name N or name CA or name \ C or name O or name CB )) or resid 229 through 239 or (resid 240 through 241 an \ d (name N or name CA or name C or name O or name CB )) or resid 242 through 247 \ or (resid 248 through 251 and (name N or name CA or name C or name O or name CB \ )) or resid 252 through 255 or (resid 256 through 261 and (name N or name CA or \ name C or name O or name CB )) or resid 262 through 266 or (resid 267 and (name \ N or name CA or name C or name O or name CB )) or resid 268 through 288 or (resi \ d 289 through 290 and (name N or name CA or name C or name O or name CB )) or re \ sid 291 through 299 or (resid 300 through 301 and (name N or name CA or name C o \ r name O or name CB )) or resid 302 through 325 or (resid 326 through 327 and (n \ ame N or name CA or name C or name O or name CB )) or resid 328 through 357)) selection = (chain 'B' and ((resid 7 and (name N or name CA or name C or name O or name CB ) \ ) or resid 8 through 41 or resid 45 through 47 or (resid 48 through 51 and (name \ N or name CA or name C or name O or name CB )) or resid 52 through 61 or resid \ 77 through 89 or (resid 92 through 95 and (name N or name CA or name C or name O \ or name CB )) or resid 96 through 121 or (resid 122 through 123 and (name N or \ name CA or name C or name O or name CB )) or resid 124 through 131 or (resid 139 \ through 145 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 46 through 148 or (resid 149 through 157 and (name N or name CA or name C or nam \ e O or name CB )) or resid 158 through 160 or (resid 161 and (name N or name CA \ or name C or name O or name CB )) or resid 162 through 189 or (resid 190 and (na \ me N or name CA or name C or name O or name CB )) or resid 193 through 198 or (r \ esid 199 through 201 and (name N or name CA or name C or name O or name CB )) or \ resid 202 through 205 or (resid 206 through 207 and (name N or name CA or name \ C or name O or name CB )) or resid 208 through 217 or (resid 218 through 219 and \ (name N or name CA or name C or name O or name CB )) or resid 220 through 226 o \ r (resid 227 through 228 and (name N or name CA or name C or name O or name CB ) \ ) or resid 229 through 240 or (resid 241 and (name N or name CA or name C or nam \ e O or name CB )) or resid 242 through 286 or (resid 287 through 290 and (name N \ or name CA or name C or name O or name CB )) or resid 291 through 349 or (resid \ 350 and (name N or name CA or name C or name O or name CB )) or resid 351 throu \ gh 357)) } ncs_group { reference = (chain 'H' and (resid 5 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 through 47 or (resid 48 through 49 and (name \ N or name CA or name C or name O or name CB )) or resid 50 through 69 or (resid \ 70 and (name N or name CA or name C or name O or name CB )) or resid 71 through \ 103 or resid 106 through 111 or (resid 112 and (name N or name CA or name C or \ name O or name CB )) or resid 113 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )))) selection = (chain 'I' and (resid 5 through 8 or (resid 9 through 10 and (name N or name CA \ or name C or name O or name CB )) or resid 11 through 19 or (resid 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 or (resid 22 and (nam \ e N or name CA or name C or name O or name CB )) or resid 23 through 27 or (resi \ d 28 and (name N or name CA or name C or name O or name CB )) or resid 29 throug \ h 33 or (resid 34 through 36 and (name N or name CA or name C or name O or name \ CB )) or resid 37 through 55 or (resid 56 through 58 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 59 through 61 and (name N or name CA or \ name C or name O or name CB )) or resid 62 through 67 or (resid 68 and (name N o \ r name CA or name C or name O or name CB )) or resid 69 through 72 or (resid 73 \ through 76 and (name N or name CA or name C or name O or name CB )) or resid 77 \ through 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) \ or resid 80 through 82 or (resid 83 and (name N or name CA or name C or name O \ or name CB )) or resid 93 or (resid 94 through 95 and (name N or name CA or name \ C or name O or name CB )) or resid 96 through 115)) } ncs_group { reference = (chain 'L' and (resid 2 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 10 or (resid 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 17 or (resid 18 through 2 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 24 through 2 \ 6 or (resid 27 through 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 39 or (resid 40 and (name N or name CA or name C or name \ O or name CB )) or resid 41 through 73 or (resid 74 and (name N or name CA or na \ me C or name O or name CB )) or resid 75 through 79 or (resid 82 through 87 and \ (name N or name CA or name C or name O or name CB )) or resid 88 through 105 or \ (resid 106 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'M' and (resid 2 through 21 or (resid 22 through 23 and (name N or name C \ A or name C or name O or name CB )) or resid 24 through 28 or (resid 29 and (nam \ e N or name CA or name C or name O or name CB )) or resid 30 or (resid 31 throug \ h 33 and (name N or name CA or name C or name O or name CB )) or resid 34 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 45 or (resid 46 and (name N or name CA or name C or na \ me O or name CB )) or resid 47 through 67 or (resid 68 and (name N or name CA or \ name C or name O or name CB )) or resid 69 through 79 or (resid 82 through 87 a \ nd (name N or name CA or name C or name O or name CB )) or resid 88 through 93 o \ r (resid 94 and (name N or name CA or name C or name O or name CB )) or resid 95 \ through 104 or (resid 105 through 106 and (name N or name CA or name C or name \ O or name CB )))) } 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 group one per residue 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: 0.900 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.360 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 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 : 0.007 0.140 7278 Z= 0.360 Angle : 0.941 16.005 10016 Z= 0.508 Chirality : 0.051 0.344 1217 Planarity : 0.007 0.082 1284 Dihedral : 14.002 86.312 2256 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.26 % Allowed : 17.01 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.26), residues: 987 helix: -1.26 (0.98), residues: 22 sheet: -0.94 (0.26), residues: 391 loop : -0.92 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 50 HIS 0.011 0.002 HIS I 38 PHE 0.018 0.002 PHE B 349 TYR 0.032 0.003 TYR B 321 ARG 0.005 0.001 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.25644 ( 254) hydrogen bonds : angle 10.67420 ( 627) SS BOND : bond 0.00315 ( 4) SS BOND : angle 1.31475 ( 8) covalent geometry : bond 0.00698 ( 7274) covalent geometry : angle 0.94077 (10008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 158 ILE cc_start: 0.7224 (mm) cc_final: 0.6869 (mt) REVERT: I 78 SER cc_start: 0.7651 (m) cc_final: 0.7294 (p) REVERT: I 103 ARG cc_start: 0.3686 (OUTLIER) cc_final: 0.3454 (ttp80) REVERT: M 49 ILE cc_start: 0.7847 (mt) cc_final: 0.7322 (mp) REVERT: M 90 GLN cc_start: 0.7017 (tm-30) cc_final: 0.6582 (tm-30) REVERT: A 103 ARG cc_start: 0.3486 (OUTLIER) cc_final: 0.2304 (mtm-85) REVERT: A 169 ARG cc_start: 0.6389 (mtp180) cc_final: 0.6076 (mtp-110) REVERT: A 326 LYS cc_start: 0.5016 (OUTLIER) cc_final: 0.3323 (tptt) REVERT: L 49 ILE cc_start: 0.7721 (mm) cc_final: 0.7361 (mm) outliers start: 13 outliers final: 5 residues processed: 150 average time/residue: 0.2377 time to fit residues: 45.9125 Evaluate side-chains 130 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain H residue 31 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 189 GLN A 237 GLN L 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.178646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.164692 restraints weight = 12928.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.166546 restraints weight = 9870.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.167970 restraints weight = 7976.228| |-----------------------------------------------------------------------------| r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7278 Z= 0.181 Angle : 0.712 11.551 10016 Z= 0.367 Chirality : 0.047 0.258 1217 Planarity : 0.006 0.056 1284 Dihedral : 7.895 73.697 1135 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 5.03 % Allowed : 18.06 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.10 (0.27), residues: 987 helix: 0.47 (1.12), residues: 22 sheet: -0.74 (0.26), residues: 412 loop : -0.68 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 39 HIS 0.004 0.001 HIS I 38 PHE 0.018 0.002 PHE B 349 TYR 0.024 0.003 TYR H 112 ARG 0.004 0.001 ARG B 7 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 254) hydrogen bonds : angle 7.06365 ( 627) SS BOND : bond 0.00929 ( 4) SS BOND : angle 1.13614 ( 8) covalent geometry : bond 0.00400 ( 7274) covalent geometry : angle 0.71197 (10008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.733 Fit side-chains REVERT: B 61 PHE cc_start: 0.5377 (t80) cc_final: 0.5130 (t80) REVERT: B 275 THR cc_start: 0.5219 (m) cc_final: 0.4991 (m) REVERT: I 78 SER cc_start: 0.7603 (m) cc_final: 0.7240 (p) REVERT: M 49 ILE cc_start: 0.7923 (mt) cc_final: 0.7458 (tt) REVERT: M 90 GLN cc_start: 0.7253 (tm-30) cc_final: 0.6927 (tm-30) REVERT: A 103 ARG cc_start: 0.4358 (OUTLIER) cc_final: 0.3118 (mtm-85) REVERT: L 49 ILE cc_start: 0.7421 (mm) cc_final: 0.7135 (mm) outliers start: 29 outliers final: 21 residues processed: 150 average time/residue: 0.1966 time to fit residues: 39.2107 Evaluate side-chains 155 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 20 optimal weight: 0.0570 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 0.0970 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN I 38 HIS A 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.180578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.164877 restraints weight = 13003.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.167315 restraints weight = 9411.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.169118 restraints weight = 7299.595| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5939 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7278 Z= 0.131 Angle : 0.636 11.517 10016 Z= 0.319 Chirality : 0.045 0.197 1217 Planarity : 0.005 0.051 1284 Dihedral : 6.733 75.037 1119 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.03 % Allowed : 19.79 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.28), residues: 987 helix: 1.52 (1.17), residues: 22 sheet: -0.62 (0.26), residues: 415 loop : -0.55 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 39 HIS 0.005 0.001 HIS I 38 PHE 0.015 0.002 PHE A 277 TYR 0.017 0.002 TYR B 54 ARG 0.003 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.02886 ( 254) hydrogen bonds : angle 6.11280 ( 627) SS BOND : bond 0.00315 ( 4) SS BOND : angle 0.79196 ( 8) covalent geometry : bond 0.00301 ( 7274) covalent geometry : angle 0.63633 (10008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.763 Fit side-chains REVERT: B 275 THR cc_start: 0.5342 (m) cc_final: 0.5128 (m) REVERT: I 78 SER cc_start: 0.7639 (m) cc_final: 0.7224 (p) REVERT: I 110 LEU cc_start: 0.7639 (tt) cc_final: 0.7402 (tt) REVERT: M 49 ILE cc_start: 0.7753 (mt) cc_final: 0.7361 (tt) REVERT: M 90 GLN cc_start: 0.7225 (tm-30) cc_final: 0.6982 (tm-30) REVERT: A 320 SER cc_start: 0.7723 (t) cc_final: 0.7467 (t) REVERT: H 50 TRP cc_start: 0.7082 (t60) cc_final: 0.6527 (t60) REVERT: H 110 LEU cc_start: 0.7262 (mp) cc_final: 0.6920 (mt) REVERT: L 49 ILE cc_start: 0.7324 (mm) cc_final: 0.6943 (mm) outliers start: 29 outliers final: 16 residues processed: 154 average time/residue: 0.1882 time to fit residues: 38.6347 Evaluate side-chains 150 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 89 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 49 optimal weight: 0.0570 chunk 70 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 0.0970 chunk 59 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN I 38 HIS A 101 GLN A 237 GLN L 38 GLN L 91 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.178510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.164642 restraints weight = 13089.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.166546 restraints weight = 9947.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.167978 restraints weight = 8011.921| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7278 Z= 0.164 Angle : 0.651 9.881 10016 Z= 0.329 Chirality : 0.046 0.210 1217 Planarity : 0.005 0.053 1284 Dihedral : 6.501 74.905 1115 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 5.21 % Allowed : 21.70 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.28), residues: 987 helix: 1.04 (1.11), residues: 24 sheet: -0.62 (0.26), residues: 413 loop : -0.56 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I 39 HIS 0.003 0.001 HIS I 38 PHE 0.014 0.002 PHE B 349 TYR 0.021 0.002 TYR H 98 ARG 0.003 0.001 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.02966 ( 254) hydrogen bonds : angle 6.09781 ( 627) SS BOND : bond 0.00558 ( 4) SS BOND : angle 0.88557 ( 8) covalent geometry : bond 0.00366 ( 7274) covalent geometry : angle 0.65098 (10008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.762 Fit side-chains REVERT: B 173 TYR cc_start: 0.6232 (m-80) cc_final: 0.5503 (m-10) REVERT: B 275 THR cc_start: 0.5549 (m) cc_final: 0.5348 (m) REVERT: B 295 HIS cc_start: 0.7311 (OUTLIER) cc_final: 0.6232 (t-90) REVERT: I 55 SER cc_start: 0.6824 (t) cc_final: 0.6257 (p) REVERT: I 78 SER cc_start: 0.7646 (m) cc_final: 0.7255 (p) REVERT: I 110 LEU cc_start: 0.7415 (tt) cc_final: 0.7156 (tt) REVERT: M 49 ILE cc_start: 0.7746 (mt) cc_final: 0.7396 (tt) REVERT: M 90 GLN cc_start: 0.7264 (tm-30) cc_final: 0.6960 (tm-30) REVERT: A 320 SER cc_start: 0.7754 (t) cc_final: 0.7442 (t) REVERT: A 346 GLU cc_start: 0.6176 (mp0) cc_final: 0.5922 (mp0) outliers start: 30 outliers final: 24 residues processed: 154 average time/residue: 0.1720 time to fit residues: 36.1563 Evaluate side-chains 160 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 89 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.0670 chunk 10 optimal weight: 0.0370 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 2 optimal weight: 0.0570 chunk 99 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN A 237 GLN L 38 GLN L 91 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.180313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.164713 restraints weight = 12940.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.167071 restraints weight = 9518.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.168584 restraints weight = 7389.556| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7278 Z= 0.127 Angle : 0.588 7.497 10016 Z= 0.297 Chirality : 0.044 0.190 1217 Planarity : 0.005 0.047 1284 Dihedral : 6.504 75.773 1115 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.03 % Allowed : 23.96 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.28), residues: 987 helix: 1.35 (1.14), residues: 24 sheet: -0.52 (0.27), residues: 405 loop : -0.58 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP I 39 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.001 PHE B 349 TYR 0.014 0.002 TYR H 98 ARG 0.003 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.02606 ( 254) hydrogen bonds : angle 5.77921 ( 627) SS BOND : bond 0.00248 ( 4) SS BOND : angle 0.80473 ( 8) covalent geometry : bond 0.00288 ( 7274) covalent geometry : angle 0.58814 (10008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.815 Fit side-chains REVERT: B 52 ARG cc_start: 0.5845 (mmm-85) cc_final: 0.5242 (mmm-85) REVERT: B 173 TYR cc_start: 0.6159 (m-80) cc_final: 0.5354 (m-10) REVERT: B 233 ILE cc_start: 0.0655 (OUTLIER) cc_final: 0.0355 (mt) REVERT: B 275 THR cc_start: 0.5496 (m) cc_final: 0.5289 (m) REVERT: B 295 HIS cc_start: 0.7162 (OUTLIER) cc_final: 0.6130 (t-90) REVERT: I 55 SER cc_start: 0.6963 (t) cc_final: 0.6505 (p) REVERT: I 78 SER cc_start: 0.7652 (m) cc_final: 0.7258 (p) REVERT: M 49 ILE cc_start: 0.7700 (mt) cc_final: 0.7328 (tt) REVERT: M 90 GLN cc_start: 0.7244 (tm-30) cc_final: 0.6930 (tm-30) REVERT: A 278 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6295 (pp) REVERT: A 320 SER cc_start: 0.7640 (t) cc_final: 0.7351 (t) REVERT: L 38 GLN cc_start: 0.4613 (tt0) cc_final: 0.4231 (mm-40) REVERT: L 78 SER cc_start: 0.7432 (m) cc_final: 0.7121 (p) outliers start: 29 outliers final: 22 residues processed: 154 average time/residue: 0.1796 time to fit residues: 37.2307 Evaluate side-chains 156 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 89 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 2 optimal weight: 0.0050 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN A 237 GLN L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.177820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.163946 restraints weight = 13074.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.165827 restraints weight = 9973.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.167227 restraints weight = 8015.565| |-----------------------------------------------------------------------------| r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7278 Z= 0.176 Angle : 0.635 7.493 10016 Z= 0.324 Chirality : 0.046 0.199 1217 Planarity : 0.005 0.054 1284 Dihedral : 6.643 74.349 1115 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 7.29 % Allowed : 24.48 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.28), residues: 987 helix: 1.15 (1.12), residues: 24 sheet: -0.63 (0.26), residues: 414 loop : -0.63 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP I 39 HIS 0.004 0.001 HIS A 210 PHE 0.014 0.002 PHE B 349 TYR 0.020 0.002 TYR H 98 ARG 0.008 0.001 ARG B 7 Details of bonding type rmsd hydrogen bonds : bond 0.02977 ( 254) hydrogen bonds : angle 6.09976 ( 627) SS BOND : bond 0.00401 ( 4) SS BOND : angle 0.96658 ( 8) covalent geometry : bond 0.00390 ( 7274) covalent geometry : angle 0.63437 (10008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 0.762 Fit side-chains REVERT: B 7 ARG cc_start: 0.6112 (tmt170) cc_final: 0.5903 (tmt170) REVERT: B 173 TYR cc_start: 0.6135 (m-80) cc_final: 0.5372 (m-10) REVERT: B 233 ILE cc_start: 0.0670 (OUTLIER) cc_final: 0.0294 (mt) REVERT: B 295 HIS cc_start: 0.7166 (OUTLIER) cc_final: 0.6020 (t-90) REVERT: I 55 SER cc_start: 0.6975 (t) cc_final: 0.6343 (p) REVERT: I 78 SER cc_start: 0.7653 (m) cc_final: 0.7254 (p) REVERT: M 49 ILE cc_start: 0.7723 (mt) cc_final: 0.7410 (tt) REVERT: M 90 GLN cc_start: 0.7251 (tm-30) cc_final: 0.6911 (tm-30) REVERT: A 278 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6463 (pp) REVERT: A 320 SER cc_start: 0.7729 (t) cc_final: 0.7445 (t) REVERT: A 346 GLU cc_start: 0.6098 (mp0) cc_final: 0.5805 (mp0) REVERT: L 38 GLN cc_start: 0.4842 (tt0) cc_final: 0.4157 (mm-40) REVERT: L 49 ILE cc_start: 0.7301 (tp) cc_final: 0.7056 (tp) REVERT: L 78 SER cc_start: 0.7524 (m) cc_final: 0.7252 (p) outliers start: 42 outliers final: 26 residues processed: 162 average time/residue: 0.1729 time to fit residues: 38.2245 Evaluate side-chains 160 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 89 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 69 optimal weight: 0.0570 chunk 21 optimal weight: 0.0370 chunk 59 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.181226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.165789 restraints weight = 12943.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.168192 restraints weight = 9472.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.169961 restraints weight = 7365.224| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7278 Z= 0.111 Angle : 0.596 9.109 10016 Z= 0.295 Chirality : 0.044 0.267 1217 Planarity : 0.005 0.048 1284 Dihedral : 6.470 76.652 1115 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 6.08 % Allowed : 26.04 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.28), residues: 987 helix: 1.61 (1.16), residues: 24 sheet: -0.63 (0.26), residues: 426 loop : -0.68 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP I 39 HIS 0.002 0.001 HIS H 38 PHE 0.016 0.001 PHE B 349 TYR 0.013 0.001 TYR H 62 ARG 0.004 0.000 ARG B 7 Details of bonding type rmsd hydrogen bonds : bond 0.02461 ( 254) hydrogen bonds : angle 5.62404 ( 627) SS BOND : bond 0.00245 ( 4) SS BOND : angle 0.66305 ( 8) covalent geometry : bond 0.00257 ( 7274) covalent geometry : angle 0.59550 (10008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.795 Fit side-chains REVERT: B 173 TYR cc_start: 0.6110 (m-80) cc_final: 0.5418 (m-10) REVERT: B 233 ILE cc_start: 0.0162 (OUTLIER) cc_final: -0.0168 (mt) REVERT: B 295 HIS cc_start: 0.7014 (OUTLIER) cc_final: 0.6112 (t-90) REVERT: B 320 SER cc_start: 0.7476 (t) cc_final: 0.7217 (p) REVERT: I 55 SER cc_start: 0.6839 (t) cc_final: 0.6437 (p) REVERT: I 78 SER cc_start: 0.7704 (m) cc_final: 0.7295 (p) REVERT: M 49 ILE cc_start: 0.7632 (mt) cc_final: 0.7336 (tt) REVERT: M 90 GLN cc_start: 0.7248 (tm-30) cc_final: 0.6896 (tm-30) REVERT: M 95 VAL cc_start: 0.7038 (OUTLIER) cc_final: 0.6798 (m) REVERT: A 278 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.6255 (pp) REVERT: A 320 SER cc_start: 0.7637 (t) cc_final: 0.7354 (t) REVERT: H 50 TRP cc_start: 0.6961 (t60) cc_final: 0.6344 (t60) REVERT: L 38 GLN cc_start: 0.4374 (tt0) cc_final: 0.4027 (mm-40) REVERT: L 49 ILE cc_start: 0.7165 (tp) cc_final: 0.6767 (tp) REVERT: L 78 SER cc_start: 0.7308 (m) cc_final: 0.6990 (p) outliers start: 35 outliers final: 24 residues processed: 157 average time/residue: 0.1839 time to fit residues: 40.6019 Evaluate side-chains 160 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 89 CYS Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 2 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 86 optimal weight: 0.2980 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.178170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.164255 restraints weight = 13072.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.166112 restraints weight = 10036.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.167528 restraints weight = 8129.130| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5996 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7278 Z= 0.172 Angle : 0.658 12.516 10016 Z= 0.327 Chirality : 0.046 0.279 1217 Planarity : 0.005 0.051 1284 Dihedral : 6.606 74.225 1115 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 6.25 % Allowed : 26.56 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.28), residues: 987 helix: 1.46 (1.13), residues: 24 sheet: -0.65 (0.26), residues: 413 loop : -0.69 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP I 39 HIS 0.004 0.001 HIS H 38 PHE 0.013 0.002 PHE B 349 TYR 0.018 0.002 TYR I 98 ARG 0.004 0.001 ARG M 67 Details of bonding type rmsd hydrogen bonds : bond 0.02886 ( 254) hydrogen bonds : angle 5.90984 ( 627) SS BOND : bond 0.00405 ( 4) SS BOND : angle 0.87754 ( 8) covalent geometry : bond 0.00385 ( 7274) covalent geometry : angle 0.65806 (10008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: B 233 ILE cc_start: 0.0297 (OUTLIER) cc_final: -0.0067 (mt) REVERT: B 295 HIS cc_start: 0.7149 (OUTLIER) cc_final: 0.6255 (t-90) REVERT: I 55 SER cc_start: 0.7004 (t) cc_final: 0.6453 (p) REVERT: I 78 SER cc_start: 0.7738 (m) cc_final: 0.7316 (p) REVERT: M 49 ILE cc_start: 0.7700 (mt) cc_final: 0.7429 (tt) REVERT: M 90 GLN cc_start: 0.7260 (tm-30) cc_final: 0.6891 (tm-30) REVERT: M 95 VAL cc_start: 0.7205 (OUTLIER) cc_final: 0.6960 (m) REVERT: A 278 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6314 (pp) REVERT: A 320 SER cc_start: 0.7778 (t) cc_final: 0.7474 (t) REVERT: L 38 GLN cc_start: 0.4730 (tt0) cc_final: 0.4008 (mm-40) REVERT: L 49 ILE cc_start: 0.7328 (tp) cc_final: 0.6942 (tp) outliers start: 36 outliers final: 26 residues processed: 153 average time/residue: 0.1941 time to fit residues: 41.5480 Evaluate side-chains 161 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 89 CYS Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 30 optimal weight: 0.0570 chunk 25 optimal weight: 0.0470 chunk 45 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.181798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.166260 restraints weight = 13127.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.168674 restraints weight = 9558.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.170448 restraints weight = 7438.103| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7278 Z= 0.106 Angle : 0.587 10.021 10016 Z= 0.291 Chirality : 0.043 0.187 1217 Planarity : 0.005 0.049 1284 Dihedral : 6.413 77.154 1115 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.51 % Allowed : 28.30 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.28), residues: 987 helix: 1.77 (1.17), residues: 24 sheet: -0.65 (0.25), residues: 429 loop : -0.64 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP H 50 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.001 PHE B 349 TYR 0.016 0.001 TYR H 62 ARG 0.004 0.000 ARG B 7 Details of bonding type rmsd hydrogen bonds : bond 0.02352 ( 254) hydrogen bonds : angle 5.38683 ( 627) SS BOND : bond 0.00259 ( 4) SS BOND : angle 0.61169 ( 8) covalent geometry : bond 0.00249 ( 7274) covalent geometry : angle 0.58712 (10008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.785 Fit side-chains REVERT: B 52 ARG cc_start: 0.5876 (mmm-85) cc_final: 0.5272 (mmm-85) REVERT: B 173 TYR cc_start: 0.6009 (m-80) cc_final: 0.5457 (m-10) REVERT: B 233 ILE cc_start: 0.0142 (OUTLIER) cc_final: -0.0211 (mt) REVERT: B 295 HIS cc_start: 0.6975 (OUTLIER) cc_final: 0.6174 (t-90) REVERT: B 320 SER cc_start: 0.7397 (t) cc_final: 0.7187 (p) REVERT: I 55 SER cc_start: 0.6689 (t) cc_final: 0.6082 (p) REVERT: I 78 SER cc_start: 0.7708 (m) cc_final: 0.7284 (p) REVERT: M 49 ILE cc_start: 0.7612 (mt) cc_final: 0.7377 (tt) REVERT: M 90 GLN cc_start: 0.7259 (tm-30) cc_final: 0.6901 (tm-30) REVERT: A 320 SER cc_start: 0.7613 (t) cc_final: 0.6956 (p) REVERT: H 50 TRP cc_start: 0.7017 (t60) cc_final: 0.6495 (t60) REVERT: L 38 GLN cc_start: 0.4636 (tt0) cc_final: 0.4176 (mm-40) REVERT: L 49 ILE cc_start: 0.7231 (tp) cc_final: 0.6951 (tt) outliers start: 26 outliers final: 20 residues processed: 151 average time/residue: 0.1717 time to fit residues: 35.8571 Evaluate side-chains 154 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 89 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.178690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.164853 restraints weight = 13171.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.166733 restraints weight = 10079.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.168125 restraints weight = 8113.741| |-----------------------------------------------------------------------------| r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7278 Z= 0.160 Angle : 0.650 11.487 10016 Z= 0.324 Chirality : 0.045 0.220 1217 Planarity : 0.005 0.049 1284 Dihedral : 6.551 74.868 1114 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.99 % Allowed : 28.82 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.28), residues: 987 helix: 1.50 (1.12), residues: 24 sheet: -0.64 (0.26), residues: 422 loop : -0.68 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP I 39 HIS 0.004 0.001 HIS H 38 PHE 0.019 0.002 PHE B 9 TYR 0.017 0.002 TYR I 98 ARG 0.004 0.000 ARG M 67 Details of bonding type rmsd hydrogen bonds : bond 0.02735 ( 254) hydrogen bonds : angle 5.75115 ( 627) SS BOND : bond 0.00365 ( 4) SS BOND : angle 0.81040 ( 8) covalent geometry : bond 0.00363 ( 7274) covalent geometry : angle 0.65015 (10008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.721 Fit side-chains REVERT: B 173 TYR cc_start: 0.6113 (m-80) cc_final: 0.5506 (m-10) REVERT: B 233 ILE cc_start: 0.0291 (OUTLIER) cc_final: -0.0083 (mt) REVERT: B 295 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.6277 (t-90) REVERT: I 55 SER cc_start: 0.6900 (t) cc_final: 0.6373 (p) REVERT: I 78 SER cc_start: 0.7781 (m) cc_final: 0.7395 (p) REVERT: M 49 ILE cc_start: 0.7675 (mt) cc_final: 0.7407 (tt) REVERT: M 90 GLN cc_start: 0.7271 (tm-30) cc_final: 0.6874 (tm-30) REVERT: M 95 VAL cc_start: 0.7237 (OUTLIER) cc_final: 0.6982 (m) REVERT: A 320 SER cc_start: 0.7721 (t) cc_final: 0.7441 (t) REVERT: L 38 GLN cc_start: 0.4928 (tt0) cc_final: 0.4122 (mm-40) REVERT: L 49 ILE cc_start: 0.7345 (tp) cc_final: 0.7086 (tt) outliers start: 23 outliers final: 18 residues processed: 146 average time/residue: 0.1715 time to fit residues: 34.7540 Evaluate side-chains 150 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 89 CYS Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 21 optimal weight: 0.0670 chunk 65 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 61 optimal weight: 0.0770 chunk 69 optimal weight: 0.0870 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.181922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.166542 restraints weight = 12976.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.168959 restraints weight = 9490.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.170695 restraints weight = 7348.832| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7278 Z= 0.108 Angle : 0.597 11.483 10016 Z= 0.295 Chirality : 0.043 0.184 1217 Planarity : 0.004 0.049 1284 Dihedral : 6.420 77.212 1114 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.82 % Allowed : 29.34 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.28), residues: 987 helix: 1.79 (1.16), residues: 24 sheet: -0.56 (0.26), residues: 424 loop : -0.61 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP H 50 HIS 0.003 0.001 HIS H 38 PHE 0.014 0.001 PHE B 9 TYR 0.016 0.001 TYR H 62 ARG 0.004 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.02314 ( 254) hydrogen bonds : angle 5.31530 ( 627) SS BOND : bond 0.00209 ( 4) SS BOND : angle 0.61635 ( 8) covalent geometry : bond 0.00256 ( 7274) covalent geometry : angle 0.59653 (10008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2657.13 seconds wall clock time: 46 minutes 56.49 seconds (2816.49 seconds total)