Starting phenix.real_space_refine on Fri Mar 15 11:44:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpd_14119/03_2024/7qpd_14119.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpd_14119/03_2024/7qpd_14119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpd_14119/03_2024/7qpd_14119.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpd_14119/03_2024/7qpd_14119.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpd_14119/03_2024/7qpd_14119.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpd_14119/03_2024/7qpd_14119.pdb" } resolution = 3.73 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= 0.002 sd= 0.018 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 42 5.16 5 C 7343 2.51 5 N 1989 2.21 5 O 2147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "T PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 11": "OE1" <-> "OE2" Residue "T GLU 43": "OE1" <-> "OE2" Residue "T ASP 159": "OD1" <-> "OD2" Residue "T PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 222": "OD1" <-> "OD2" Residue "T PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 337": "OD1" <-> "OD2" Residue "E TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 286": "OE1" <-> "OE2" Residue "E PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 128": "OE1" <-> "OE2" Residue "M ASP 183": "OD1" <-> "OD2" Residue "M TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 212": "OE1" <-> "OE2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 11521 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 803 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "T" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2569 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 304} Chain breaks: 4 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 Chain: "E" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3365 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 435} Chain breaks: 1 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 15, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 170 Chain: "M" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2110 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 260} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 95 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 100 Chain: "C" Number of atoms: 2552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2552 Classifications: {'peptide': 364} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 119} Link IDs: {'PTRANS': 24, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 457 Unresolved non-hydrogen angles: 576 Unresolved non-hydrogen dihedrals: 387 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 5, 'ASP:plan': 27, 'GLU:plan': 23, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 298 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'GLC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.74, per 1000 atoms: 0.59 Number of scatterers: 11521 At special positions: 0 Unit cell: (99.75, 136.5, 131.25, 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 42 16.00 O 2147 8.00 N 1989 7.00 C 7343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS T 7 " - pdb=" SG CYS T 71 " distance=2.03 Simple disulfide: pdb=" SG CYS T 95 " - pdb=" SG CYS E 33 " distance=2.03 Simple disulfide: pdb=" SG CYS T 295 " - pdb=" SG CYS T 362 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 382 " - pdb=" SG CYS E 385 " distance=2.03 Simple disulfide: pdb=" SG CYS M 101 " - pdb=" SG CYS M 164 " distance=2.03 Simple disulfide: pdb=" SG CYS M 203 " - pdb=" SG CYS M 259 " distance=2.04 Simple disulfide: pdb=" SG CYS C 88 " - pdb=" SG CYS C 120 " distance=2.04 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 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN D 5 " - " MAN D 6 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " MAN D 6 " - " GLC D 7 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A 1 " - " ASN T 233 " " NAG D 1 " - " ASN M 86 " Time building additional restraints: 4.89 Conformation dependent library (CDL) restraints added in 2.0 seconds 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2882 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 27 sheets defined 23.9% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'T' and resid 41 through 44 Processing helix chain 'T' and resid 53 through 61 removed outlier: 3.629A pdb=" N ALA T 57 " --> pdb=" O GLY T 53 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 90 removed outlier: 4.387A pdb=" N GLY T 88 " --> pdb=" O TRP T 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 100 No H-bonds generated for 'chain 'T' and resid 98 through 100' Processing helix chain 'T' and resid 242 through 246 Processing helix chain 'E' and resid 7 through 9 No H-bonds generated for 'chain 'E' and resid 7 through 9' Processing helix chain 'E' and resid 10 through 16 removed outlier: 3.929A pdb=" N SER E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 50 removed outlier: 3.787A pdb=" N LYS E 37 " --> pdb=" O CYS E 33 " (cutoff:3.500A) Proline residue: E 41 - end of helix Processing helix chain 'E' and resid 64 through 72 removed outlier: 4.257A pdb=" N CYS E 68 " --> pdb=" O ASN E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 109 removed outlier: 3.556A pdb=" N GLY E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'E' and resid 141 through 154 Processing helix chain 'E' and resid 165 through 171 Processing helix chain 'E' and resid 184 through 188 removed outlier: 3.949A pdb=" N THR E 188 " --> pdb=" O SER E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.525A pdb=" N ILE E 231 " --> pdb=" O ASN E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 270 removed outlier: 8.156A pdb=" N LYS E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 290 removed outlier: 3.935A pdb=" N SER E 288 " --> pdb=" O SER E 284 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP E 289 " --> pdb=" O HIS E 285 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 335 Processing helix chain 'E' and resid 361 through 366 Processing helix chain 'E' and resid 382 through 399 Proline residue: E 390 - end of helix Processing helix chain 'E' and resid 400 through 402 No H-bonds generated for 'chain 'E' and resid 400 through 402' Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'M' and resid 49 through 54 removed outlier: 4.034A pdb=" N GLN M 54 " --> pdb=" O PRO M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 86 removed outlier: 3.734A pdb=" N VAL M 76 " --> pdb=" O GLN M 72 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN M 86 " --> pdb=" O ARG M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 151 removed outlier: 3.541A pdb=" N ALA M 150 " --> pdb=" O LYS M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 162 removed outlier: 3.521A pdb=" N ALA M 158 " --> pdb=" O GLU M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 175 Processing helix chain 'C' and resid 15 through 20 removed outlier: 3.818A pdb=" N ARG C 19 " --> pdb=" O GLY C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 Processing helix chain 'C' and resid 285 through 289 removed outlier: 4.172A pdb=" N TYR C 289 " --> pdb=" O PRO C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 369 removed outlier: 4.446A pdb=" N VAL C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 335 " --> pdb=" O GLY C 331 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 8 through 9 removed outlier: 3.646A pdb=" N SER B 55 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'B' and resid 44 through 45 removed outlier: 3.632A pdb=" N GLU B 44 " --> pdb=" O LYS B 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'T' and resid 9 through 10 Processing sheet with id=AA5, first strand: chain 'T' and resid 46 through 49 removed outlier: 3.600A pdb=" N ALA T 135 " --> pdb=" O SER T 47 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL T 137 " --> pdb=" O HIS T 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 95 through 96 Processing sheet with id=AA7, first strand: chain 'T' and resid 139 through 142 Processing sheet with id=AA8, first strand: chain 'T' and resid 149 through 151 removed outlier: 6.256A pdb=" N VAL T 150 " --> pdb=" O TYR T 269 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY T 247 " --> pdb=" O LEU T 266 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR T 248 " --> pdb=" O GLN T 189 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU T 198 " --> pdb=" O TRP T 186 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARG T 188 " --> pdb=" O LEU T 196 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU T 196 " --> pdb=" O ARG T 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 149 through 151 removed outlier: 6.256A pdb=" N VAL T 150 " --> pdb=" O TYR T 269 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY T 247 " --> pdb=" O LEU T 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 156 through 158 Processing sheet with id=AB2, first strand: chain 'T' and resid 274 through 277 Processing sheet with id=AB3, first strand: chain 'T' and resid 321 through 322 Processing sheet with id=AB4, first strand: chain 'T' and resid 334 through 335 removed outlier: 4.470A pdb=" N TRP M 244 " --> pdb=" O VAL M 231 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N THR M 233 " --> pdb=" O GLN M 242 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLN M 242 " --> pdb=" O THR M 233 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N PHE M 241 " --> pdb=" O GLY M 207 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 4 through 5 removed outlier: 6.090A pdb=" N LEU E 4 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ASP E 60 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ILE E 81 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 113 through 115 removed outlier: 3.761A pdb=" N GLY E 178 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 276 through 279 removed outlier: 6.140A pdb=" N ALA E 239 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 355 through 357 removed outlier: 4.271A pdb=" N ASP E 411 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASP E 372 " --> pdb=" O VAL E 406 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA E 408 " --> pdb=" O ASP E 372 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU E 374 " --> pdb=" O ALA E 408 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N MET E 410 " --> pdb=" O LEU E 374 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU E 376 " --> pdb=" O MET E 410 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 31 through 37 removed outlier: 5.308A pdb=" N GLN M 32 " --> pdb=" O VAL M 28 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL M 28 " --> pdb=" O GLN M 32 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL M 34 " --> pdb=" O GLY M 26 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG M 114 " --> pdb=" O LEU M 126 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N TYR M 118 " --> pdb=" O ASP M 122 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP M 122 " --> pdb=" O TYR M 118 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 222 through 223 Processing sheet with id=AC2, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AC3, first strand: chain 'C' and resid 6 through 8 removed outlier: 4.197A pdb=" N PHE C 313 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLN C 77 " --> pdb=" O PHE C 313 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE C 315 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 75 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR C 164 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TYR C 165 " --> pdb=" O SER C 176 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER C 176 " --> pdb=" O TYR C 165 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 167 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 21 through 22 removed outlier: 9.904A pdb=" N SER C 63 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N GLY C 298 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N GLU C 65 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL C 296 " --> pdb=" O GLU C 65 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE C 96 " --> pdb=" O GLY C 295 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU C 297 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS C 94 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 113 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 56 through 57 removed outlier: 3.608A pdb=" N ARG C 56 " --> pdb=" O GLN C 303 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN C 303 " --> pdb=" O ARG C 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 88 through 90 removed outlier: 3.612A pdb=" N ASP C 118 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS C 126 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 190 through 192 Processing sheet with id=AC8, first strand: chain 'C' and resid 207 through 208 Processing sheet with id=AC9, first strand: chain 'C' and resid 224 through 226 467 hydrogen bonds defined for protein. 1230 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: 4.01 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3754 1.34 - 1.46: 2826 1.46 - 1.59: 5195 1.59 - 1.71: 0 1.71 - 1.83: 63 Bond restraints: 11838 Sorted by residual: bond pdb=" N VAL C 174 " pdb=" CA VAL C 174 " ideal model delta sigma weight residual 1.456 1.496 -0.039 9.50e-03 1.11e+04 1.70e+01 bond pdb=" N PRO M 50 " pdb=" CD PRO M 50 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.20e+01 bond pdb=" N VAL C 93 " pdb=" CA VAL C 93 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.19e+01 bond pdb=" N ILE C 86 " pdb=" CA ILE C 86 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.83e+00 bond pdb=" N GLU B 74 " pdb=" CA GLU B 74 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.12e-02 7.97e+03 9.26e+00 ... (remaining 11833 not shown) Histogram of bond angle deviations from ideal: 97.68 - 104.99: 343 104.99 - 112.29: 5921 112.29 - 119.60: 3808 119.60 - 126.90: 5900 126.90 - 134.21: 201 Bond angle restraints: 16173 Sorted by residual: angle pdb=" N ASP M 29 " pdb=" CA ASP M 29 " pdb=" C ASP M 29 " ideal model delta sigma weight residual 108.00 100.75 7.25 1.48e+00 4.57e-01 2.40e+01 angle pdb=" N VAL M 28 " pdb=" CA VAL M 28 " pdb=" C VAL M 28 " ideal model delta sigma weight residual 107.80 100.82 6.98 1.45e+00 4.76e-01 2.31e+01 angle pdb=" N ASP C 87 " pdb=" CA ASP C 87 " pdb=" C ASP C 87 " ideal model delta sigma weight residual 113.12 107.95 5.17 1.25e+00 6.40e-01 1.71e+01 angle pdb=" N LYS T 193 " pdb=" CA LYS T 193 " pdb=" C LYS T 193 " ideal model delta sigma weight residual 112.12 106.59 5.53 1.34e+00 5.57e-01 1.70e+01 angle pdb=" N VAL C 174 " pdb=" CA VAL C 174 " pdb=" C VAL C 174 " ideal model delta sigma weight residual 113.53 109.60 3.93 9.80e-01 1.04e+00 1.61e+01 ... (remaining 16168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 6816 21.64 - 43.27: 256 43.27 - 64.91: 29 64.91 - 86.55: 17 86.55 - 108.18: 9 Dihedral angle restraints: 7127 sinusoidal: 2656 harmonic: 4471 Sorted by residual: dihedral pdb=" CB CYS E 61 " pdb=" SG CYS E 61 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual 93.00 178.31 -85.31 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CA ILE E 304 " pdb=" C ILE E 304 " pdb=" N ARG E 305 " pdb=" CA ARG E 305 " ideal model delta harmonic sigma weight residual 180.00 160.76 19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" O4 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C5 BMA A 3 " pdb=" O5 BMA A 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.47 108.18 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 7124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1456 0.059 - 0.118: 286 0.118 - 0.177: 40 0.177 - 0.236: 7 0.236 - 0.295: 4 Chirality restraints: 1793 Sorted by residual: chirality pdb=" CA ILE C 113 " pdb=" N ILE C 113 " pdb=" C ILE C 113 " pdb=" CB ILE C 113 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 1790 not shown) Planarity restraints: 2121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR M 27 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C TYR M 27 " -0.061 2.00e-02 2.50e+03 pdb=" O TYR M 27 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL M 28 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 60 " 0.015 2.00e-02 2.50e+03 1.43e-02 5.09e+00 pdb=" CG TRP M 60 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP M 60 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP M 60 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP M 60 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP M 60 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP M 60 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 60 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 60 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP M 60 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP M 29 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.76e+00 pdb=" C ASP M 29 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP M 29 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP M 30 " 0.013 2.00e-02 2.50e+03 ... (remaining 2118 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1591 2.76 - 3.29: 10755 3.29 - 3.83: 18482 3.83 - 4.36: 21025 4.36 - 4.90: 36894 Nonbonded interactions: 88747 Sorted by model distance: nonbonded pdb=" OH TYR B 10 " pdb=" O PRO M 235 " model vdw 2.225 2.440 nonbonded pdb=" O GLN T 245 " pdb=" OH TYR T 249 " model vdw 2.237 2.440 nonbonded pdb=" N GLY C 30 " pdb=" O PHE C 57 " model vdw 2.323 2.520 nonbonded pdb=" OE2 GLU E 286 " pdb=" NH2 ARG E 305 " model vdw 2.358 2.520 nonbonded pdb=" NH1 ARG B 45 " pdb=" O ILE B 46 " model vdw 2.388 2.520 ... (remaining 88742 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 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: 3.190 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: 10.020 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 34.430 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 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: 0.020 Load rotamer database and sin/cos tables:3.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 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 : 0.005 0.049 11838 Z= 0.325 Angle : 0.809 8.835 16173 Z= 0.492 Chirality : 0.051 0.295 1793 Planarity : 0.005 0.050 2119 Dihedral : 12.543 108.182 4218 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.93 % Favored : 95.01 % Rotamer: Outliers : 0.09 % Allowed : 0.94 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % 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: -1.20 (0.22), residues: 1522 helix: 1.11 (0.30), residues: 297 sheet: -1.59 (0.24), residues: 416 loop : -1.03 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP M 60 HIS 0.004 0.001 HIS T 345 PHE 0.031 0.002 PHE C 325 TYR 0.012 0.001 TYR B 63 ARG 0.009 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 40 LEU cc_start: 0.6629 (mt) cc_final: 0.6338 (mt) REVERT: T 87 SER cc_start: 0.8633 (p) cc_final: 0.8368 (t) REVERT: C 92 TYR cc_start: 0.6936 (p90) cc_final: 0.6668 (p90) outliers start: 1 outliers final: 1 residues processed: 219 average time/residue: 0.2931 time to fit residues: 85.6678 Evaluate side-chains 122 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 28 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 chunk 61 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 242 GLN M 72 GLN M 192 HIS C 137 ASN C 173 GLN ** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11838 Z= 0.221 Angle : 0.650 9.043 16173 Z= 0.325 Chirality : 0.045 0.288 1793 Planarity : 0.005 0.043 2119 Dihedral : 8.034 66.843 1849 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.26 % Favored : 94.68 % Rotamer: Outliers : 2.17 % Allowed : 8.21 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % 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: -0.88 (0.22), residues: 1522 helix: 1.35 (0.30), residues: 308 sheet: -1.24 (0.25), residues: 421 loop : -0.94 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 204 HIS 0.010 0.001 HIS C 153 PHE 0.019 0.002 PHE T 236 TYR 0.025 0.002 TYR C 321 ARG 0.013 0.001 ARG M 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 40 LEU cc_start: 0.7234 (mt) cc_final: 0.6844 (mt) REVERT: T 87 SER cc_start: 0.8538 (p) cc_final: 0.8290 (t) REVERT: C 321 TYR cc_start: 0.6942 (OUTLIER) cc_final: 0.6612 (t80) REVERT: C 349 ARG cc_start: 0.8648 (tmm-80) cc_final: 0.8296 (tmm-80) outliers start: 23 outliers final: 12 residues processed: 146 average time/residue: 0.2291 time to fit residues: 48.1742 Evaluate side-chains 127 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain T residue 100 ASP Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 150 VAL Chi-restraints excluded: chain T residue 227 TRP Chi-restraints excluded: chain T residue 277 MET Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain M residue 72 GLN Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 321 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 136 optimal weight: 0.0000 chunk 46 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 70 HIS ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11838 Z= 0.400 Angle : 0.708 10.069 16173 Z= 0.356 Chirality : 0.046 0.341 1793 Planarity : 0.005 0.048 2119 Dihedral : 7.207 59.271 1848 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.11 % Favored : 93.82 % Rotamer: Outliers : 2.26 % Allowed : 12.45 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.22), residues: 1522 helix: 1.37 (0.30), residues: 306 sheet: -1.24 (0.25), residues: 435 loop : -1.07 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 204 HIS 0.006 0.001 HIS M 93 PHE 0.028 0.003 PHE B 30 TYR 0.030 0.002 TYR B 67 ARG 0.003 0.001 ARG M 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 ASN cc_start: 0.7434 (t0) cc_final: 0.7225 (t0) REVERT: T 40 LEU cc_start: 0.7302 (mt) cc_final: 0.6821 (mt) REVERT: T 87 SER cc_start: 0.8677 (p) cc_final: 0.8369 (t) REVERT: T 90 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8301 (p) REVERT: T 165 MET cc_start: 0.7159 (tpp) cc_final: 0.6837 (tpp) REVERT: M 138 MET cc_start: 0.7952 (ttm) cc_final: 0.7677 (ttp) REVERT: C 92 TYR cc_start: 0.6720 (p90) cc_final: 0.6492 (p90) REVERT: C 254 TYR cc_start: 0.5152 (t80) cc_final: 0.3976 (t80) outliers start: 24 outliers final: 13 residues processed: 131 average time/residue: 0.2217 time to fit residues: 43.1531 Evaluate side-chains 123 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 100 ASP Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 150 VAL Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain T residue 227 TRP Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 259 CYS Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 303 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 72 GLN C 173 GLN C 303 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11838 Z= 0.261 Angle : 0.656 14.939 16173 Z= 0.322 Chirality : 0.044 0.306 1793 Planarity : 0.005 0.044 2119 Dihedral : 6.214 58.222 1848 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.19 % Favored : 94.74 % Rotamer: Outliers : 2.08 % Allowed : 13.58 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % 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: -0.85 (0.22), residues: 1522 helix: 1.54 (0.30), residues: 306 sheet: -1.19 (0.25), residues: 431 loop : -1.00 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 204 HIS 0.007 0.001 HIS M 192 PHE 0.022 0.002 PHE C 115 TYR 0.026 0.002 TYR B 67 ARG 0.003 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 ASN cc_start: 0.7509 (t0) cc_final: 0.7228 (t0) REVERT: T 40 LEU cc_start: 0.7491 (mt) cc_final: 0.7040 (mt) REVERT: T 87 SER cc_start: 0.8613 (p) cc_final: 0.8284 (t) REVERT: T 90 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8261 (p) REVERT: T 165 MET cc_start: 0.7246 (tpp) cc_final: 0.7013 (tpp) REVERT: T 347 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8751 (tp40) REVERT: E 24 MET cc_start: 0.4428 (tpt) cc_final: 0.4070 (tpp) REVERT: C 254 TYR cc_start: 0.4690 (t80) cc_final: 0.3767 (t80) REVERT: C 349 ARG cc_start: 0.8682 (tmm-80) cc_final: 0.8242 (tmm-80) outliers start: 22 outliers final: 13 residues processed: 135 average time/residue: 0.2114 time to fit residues: 42.5908 Evaluate side-chains 131 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 100 ASP Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 150 VAL Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain T residue 227 TRP Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 259 CYS Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain C residue 157 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.3428 > 50: distance: 28 - 33: 19.519 distance: 33 - 34: 3.933 distance: 33 - 137: 20.762 distance: 34 - 35: 8.906 distance: 34 - 37: 6.257 distance: 35 - 36: 5.268 distance: 35 - 41: 43.545 distance: 37 - 38: 6.602 distance: 38 - 39: 17.840 distance: 38 - 40: 24.174 distance: 41 - 42: 35.019 distance: 42 - 43: 19.422 distance: 42 - 45: 24.625 distance: 43 - 44: 11.039 distance: 43 - 52: 17.737 distance: 44 - 154: 22.111 distance: 45 - 46: 12.458 distance: 46 - 47: 10.273 distance: 46 - 48: 18.335 distance: 47 - 49: 28.131 distance: 48 - 50: 24.692 distance: 49 - 51: 15.811 distance: 50 - 51: 5.502 distance: 52 - 53: 22.832 distance: 52 - 58: 34.851 distance: 53 - 54: 10.869 distance: 53 - 56: 19.605 distance: 54 - 55: 55.893 distance: 54 - 59: 16.681 distance: 56 - 57: 5.444 distance: 57 - 58: 19.411 distance: 59 - 60: 6.121 distance: 60 - 61: 34.936 distance: 60 - 63: 24.169 distance: 61 - 62: 37.097 distance: 61 - 64: 13.253 distance: 64 - 65: 28.404 distance: 65 - 66: 17.286 distance: 65 - 68: 23.201 distance: 66 - 67: 30.688 distance: 66 - 69: 25.169 distance: 69 - 70: 25.275 distance: 70 - 71: 26.891 distance: 70 - 73: 56.092 distance: 71 - 72: 27.136 distance: 71 - 74: 14.271 distance: 74 - 75: 6.243 distance: 75 - 76: 34.107 distance: 75 - 78: 25.008 distance: 76 - 77: 17.693 distance: 76 - 82: 39.959 distance: 78 - 79: 8.275 distance: 79 - 80: 22.965 distance: 79 - 81: 33.753 distance: 82 - 83: 35.797 distance: 83 - 84: 28.290 distance: 83 - 86: 39.512 distance: 84 - 85: 36.758 distance: 84 - 87: 30.383 distance: 87 - 88: 15.302 distance: 88 - 89: 16.031 distance: 88 - 91: 40.844 distance: 89 - 90: 26.270 distance: 89 - 94: 15.579 distance: 91 - 92: 20.583 distance: 91 - 93: 14.163 distance: 94 - 95: 18.030 distance: 95 - 96: 6.474 distance: 95 - 98: 34.878 distance: 96 - 97: 18.097 distance: 96 - 99: 8.298