Starting phenix.real_space_refine on Thu Mar 14 14:49:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sr8_25399/03_2024/7sr8_25399.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sr8_25399/03_2024/7sr8_25399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sr8_25399/03_2024/7sr8_25399.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sr8_25399/03_2024/7sr8_25399.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sr8_25399/03_2024/7sr8_25399.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sr8_25399/03_2024/7sr8_25399.pdb" } resolution = 3.3 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5790 2.51 5 N 1547 2.21 5 O 1682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "E GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9083 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1850 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 453 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "E" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1800 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2373 Unusual residues: {'A6F': 1, 'OLA': 4} Classifications: {'peptide': 283, 'undetermined': 5} Link IDs: {'PTRANS': 8, 'TRANS': 274, None: 5} Not linked: pdbres="SER R 380 " pdbres="A6F R 501 " Not linked: pdbres="A6F R 501 " pdbres="OLA R 502 " Not linked: pdbres="OLA R 502 " pdbres="OLA R 503 " Not linked: pdbres="OLA R 503 " pdbres="OLA R 504 " Not linked: pdbres="OLA R 504 " pdbres="OLA R 505 " Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'OLA:plan-2': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 5.58, per 1000 atoms: 0.61 Number of scatterers: 9083 At special positions: 0 Unit cell: (118.8, 113.4, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1682 8.00 N 1547 7.00 C 5790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 210 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.73 Conformation dependent library (CDL) restraints added in 1.8 seconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 38.3% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 109 through 123 Processing helix chain 'A' and resid 124 through 127 removed outlier: 3.734A pdb=" N ARG A 127 " --> pdb=" O ARG A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 124 through 127' Processing helix chain 'A' and resid 137 through 148 removed outlier: 3.602A pdb=" N GLY A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.898A pdb=" N ALA A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 196 removed outlier: 4.488A pdb=" N SER A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 235 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.516A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 removed outlier: 4.172A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 82 Processing helix chain 'R' and resid 87 through 117 removed outlier: 3.712A pdb=" N PHE R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE R 93 " --> pdb=" O THR R 89 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU R 108 " --> pdb=" O THR R 104 " (cutoff:3.500A) Proline residue: R 109 - end of helix Processing helix chain 'R' and resid 123 through 158 Proline residue: R 131 - end of helix Processing helix chain 'R' and resid 165 through 184 Processing helix chain 'R' and resid 184 through 190 Processing helix chain 'R' and resid 218 through 232 Processing helix chain 'R' and resid 232 through 252 Processing helix chain 'R' and resid 294 through 329 removed outlier: 3.729A pdb=" N VAL R 309 " --> pdb=" O MET R 305 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) Proline residue: R 319 - end of helix Processing helix chain 'R' and resid 338 through 366 removed outlier: 4.060A pdb=" N VAL R 342 " --> pdb=" O ASP R 338 " (cutoff:3.500A) Proline residue: R 361 - end of helix removed outlier: 4.084A pdb=" N ASN R 365 " --> pdb=" O PRO R 361 " (cutoff:3.500A) Processing helix chain 'R' and resid 368 through 380 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 68 removed outlier: 3.506A pdb=" N LEU A 34 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A 76 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 38 " --> pdb=" O PHE A 76 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ARG A 35 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ILE A 99 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 37 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL A 101 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU A 39 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N ASP A 103 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 98 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N PHE A 134 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE A 100 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASN A 136 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A 102 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL A 131 " --> pdb=" O TYR A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.430A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.732A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP B 82 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.484A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 152 removed outlier: 3.623A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.440A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.740A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.418A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.772A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.686A pdb=" N ARG E 160 " --> pdb=" O THR E 141 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 149 removed outlier: 3.502A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 149 removed outlier: 3.502A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 192 through 196 462 hydrogen bonds defined for protein. 1302 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: 2.69 Time building geometry restraints manager: 3.98 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: 1973 1.33 - 1.45: 2129 1.45 - 1.57: 5078 1.57 - 1.69: 1 1.69 - 1.81: 92 Bond restraints: 9273 Sorted by residual: bond pdb=" C10 OLA R 504 " pdb=" C9 OLA R 504 " ideal model delta sigma weight residual 1.332 1.466 -0.134 2.00e-02 2.50e+03 4.46e+01 bond pdb=" C10 OLA R 505 " pdb=" C9 OLA R 505 " ideal model delta sigma weight residual 1.332 1.464 -0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" O27 A6F R 501 " pdb=" S26 A6F R 501 " ideal model delta sigma weight residual 1.455 1.528 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" O28 A6F R 501 " pdb=" S26 A6F R 501 " ideal model delta sigma weight residual 1.458 1.530 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" N25 A6F R 501 " pdb=" S26 A6F R 501 " ideal model delta sigma weight residual 1.647 1.600 0.047 2.00e-02 2.50e+03 5.44e+00 ... (remaining 9268 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.11: 164 106.11 - 113.08: 5026 113.08 - 120.04: 3155 120.04 - 127.01: 4105 127.01 - 133.98: 102 Bond angle restraints: 12552 Sorted by residual: angle pdb=" CA ILE R 130 " pdb=" C ILE R 130 " pdb=" N PRO R 131 " ideal model delta sigma weight residual 120.83 123.22 -2.39 6.10e-01 2.69e+00 1.53e+01 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 angle pdb=" CA PRO R 186 " pdb=" N PRO R 186 " pdb=" CD PRO R 186 " ideal model delta sigma weight residual 112.00 106.70 5.30 1.40e+00 5.10e-01 1.43e+01 angle pdb=" O ILE R 130 " pdb=" C ILE R 130 " pdb=" N PRO R 131 " ideal model delta sigma weight residual 120.42 118.27 2.15 6.40e-01 2.44e+00 1.12e+01 angle pdb=" O27 A6F R 501 " pdb=" S26 A6F R 501 " pdb=" O28 A6F R 501 " ideal model delta sigma weight residual 118.66 108.90 9.76 3.00e+00 1.11e-01 1.06e+01 ... (remaining 12547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.54: 5425 32.54 - 65.09: 109 65.09 - 97.63: 4 97.63 - 130.18: 0 130.18 - 162.72: 1 Dihedral angle restraints: 5539 sinusoidal: 2219 harmonic: 3320 Sorted by residual: dihedral pdb=" CB CYS R 127 " pdb=" SG CYS R 127 " pdb=" SG CYS R 210 " pdb=" CB CYS R 210 " ideal model delta sinusoidal sigma weight residual -86.00 -171.00 85.00 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 50.71 42.29 1 1.00e+01 1.00e-02 2.50e+01 dihedral pdb=" C3 A6F R 501 " pdb=" N25 A6F R 501 " pdb=" S26 A6F R 501 " pdb=" O28 A6F R 501 " ideal model delta sinusoidal sigma weight residual 328.43 165.71 162.72 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 5536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1080 0.045 - 0.090: 242 0.090 - 0.135: 86 0.135 - 0.180: 1 0.180 - 0.225: 3 Chirality restraints: 1412 Sorted by residual: chirality pdb=" C16 A6F R 501 " pdb=" C15 A6F R 501 " pdb=" C17 A6F R 501 " pdb=" C19 A6F R 501 " both_signs ideal model delta sigma weight residual False -2.50 -2.72 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C2 A6F R 501 " pdb=" C11 A6F R 501 " pdb=" C3 A6F R 501 " pdb=" N1 A6F R 501 " both_signs ideal model delta sigma weight residual False -2.28 -2.49 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3 A6F R 501 " pdb=" C2 A6F R 501 " pdb=" C4 A6F R 501 " pdb=" N25 A6F R 501 " both_signs ideal model delta sigma weight residual False 2.34 2.52 -0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 1409 not shown) Planarity restraints: 1585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA R 505 " 0.206 2.00e-02 2.50e+03 1.59e-01 2.54e+02 pdb=" C11 OLA R 505 " -0.091 2.00e-02 2.50e+03 pdb=" C8 OLA R 505 " 0.092 2.00e-02 2.50e+03 pdb=" C9 OLA R 505 " -0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA R 504 " -0.154 2.00e-02 2.50e+03 1.20e-01 1.45e+02 pdb=" C11 OLA R 504 " 0.073 2.00e-02 2.50e+03 pdb=" C8 OLA R 504 " -0.072 2.00e-02 2.50e+03 pdb=" C9 OLA R 504 " 0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 185 " -0.075 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO R 186 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO R 186 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO R 186 " -0.060 5.00e-02 4.00e+02 ... (remaining 1582 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 178 2.69 - 3.24: 8669 3.24 - 3.79: 14062 3.79 - 4.35: 18382 4.35 - 4.90: 31541 Nonbonded interactions: 72832 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.134 2.440 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.141 2.440 nonbonded pdb=" O ARG E 67 " pdb=" OG1 THR E 84 " model vdw 2.145 2.440 nonbonded pdb=" O PHE E 32 " pdb=" NH2 ARG E 72 " model vdw 2.197 2.520 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.236 2.440 ... (remaining 72827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 2.540 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.480 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 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 : 0.004 0.134 9273 Z= 0.233 Angle : 0.619 9.761 12552 Z= 0.300 Chirality : 0.042 0.225 1412 Planarity : 0.007 0.159 1585 Dihedral : 12.325 162.724 3384 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.51 (0.26), residues: 1123 helix: 2.45 (0.26), residues: 392 sheet: 0.75 (0.31), residues: 295 loop : -0.11 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 120 HIS 0.010 0.001 HIS R 224 PHE 0.019 0.001 PHE R 375 TYR 0.026 0.001 TYR R 354 ARG 0.006 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.000 Fit side-chains REVERT: A 133 LEU cc_start: 0.8234 (mm) cc_final: 0.7975 (mm) REVERT: A 187 LYS cc_start: 0.8389 (tmtt) cc_final: 0.7854 (tptp) REVERT: B 105 TYR cc_start: 0.8303 (t80) cc_final: 0.8073 (t80) REVERT: R 85 MET cc_start: 0.6486 (ttp) cc_final: 0.6281 (ttm) REVERT: R 100 ASP cc_start: 0.8329 (m-30) cc_final: 0.8083 (m-30) REVERT: R 296 ILE cc_start: 0.7481 (mt) cc_final: 0.7258 (tp) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1942 time to fit residues: 60.6211 Evaluate side-chains 178 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 0.0470 chunk 100 optimal weight: 4.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9273 Z= 0.239 Angle : 0.556 7.279 12552 Z= 0.294 Chirality : 0.043 0.146 1412 Planarity : 0.004 0.077 1585 Dihedral : 8.020 168.856 1317 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.93 % Allowed : 8.23 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.33 (0.26), residues: 1123 helix: 2.28 (0.26), residues: 392 sheet: 0.57 (0.30), residues: 309 loop : -0.15 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.008 0.001 HIS R 224 PHE 0.018 0.002 PHE A 73 TYR 0.027 0.002 TYR R 354 ARG 0.006 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 203 time to evaluate : 1.046 Fit side-chains REVERT: A 74 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6232 (t-90) REVERT: A 133 LEU cc_start: 0.8143 (mm) cc_final: 0.7872 (mm) REVERT: A 187 LYS cc_start: 0.8216 (tmtt) cc_final: 0.7770 (tptp) REVERT: E 192 MET cc_start: 0.7651 (ptt) cc_final: 0.7101 (ptt) REVERT: R 72 ASN cc_start: 0.8589 (m-40) cc_final: 0.8312 (m-40) REVERT: R 229 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7971 (tp) REVERT: R 354 TYR cc_start: 0.8168 (m-10) cc_final: 0.7528 (m-10) outliers start: 19 outliers final: 14 residues processed: 208 average time/residue: 0.2042 time to fit residues: 58.7596 Evaluate side-chains 203 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 187 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 244 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9273 Z= 0.268 Angle : 0.554 6.116 12552 Z= 0.294 Chirality : 0.043 0.162 1412 Planarity : 0.004 0.071 1585 Dihedral : 7.718 163.197 1317 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.74 % Allowed : 11.89 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.13 (0.25), residues: 1123 helix: 2.14 (0.26), residues: 393 sheet: 0.43 (0.30), residues: 302 loop : -0.26 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.008 0.001 HIS R 224 PHE 0.013 0.002 PHE A 73 TYR 0.014 0.001 TYR R 354 ARG 0.004 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 187 time to evaluate : 1.077 Fit side-chains REVERT: A 74 HIS cc_start: 0.7311 (OUTLIER) cc_final: 0.6236 (t-90) REVERT: A 187 LYS cc_start: 0.8296 (tmtt) cc_final: 0.7805 (tptp) REVERT: B 55 LEU cc_start: 0.7724 (mt) cc_final: 0.7417 (pp) REVERT: E 140 MET cc_start: 0.6483 (mtm) cc_final: 0.6270 (mtm) REVERT: E 192 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7260 (ptt) REVERT: R 85 MET cc_start: 0.6678 (ttp) cc_final: 0.6425 (ttm) REVERT: R 305 MET cc_start: 0.8664 (tpt) cc_final: 0.7954 (tpt) outliers start: 27 outliers final: 17 residues processed: 195 average time/residue: 0.1944 time to fit residues: 53.0873 Evaluate side-chains 200 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 181 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 315 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.0770 chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9273 Z= 0.200 Angle : 0.523 6.187 12552 Z= 0.277 Chirality : 0.042 0.172 1412 Planarity : 0.004 0.066 1585 Dihedral : 7.424 157.486 1317 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.05 % Allowed : 13.31 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.15 (0.25), residues: 1123 helix: 2.17 (0.26), residues: 393 sheet: 0.40 (0.29), residues: 317 loop : -0.26 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.007 0.001 HIS R 224 PHE 0.013 0.001 PHE A 73 TYR 0.025 0.001 TYR R 354 ARG 0.005 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 186 time to evaluate : 1.025 Fit side-chains REVERT: A 74 HIS cc_start: 0.7379 (OUTLIER) cc_final: 0.6364 (t-90) REVERT: A 187 LYS cc_start: 0.8204 (tmtt) cc_final: 0.7715 (tptp) REVERT: B 55 LEU cc_start: 0.7676 (mt) cc_final: 0.7423 (pp) REVERT: E 140 MET cc_start: 0.6406 (mtm) cc_final: 0.6131 (mtm) REVERT: E 192 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7269 (ptt) REVERT: R 72 ASN cc_start: 0.8696 (m-40) cc_final: 0.8459 (m-40) REVERT: R 229 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8030 (tp) REVERT: R 305 MET cc_start: 0.8685 (tpt) cc_final: 0.8389 (tpp) outliers start: 30 outliers final: 19 residues processed: 200 average time/residue: 0.1833 time to fit residues: 52.2440 Evaluate side-chains 197 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 175 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 30.0000 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9273 Z= 0.250 Angle : 0.545 6.189 12552 Z= 0.288 Chirality : 0.043 0.158 1412 Planarity : 0.004 0.064 1585 Dihedral : 7.192 149.249 1317 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.66 % Allowed : 15.04 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.04 (0.25), residues: 1123 helix: 2.08 (0.26), residues: 393 sheet: 0.41 (0.30), residues: 299 loop : -0.36 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS R 224 PHE 0.013 0.001 PHE A 73 TYR 0.013 0.001 TYR E 102 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 1.034 Fit side-chains REVERT: A 72 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8171 (p0) REVERT: A 74 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.6291 (t-90) REVERT: A 187 LYS cc_start: 0.8220 (tmtt) cc_final: 0.7706 (tptp) REVERT: B 55 LEU cc_start: 0.7719 (mt) cc_final: 0.7462 (pp) REVERT: B 339 TRP cc_start: 0.7807 (OUTLIER) cc_final: 0.7454 (m100) REVERT: E 192 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7221 (ptt) REVERT: R 305 MET cc_start: 0.8649 (tpt) cc_final: 0.8275 (tpp) outliers start: 36 outliers final: 24 residues processed: 200 average time/residue: 0.1963 time to fit residues: 55.0684 Evaluate side-chains 203 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 175 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain R residue 84 HIS Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 366 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 0.3980 chunk 107 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9273 Z= 0.209 Angle : 0.535 6.738 12552 Z= 0.283 Chirality : 0.042 0.192 1412 Planarity : 0.004 0.062 1585 Dihedral : 6.959 144.176 1317 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.46 % Allowed : 16.46 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.02 (0.25), residues: 1123 helix: 2.12 (0.26), residues: 393 sheet: 0.35 (0.29), residues: 308 loop : -0.39 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS R 224 PHE 0.011 0.001 PHE R 333 TYR 0.015 0.001 TYR R 343 ARG 0.004 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 177 time to evaluate : 0.932 Fit side-chains REVERT: A 74 HIS cc_start: 0.7383 (OUTLIER) cc_final: 0.6318 (t-90) REVERT: A 187 LYS cc_start: 0.8075 (tmtt) cc_final: 0.7596 (tptp) REVERT: B 55 LEU cc_start: 0.7736 (mt) cc_final: 0.7461 (pp) REVERT: B 339 TRP cc_start: 0.7767 (OUTLIER) cc_final: 0.7418 (m100) REVERT: E 192 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7287 (ptt) REVERT: R 305 MET cc_start: 0.8634 (tpt) cc_final: 0.8286 (tpp) outliers start: 34 outliers final: 25 residues processed: 191 average time/residue: 0.1999 time to fit residues: 53.6506 Evaluate side-chains 201 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain R residue 84 HIS Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 366 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 42 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 0.0770 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9273 Z= 0.164 Angle : 0.526 11.238 12552 Z= 0.274 Chirality : 0.042 0.193 1412 Planarity : 0.004 0.061 1585 Dihedral : 6.524 134.566 1317 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.85 % Allowed : 17.58 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.21 (0.26), residues: 1123 helix: 2.29 (0.26), residues: 394 sheet: 0.47 (0.30), residues: 308 loop : -0.33 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS R 224 PHE 0.015 0.001 PHE E 68 TYR 0.012 0.001 TYR E 190 ARG 0.006 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 74 HIS cc_start: 0.7423 (OUTLIER) cc_final: 0.6475 (t-90) REVERT: A 187 LYS cc_start: 0.7978 (tmtt) cc_final: 0.7497 (tptp) REVERT: B 55 LEU cc_start: 0.7718 (mt) cc_final: 0.7452 (pp) REVERT: B 339 TRP cc_start: 0.7662 (OUTLIER) cc_final: 0.7249 (m100) REVERT: E 192 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7046 (ptt) REVERT: R 229 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8081 (tp) REVERT: R 305 MET cc_start: 0.8597 (tpt) cc_final: 0.8274 (tpp) outliers start: 28 outliers final: 21 residues processed: 194 average time/residue: 0.1801 time to fit residues: 49.7851 Evaluate side-chains 199 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain R residue 84 HIS Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 366 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN B 175 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9273 Z= 0.237 Angle : 0.556 6.900 12552 Z= 0.292 Chirality : 0.043 0.218 1412 Planarity : 0.004 0.060 1585 Dihedral : 6.384 125.584 1317 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.46 % Allowed : 18.09 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.05 (0.25), residues: 1123 helix: 2.18 (0.26), residues: 394 sheet: 0.38 (0.30), residues: 303 loop : -0.44 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.007 0.001 HIS R 224 PHE 0.012 0.001 PHE E 68 TYR 0.012 0.001 TYR E 102 ARG 0.004 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 1.045 Fit side-chains REVERT: A 72 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.8101 (p0) REVERT: A 74 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.6494 (t-90) REVERT: A 133 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7661 (mm) REVERT: A 187 LYS cc_start: 0.8033 (tmtt) cc_final: 0.7508 (tptp) REVERT: B 55 LEU cc_start: 0.7740 (mt) cc_final: 0.7493 (pp) REVERT: B 339 TRP cc_start: 0.7751 (OUTLIER) cc_final: 0.7426 (m100) REVERT: E 192 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7275 (ptt) REVERT: R 233 MET cc_start: 0.6690 (tpt) cc_final: 0.6456 (ttp) REVERT: R 305 MET cc_start: 0.8607 (tpt) cc_final: 0.8292 (tpp) outliers start: 34 outliers final: 25 residues processed: 189 average time/residue: 0.1867 time to fit residues: 50.5343 Evaluate side-chains 201 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 171 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain R residue 84 HIS Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 252 CYS Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 366 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9273 Z= 0.274 Angle : 0.592 16.158 12552 Z= 0.308 Chirality : 0.044 0.225 1412 Planarity : 0.004 0.060 1585 Dihedral : 6.374 120.628 1317 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.35 % Allowed : 18.50 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.92 (0.25), residues: 1123 helix: 2.11 (0.26), residues: 394 sheet: 0.28 (0.30), residues: 304 loop : -0.52 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.007 0.001 HIS R 224 PHE 0.017 0.002 PHE A 73 TYR 0.013 0.001 TYR E 102 ARG 0.004 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 1.025 Fit side-chains REVERT: A 74 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.6492 (t-90) REVERT: A 133 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7677 (mm) REVERT: A 187 LYS cc_start: 0.8049 (tmtt) cc_final: 0.7300 (tptp) REVERT: B 339 TRP cc_start: 0.7800 (OUTLIER) cc_final: 0.7483 (m100) REVERT: E 192 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7361 (ptt) REVERT: R 305 MET cc_start: 0.8615 (tpt) cc_final: 0.8302 (tpp) outliers start: 33 outliers final: 26 residues processed: 181 average time/residue: 0.1813 time to fit residues: 46.8935 Evaluate side-chains 197 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 147 CYS Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 252 CYS Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 366 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9273 Z= 0.198 Angle : 0.564 15.455 12552 Z= 0.293 Chirality : 0.043 0.217 1412 Planarity : 0.004 0.060 1585 Dihedral : 6.156 113.848 1317 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.15 % Allowed : 18.60 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.96 (0.26), residues: 1123 helix: 2.16 (0.26), residues: 394 sheet: 0.21 (0.29), residues: 318 loop : -0.46 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.007 0.001 HIS R 224 PHE 0.028 0.001 PHE E 68 TYR 0.012 0.001 TYR E 102 ARG 0.005 0.000 ARG A 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 74 HIS cc_start: 0.7394 (OUTLIER) cc_final: 0.6423 (t-90) REVERT: A 133 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7666 (mm) REVERT: A 187 LYS cc_start: 0.8030 (tmtt) cc_final: 0.7512 (tptp) REVERT: B 16 ASN cc_start: 0.7565 (m-40) cc_final: 0.7100 (m110) REVERT: B 55 LEU cc_start: 0.7747 (mt) cc_final: 0.7481 (pp) REVERT: B 339 TRP cc_start: 0.7722 (OUTLIER) cc_final: 0.7405 (m100) REVERT: G 21 MET cc_start: 0.3883 (mtp) cc_final: 0.3460 (mtp) REVERT: E 192 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7311 (ptt) REVERT: R 132 TYR cc_start: 0.7932 (t80) cc_final: 0.7638 (t80) REVERT: R 305 MET cc_start: 0.8624 (tpt) cc_final: 0.8329 (tpp) outliers start: 31 outliers final: 24 residues processed: 189 average time/residue: 0.1907 time to fit residues: 51.4427 Evaluate side-chains 201 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 147 CYS Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 366 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.165911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132757 restraints weight = 12397.849| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.48 r_work: 0.3444 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 0.004 0.037 9273 Z= 0.237 Angle : 0.582 15.425 12552 Z= 0.303 Chirality : 0.044 0.235 1412 Planarity : 0.004 0.060 1585 Dihedral : 6.118 108.012 1317 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.25 % Allowed : 18.70 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.92 (0.25), residues: 1123 helix: 2.22 (0.26), residues: 388 sheet: 0.08 (0.29), residues: 311 loop : -0.42 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.007 0.001 HIS R 224 PHE 0.030 0.001 PHE E 68 TYR 0.012 0.001 TYR E 102 ARG 0.004 0.000 ARG A 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2108.14 seconds wall clock time: 38 minutes 38.76 seconds (2318.76 seconds total)