Starting phenix.real_space_refine on Mon Aug 5 06:07:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc5_34652/08_2024/8hc5_34652.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc5_34652/08_2024/8hc5_34652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc5_34652/08_2024/8hc5_34652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc5_34652/08_2024/8hc5_34652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc5_34652/08_2024/8hc5_34652.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc5_34652/08_2024/8hc5_34652.cif" } resolution = 3.43 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= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1488 atoms to isotropic. 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 45 5.16 5 C 7218 2.51 5 N 1906 2.21 5 O 2231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "L ASP 17": "OD1" <-> "OD2" Residue "L TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 144": "OE1" <-> "OE2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 155": "OD1" <-> "OD2" Residue "D TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11400 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4948 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 31, 'TRANS': 592} Chain breaks: 2 Chain: "H" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1588 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Chain breaks: 1 Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 203} Chain: "D" Number of atoms: 1665 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1690 Chain: "E" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.56, per 1000 atoms: 0.66 Number of scatterers: 11400 At special positions: 0 Unit cell: (99.552, 171.288, 161.04, 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 45 16.00 O 2231 8.00 N 1906 7.00 C 7218 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 143 " - pdb=" SG CYS H 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 219 " - pdb=" SG CYS L 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 151 " - pdb=" SG CYS D 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 139 " - pdb=" SG CYS E 198 " 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 Links applied NAG-ASN " NAG C 701 " - " ASN C 343 " Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 2.5 seconds 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2748 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 34 sheets defined 4.8% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.986A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.928A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.596A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 409 through 411 No H-bonds generated for 'chain 'C' and resid 409 through 411' Processing helix chain 'H' and resid 86 through 90 removed outlier: 4.049A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 161 No H-bonds generated for 'chain 'H' and resid 159 through 161' Processing helix chain 'H' and resid 188 through 192 removed outlier: 3.524A pdb=" N SER H 191 " --> pdb=" O PRO H 188 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU H 192 " --> pdb=" O SER H 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 188 through 192' Processing helix chain 'L' and resid 122 through 127 removed outlier: 3.612A pdb=" N LYS L 127 " --> pdb=" O GLU L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 188 removed outlier: 3.566A pdb=" N GLU L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 184 through 188' Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.962A pdb=" N GLU E 85 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 removed outlier: 3.872A pdb=" N GLN E 131 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN E 133 " --> pdb=" O LEU E 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.142A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR C 279 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 63 through 67 removed outlier: 3.509A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.504A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.490A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.555A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.504A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 312 through 313 removed outlier: 3.710A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.708A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA C 435 " --> pdb=" O SER C 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.737A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.087A pdb=" N ARG C 466 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY D 104 " --> pdb=" O ARG C 466 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE C 468 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D 102 " --> pdb=" O ILE C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.750A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 664 through 667 removed outlier: 3.670A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C 672 " --> pdb=" O ILE C 664 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.189A pdb=" N TYR H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.129A pdb=" N ARG H 97 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 123 through 127 removed outlier: 4.202A pdb=" N GLY H 142 " --> pdb=" O LEU H 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER H 183 " --> pdb=" O CYS H 143 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP H 147 " --> pdb=" O TYR H 179 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR H 179 " --> pdb=" O ASP H 147 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL H 184 " --> pdb=" O HIS H 167 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 123 through 127 removed outlier: 4.202A pdb=" N GLY H 142 " --> pdb=" O LEU H 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER H 183 " --> pdb=" O CYS H 143 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP H 147 " --> pdb=" O TYR H 179 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR H 179 " --> pdb=" O ASP H 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 154 through 157 removed outlier: 3.559A pdb=" N THR H 154 " --> pdb=" O ASN H 202 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN H 202 " --> pdb=" O THR H 154 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS H 199 " --> pdb=" O LYS H 212 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS H 212 " --> pdb=" O CYS H 199 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL H 201 " --> pdb=" O VAL H 210 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL H 210 " --> pdb=" O VAL H 201 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.650A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.822A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.677A pdb=" N GLN L 90 " --> pdb=" O THR L 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 112 through 119 removed outlier: 7.156A pdb=" N ALA L 113 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE L 140 " --> pdb=" O ALA L 113 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN L 138 " --> pdb=" O SER L 115 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL L 133 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU L 180 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N CYS L 135 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER L 178 " --> pdb=" O CYS L 135 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 154 through 155 removed outlier: 3.792A pdb=" N TYR L 193 " --> pdb=" O PHE L 210 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE L 210 " --> pdb=" O TYR L 193 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS L 195 " --> pdb=" O LYS L 208 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL L 197 " --> pdb=" O VAL L 206 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL L 206 " --> pdb=" O VAL L 197 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.034A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.670A pdb=" N ASN D 100 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE D 111 " --> pdb=" O ASN D 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 68 through 69 Processing sheet with id=AD1, first strand: chain 'D' and resid 131 through 135 removed outlier: 3.675A pdb=" N LYS D 154 " --> pdb=" O SER D 131 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE D 133 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU D 152 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY D 150 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 149 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 163 through 165 removed outlier: 3.690A pdb=" N SER D 164 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN D 208 " --> pdb=" O SER D 164 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR D 205 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS D 207 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS D 220 " --> pdb=" O CYS D 207 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL D 209 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL D 218 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR D 216 " --> pdb=" O HIS D 211 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.941A pdb=" N THR E 109 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR E 88 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP E 37 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.941A pdb=" N THR E 109 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR E 88 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 17 through 22 removed outlier: 4.166A pdb=" N VAL E 18 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE E 77 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE E 20 " --> pdb=" O LEU E 75 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 119 through 123 removed outlier: 3.586A pdb=" N SER E 181 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE E 141 " --> pdb=" O ALA E 179 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA E 179 " --> pdb=" O ILE E 141 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP E 143 " --> pdb=" O TYR E 177 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N TYR E 177 " --> pdb=" O ASP E 143 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 150 through 154 removed outlier: 4.277A pdb=" N THR E 150 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR E 201 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS E 154 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER E 197 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR E 196 " --> pdb=" O VAL E 211 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS E 198 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS E 209 " --> pdb=" O CYS E 198 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL E 200 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL E 207 " --> pdb=" O VAL E 200 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 768 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: 3.95 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3657 1.35 - 1.46: 2889 1.46 - 1.58: 5078 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 11678 Sorted by residual: bond pdb=" C1 NAG C 701 " pdb=" O5 NAG C 701 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" CB GLU D 89 " pdb=" CG GLU D 89 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" CA PHE D 157 " pdb=" C PHE D 157 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.68e+00 bond pdb=" C5 NAG C 701 " pdb=" O5 NAG C 701 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.40e+00 bond pdb=" CA LYS H 213 " pdb=" C LYS H 213 " ideal model delta sigma weight residual 1.526 1.509 0.017 1.42e-02 4.96e+03 1.38e+00 ... (remaining 11673 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.34: 417 107.34 - 114.00: 6451 114.00 - 120.66: 4271 120.66 - 127.32: 4644 127.32 - 133.98: 122 Bond angle restraints: 15905 Sorted by residual: angle pdb=" CA GLU D 89 " pdb=" CB GLU D 89 " pdb=" CG GLU D 89 " ideal model delta sigma weight residual 114.10 120.50 -6.40 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA GLU D 159 " pdb=" C GLU D 159 " pdb=" N PRO D 160 " ideal model delta sigma weight residual 120.79 117.78 3.01 9.70e-01 1.06e+00 9.65e+00 angle pdb=" CA LEU H 181 " pdb=" CB LEU H 181 " pdb=" CG LEU H 181 " ideal model delta sigma weight residual 116.30 126.58 -10.28 3.50e+00 8.16e-02 8.63e+00 angle pdb=" N LYS H 204 " pdb=" CA LYS H 204 " pdb=" C LYS H 204 " ideal model delta sigma weight residual 109.81 116.20 -6.39 2.21e+00 2.05e-01 8.35e+00 angle pdb=" CB GLU D 89 " pdb=" CG GLU D 89 " pdb=" CD GLU D 89 " ideal model delta sigma weight residual 112.60 117.50 -4.90 1.70e+00 3.46e-01 8.31e+00 ... (remaining 15900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 6093 17.58 - 35.17: 656 35.17 - 52.75: 177 52.75 - 70.33: 21 70.33 - 87.91: 14 Dihedral angle restraints: 6961 sinusoidal: 2652 harmonic: 4309 Sorted by residual: dihedral pdb=" CB CYS H 143 " pdb=" SG CYS H 143 " pdb=" SG CYS H 199 " pdb=" CB CYS H 199 " ideal model delta sinusoidal sigma weight residual 93.00 165.28 -72.28 1 1.00e+01 1.00e-02 6.68e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 145.44 -52.44 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 63.78 29.22 1 1.00e+01 1.00e-02 1.22e+01 ... (remaining 6958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1360 0.043 - 0.086: 278 0.086 - 0.130: 147 0.130 - 0.173: 4 0.173 - 0.216: 1 Chirality restraints: 1790 Sorted by residual: chirality pdb=" CB THR H 90 " pdb=" CA THR H 90 " pdb=" OG1 THR H 90 " pdb=" CG2 THR H 90 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB VAL L 147 " pdb=" CA VAL L 147 " pdb=" CG1 VAL L 147 " pdb=" CG2 VAL L 147 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA VAL D 161 " pdb=" N VAL D 161 " pdb=" C VAL D 161 " pdb=" CB VAL D 161 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 1787 not shown) Planarity restraints: 2049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 112 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C GLY E 112 " 0.047 2.00e-02 2.50e+03 pdb=" O GLY E 112 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN E 113 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS H 204 " -0.045 5.00e-02 4.00e+02 6.81e-02 7.42e+00 pdb=" N PRO H 205 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO H 205 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 205 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 133 " -0.010 2.00e-02 2.50e+03 1.46e-02 3.71e+00 pdb=" CG PHE D 133 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE D 133 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE D 133 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE D 133 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 133 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 133 " 0.000 2.00e-02 2.50e+03 ... (remaining 2046 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2089 2.78 - 3.31: 9272 3.31 - 3.84: 18298 3.84 - 4.37: 19741 4.37 - 4.90: 35658 Nonbonded interactions: 85058 Sorted by model distance: nonbonded pdb=" OD1 ASN L 92 " pdb=" N SER L 93 " model vdw 2.249 3.120 nonbonded pdb=" O LEU C 455 " pdb=" OH TYR H 33 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.300 3.040 nonbonded pdb=" O CYS D 151 " pdb=" OG SER D 191 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR E 33 " pdb=" OG SER E 95 " model vdw 2.337 3.040 ... (remaining 85053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.890 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5695 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 : 0.002 0.042 11678 Z= 0.141 Angle : 0.527 10.282 15905 Z= 0.275 Chirality : 0.043 0.216 1790 Planarity : 0.004 0.068 2048 Dihedral : 15.559 87.915 4156 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 23.19 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.79 (0.21), residues: 1479 helix: -3.27 (0.45), residues: 57 sheet: 0.50 (0.25), residues: 460 loop : -0.89 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.003 0.000 HIS H 203 PHE 0.033 0.001 PHE D 133 TYR 0.027 0.001 TYR L 141 ARG 0.002 0.000 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: D 89 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7870 (tm-30) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1893 time to fit residues: 22.9434 Evaluate side-chains 65 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 40.0000 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 85 optimal weight: 0.4980 chunk 133 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 72 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 ASN E 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11678 Z= 0.224 Angle : 0.549 7.922 15905 Z= 0.285 Chirality : 0.044 0.165 1790 Planarity : 0.005 0.068 2048 Dihedral : 3.423 22.840 1628 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.81 % Allowed : 21.46 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.58 (0.22), residues: 1479 helix: -2.74 (0.56), residues: 56 sheet: 0.38 (0.24), residues: 502 loop : -0.66 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 114 HIS 0.003 0.001 HIS H 35 PHE 0.016 0.001 PHE C 429 TYR 0.013 0.001 TYR D 95 ARG 0.006 0.001 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 72 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: D 51 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7991 (tt) outliers start: 23 outliers final: 13 residues processed: 92 average time/residue: 0.2170 time to fit residues: 30.6176 Evaluate side-chains 78 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 55 ASN Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 138 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 144 optimal weight: 50.0000 chunk 119 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11678 Z= 0.214 Angle : 0.528 7.724 15905 Z= 0.270 Chirality : 0.044 0.150 1790 Planarity : 0.004 0.048 2048 Dihedral : 3.591 23.340 1628 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.83 % Allowed : 20.99 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.60 (0.22), residues: 1479 helix: -2.17 (0.67), residues: 48 sheet: 0.16 (0.23), residues: 527 loop : -0.61 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.005 0.001 HIS L 199 PHE 0.015 0.001 PHE H 67 TYR 0.019 0.001 TYR L 193 ARG 0.003 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 66 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: L 77 SER cc_start: 0.6593 (OUTLIER) cc_final: 0.6325 (p) REVERT: E 83 GLU cc_start: 0.5511 (tt0) cc_final: 0.5287 (tt0) outliers start: 36 outliers final: 18 residues processed: 100 average time/residue: 0.2137 time to fit residues: 33.0456 Evaluate side-chains 79 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 143 CYS Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 55 ASN Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 149 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 14 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 142 optimal weight: 50.0000 chunk 70 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11678 Z= 0.188 Angle : 0.499 6.427 15905 Z= 0.256 Chirality : 0.043 0.167 1790 Planarity : 0.004 0.056 2048 Dihedral : 3.554 23.390 1628 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.20 % Allowed : 21.15 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.59 (0.22), residues: 1479 helix: -2.00 (0.69), residues: 48 sheet: 0.15 (0.23), residues: 530 loop : -0.60 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 36 HIS 0.003 0.001 HIS L 199 PHE 0.011 0.001 PHE C 429 TYR 0.012 0.001 TYR C 396 ARG 0.006 0.000 ARG L 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 66 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: C 377 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.5405 (m-80) REVERT: C 405 ASP cc_start: 0.6801 (t70) cc_final: 0.6435 (t0) REVERT: L 77 SER cc_start: 0.6694 (OUTLIER) cc_final: 0.6345 (p) REVERT: E 81 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.6025 (mm110) outliers start: 28 outliers final: 17 residues processed: 92 average time/residue: 0.2032 time to fit residues: 29.3583 Evaluate side-chains 84 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 64 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 143 CYS Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 149 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 53.898 > 50: distance: 15 - 21: 9.747 distance: 21 - 22: 12.530 distance: 22 - 23: 5.063 distance: 22 - 25: 8.499 distance: 23 - 24: 11.675 distance: 23 - 28: 5.849 distance: 25 - 26: 14.412 distance: 25 - 27: 16.408 distance: 28 - 29: 5.505 distance: 29 - 30: 3.006 distance: 30 - 31: 6.100 distance: 30 - 34: 7.266 distance: 32 - 33: 19.278 distance: 34 - 35: 6.792 distance: 35 - 36: 5.021 distance: 36 - 37: 17.421 distance: 36 - 38: 18.872 distance: 39 - 40: 9.246 distance: 39 - 42: 4.688 distance: 40 - 41: 14.691 distance: 40 - 45: 8.044 distance: 42 - 43: 18.494 distance: 42 - 44: 21.176 distance: 45 - 46: 9.704 distance: 46 - 47: 11.004 distance: 46 - 49: 9.659 distance: 47 - 48: 19.260 distance: 47 - 55: 3.726 distance: 49 - 50: 9.888 distance: 50 - 51: 10.415 distance: 50 - 52: 12.226 distance: 51 - 53: 6.309 distance: 52 - 54: 5.197 distance: 53 - 54: 5.533 distance: 55 - 56: 11.628 distance: 56 - 57: 13.798 distance: 56 - 59: 18.294 distance: 57 - 58: 24.386 distance: 57 - 62: 20.727 distance: 59 - 60: 23.580 distance: 59 - 61: 16.832 distance: 62 - 63: 17.797 distance: 63 - 64: 24.393 distance: 63 - 66: 11.812 distance: 64 - 65: 10.750 distance: 64 - 73: 19.002 distance: 66 - 67: 17.733 distance: 67 - 68: 13.908 distance: 67 - 69: 6.247 distance: 68 - 70: 19.751 distance: 69 - 71: 8.221 distance: 70 - 72: 18.234 distance: 71 - 72: 16.499 distance: 73 - 74: 10.283 distance: 73 - 79: 28.476 distance: 74 - 75: 11.198 distance: 74 - 77: 13.876 distance: 75 - 76: 9.349 distance: 75 - 80: 9.098 distance: 77 - 78: 7.533 distance: 78 - 79: 14.188 distance: 80 - 81: 25.355 distance: 81 - 82: 20.074 distance: 81 - 84: 20.014 distance: 82 - 83: 17.020 distance: 82 - 85: 16.728 distance: 85 - 86: 14.520 distance: 86 - 87: 10.055 distance: 86 - 89: 17.753 distance: 87 - 92: 34.704 distance: 89 - 90: 15.900 distance: 89 - 91: 16.589