Starting phenix.real_space_refine on Sat Dec 16 21:32:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foi_29350/12_2023/8foi_29350_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foi_29350/12_2023/8foi_29350.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foi_29350/12_2023/8foi_29350_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foi_29350/12_2023/8foi_29350_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foi_29350/12_2023/8foi_29350_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foi_29350/12_2023/8foi_29350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foi_29350/12_2023/8foi_29350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foi_29350/12_2023/8foi_29350_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foi_29350/12_2023/8foi_29350_trim_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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: 6 Type Number sf(0) Gaussians P 11 5.49 5 S 94 5.16 5 C 11972 2.51 5 N 2832 2.21 5 O 3377 1.98 5 H 16834 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 35120 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 5585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 5585 Classifications: {'peptide': 346} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 331} Chain breaks: 1 Chain: "B" Number of atoms: 5454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5454 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain breaks: 1 Chain: "C" Number of atoms: 5585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 5585 Classifications: {'peptide': 346} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 331} Chain breaks: 1 Chain: "D" Number of atoms: 5186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5186 Classifications: {'peptide': 318} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 304} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 5455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5455 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain breaks: 1 Chain: "H" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1783 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'GLU%NH3:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1783 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'GLU%NH3:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "K" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1552 Classifications: {'peptide': 105} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1542 Classifications: {'peptide': 105} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Chain: "N" 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 207 Unusual residues: {'D12': 2, 'OCT': 4, 'PIO': 1, 'POV': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 114 Unusual residues: {'ABU': 1, 'D12': 7, 'Y4B': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 199 Unusual residues: {'D12': 2, 'OCT': 3, 'PIO': 1, 'POV': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 78 Unusual residues: {'D12': 2, 'NAG': 1, 'OCT': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 170 Unusual residues: {'ABU': 1, 'D12': 4, 'OCT': 5, 'POV': 1, 'Y4B': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 15.93, per 1000 atoms: 0.45 Number of scatterers: 35120 At special positions: 0 Unit cell: (102.213, 166.2, 133.791, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 94 16.00 P 11 15.00 O 3377 8.00 N 2832 7.00 C 11972 6.00 H 16834 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 151 " - pdb=" SG CYS D 165 " distance=2.04 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 ALPHA1-2 " MAN F 4 " - " MAN F 5 " ALPHA1-3 " BMA F 3 " - " MAN F 4 " " MAN F 6 " - " MAN F 7 " " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " ALPHA1-6 " BMA F 3 " - " MAN F 6 " " BMA G 3 " - " MAN G 5 " " BMA I 3 " - " MAN I 5 " " BMA M 3 " - " MAN M 5 " " BMA O 3 " - " MAN O 5 " " BMA P 3 " - " MAN P 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG D 501 " - " ASN D 90 " " NAG F 1 " - " ASN A 110 " " NAG G 1 " - " ASN B 80 " " NAG I 1 " - " ASN B 149 " " NAG M 1 " - " ASN C 110 " " NAG N 1 " - " ASN D 208 " " NAG O 1 " - " ASN E 80 " " NAG P 1 " - " ASN E 149 " Time building additional restraints: 32.10 Conformation dependent library (CDL) restraints added in 3.6 seconds 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4014 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 28 sheets defined 29.2% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.31 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 223 through 228 removed outlier: 3.660A pdb=" N ILE A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 245 removed outlier: 3.916A pdb=" N SER A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TRP A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 275 removed outlier: 3.623A pdb=" N ARG A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 309 removed outlier: 3.631A pdb=" N PHE A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 415 removed outlier: 4.041A pdb=" N ILE A 397 " --> pdb=" O ARG A 393 " (cutoff:3.500A) Proline residue: A 400 - end of helix Processing helix chain 'B' and resid 7 through 20 removed outlier: 3.647A pdb=" N LEU B 20 " --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.629A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 241 removed outlier: 3.556A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 3.909A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 307 removed outlier: 3.564A pdb=" N PHE B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 486 removed outlier: 3.573A pdb=" N ARG B 468 " --> pdb=" O ASP B 464 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) Proline residue: B 472 - end of helix Processing helix chain 'C' and resid 11 through 22 removed outlier: 3.578A pdb=" N ILE C 17 " --> pdb=" O VAL C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 87 through 92 removed outlier: 3.565A pdb=" N SER C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 223 through 228 removed outlier: 3.658A pdb=" N ILE C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 244 removed outlier: 4.212A pdb=" N SER C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N PHE C 244 " --> pdb=" O SER C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 275 removed outlier: 3.563A pdb=" N ASN C 274 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 309 removed outlier: 3.625A pdb=" N PHE C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 415 removed outlier: 4.663A pdb=" N ILE C 397 " --> pdb=" O ARG C 393 " (cutoff:3.500A) Proline residue: C 400 - end of helix Processing helix chain 'D' and resid 28 through 35 Processing helix chain 'D' and resid 85 through 87 No H-bonds generated for 'chain 'D' and resid 85 through 87' Processing helix chain 'D' and resid 100 through 105 removed outlier: 4.176A pdb=" N GLY D 104 " --> pdb=" O ASN D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 234 through 239 removed outlier: 3.514A pdb=" N ILE D 238 " --> pdb=" O GLY D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 256 removed outlier: 3.851A pdb=" N SER D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP D 256 " --> pdb=" O TRP D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 285 Processing helix chain 'D' and resid 295 through 318 Processing helix chain 'D' and resid 411 through 431 removed outlier: 3.511A pdb=" N ILE D 416 " --> pdb=" O SER D 412 " (cutoff:3.500A) Proline residue: D 419 - end of helix removed outlier: 3.500A pdb=" N VAL D 431 " --> pdb=" O LEU D 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 20 Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 85 through 90 Processing helix chain 'E' and resid 219 through 224 removed outlier: 3.574A pdb=" N LEU E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 240 removed outlier: 3.864A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 270 Processing helix chain 'E' and resid 280 through 307 removed outlier: 3.542A pdb=" N PHE E 291 " --> pdb=" O GLY E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 487 Proline residue: E 472 - end of helix Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'J' and resid 84 through 86 No H-bonds generated for 'chain 'J' and resid 84 through 86' Processing helix chain 'K' and resid 80 through 82 No H-bonds generated for 'chain 'K' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'A' and resid 166 through 170 removed outlier: 5.912A pdb=" N THR A 38 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU A 169 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 40 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU A 39 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS A 70 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASP A 62 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N PHE A 49 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR A 60 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 118 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 44 through 46 Processing sheet with id= C, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.507A pdb=" N SER A 158 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL A 210 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 194 " --> pdb=" O HIS A 217 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LYS A 219 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU A 192 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.237A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARG B 68 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.808A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B 190 " --> pdb=" O LYS B 213 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.748A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 166 through 170 removed outlier: 6.153A pdb=" N THR C 38 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLU C 169 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL C 40 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU C 39 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS C 70 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP C 62 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N PHE C 49 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR C 60 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR C 125 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 118 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 44 through 46 Processing sheet with id= I, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.539A pdb=" N SER C 158 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL C 210 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY C 194 " --> pdb=" O HIS C 217 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LYS C 219 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU C 192 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 179 through 183 removed outlier: 5.857A pdb=" N THR D 51 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN D 182 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE D 53 " --> pdb=" O GLN D 182 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU D 52 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR D 83 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP D 75 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE D 62 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR D 73 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 95 through 98 Processing sheet with id= L, first strand: chain 'D' and resid 111 through 113 removed outlier: 4.752A pdb=" N SER D 171 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL D 221 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER D 224 " --> pdb=" O THR D 209 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D 205 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N SER D 230 " --> pdb=" O PHE D 203 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHE D 203 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.148A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG E 68 " --> pdb=" O ALA E 37 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 49 through 51 removed outlier: 3.889A pdb=" N MET E 49 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.768A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP E 190 " --> pdb=" O LYS E 213 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 147 through 150 Processing sheet with id= Q, first strand: chain 'E' and resid 44 through 47 removed outlier: 6.618A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.988A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 18 through 23 removed outlier: 3.927A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 89 through 94 removed outlier: 3.739A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 4 through 6 Processing sheet with id= V, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.679A pdb=" N THR J 110 " --> pdb=" O GLU J 10 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 89 through 94 removed outlier: 3.707A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TRP J 47 " --> pdb=" O LYS J 38 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.218A pdb=" N LYS K 102 " --> pdb=" O MET K 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'K' and resid 19 through 24 Processing sheet with id= Z, first strand: chain 'K' and resid 85 through 90 removed outlier: 6.066A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 19 through 23 Processing sheet with id= AB, first strand: chain 'L' and resid 85 through 90 removed outlier: 6.224A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) 712 hydrogen bonds defined for protein. 2031 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: 14.20 Time building geometry restraints manager: 32.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16825 1.03 - 1.23: 68 1.23 - 1.42: 7759 1.42 - 1.62: 10699 1.62 - 1.82: 179 Bond restraints: 35530 Sorted by residual: bond pdb=" C13 Y4B E 501 " pdb=" C16 Y4B E 501 " ideal model delta sigma weight residual 1.734 1.521 0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C13 Y4B B 502 " pdb=" C16 Y4B B 502 " ideal model delta sigma weight residual 1.734 1.524 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C29 POV C 608 " pdb="C210 POV C 608 " ideal model delta sigma weight residual 1.333 1.527 -0.194 2.00e-02 2.50e+03 9.44e+01 bond pdb=" C29 POV E 511 " pdb="C210 POV E 511 " ideal model delta sigma weight residual 1.333 1.525 -0.192 2.00e-02 2.50e+03 9.18e+01 bond pdb=" C29 POV C 607 " pdb="C210 POV C 607 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.16e+01 ... (remaining 35525 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.07: 434 106.07 - 113.07: 40009 113.07 - 120.08: 11283 120.08 - 127.08: 11283 127.08 - 134.09: 221 Bond angle restraints: 63230 Sorted by residual: angle pdb=" O13 POV A 608 " pdb=" P POV A 608 " pdb=" O14 POV A 608 " ideal model delta sigma weight residual 121.11 101.04 20.07 3.00e+00 1.11e-01 4.47e+01 angle pdb=" O13 POV E 511 " pdb=" P POV E 511 " pdb=" O14 POV E 511 " ideal model delta sigma weight residual 121.11 101.15 19.96 3.00e+00 1.11e-01 4.43e+01 angle pdb=" O13 POV C 608 " pdb=" P POV C 608 " pdb=" O14 POV C 608 " ideal model delta sigma weight residual 121.11 101.17 19.94 3.00e+00 1.11e-01 4.42e+01 angle pdb=" O13 POV A 609 " pdb=" P POV A 609 " pdb=" O14 POV A 609 " ideal model delta sigma weight residual 121.11 101.51 19.60 3.00e+00 1.11e-01 4.27e+01 angle pdb=" O13 POV C 607 " pdb=" P POV C 607 " pdb=" O14 POV C 607 " ideal model delta sigma weight residual 121.11 101.62 19.49 3.00e+00 1.11e-01 4.22e+01 ... (remaining 63225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.63: 16433 31.63 - 63.27: 441 63.27 - 94.90: 31 94.90 - 126.53: 4 126.53 - 158.17: 5 Dihedral angle restraints: 16914 sinusoidal: 9161 harmonic: 7753 Sorted by residual: dihedral pdb=" C29 POV C 607 " pdb="C210 POV C 607 " pdb="C211 POV C 607 " pdb="C212 POV C 607 " ideal model delta sinusoidal sigma weight residual 112.25 -89.58 -158.17 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C27 POV A 608 " pdb=" C28 POV A 608 " pdb=" C29 POV A 608 " pdb="C210 POV A 608 " ideal model delta sinusoidal sigma weight residual 127.48 -79.45 -153.07 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C27 POV C 607 " pdb=" C28 POV C 607 " pdb=" C29 POV C 607 " pdb="C210 POV C 607 " ideal model delta sinusoidal sigma weight residual 127.48 -84.85 -147.67 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 16911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2659 0.085 - 0.170: 210 0.170 - 0.255: 17 0.255 - 0.340: 7 0.340 - 0.425: 4 Chirality restraints: 2897 Sorted by residual: chirality pdb=" C08 Y4B E 501 " pdb=" C07 Y4B E 501 " pdb=" C14 Y4B E 501 " pdb=" C17 Y4B E 501 " both_signs ideal model delta sigma weight residual False -2.73 -2.31 -0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN C 110 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C08 Y4B B 502 " pdb=" C07 Y4B B 502 " pdb=" C14 Y4B B 502 " pdb=" C17 Y4B B 502 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 2894 not shown) Planarity restraints: 5033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV E 511 " -0.158 2.00e-02 2.50e+03 3.10e-01 9.61e+02 pdb=" C29 POV E 511 " 0.417 2.00e-02 2.50e+03 pdb="C210 POV E 511 " -0.405 2.00e-02 2.50e+03 pdb="C211 POV E 511 " 0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 608 " 0.075 2.00e-02 2.50e+03 7.49e-02 5.61e+01 pdb=" C29 POV C 608 " -0.076 2.00e-02 2.50e+03 pdb="C210 POV C 608 " -0.074 2.00e-02 2.50e+03 pdb="C211 POV C 608 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 609 " -0.035 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C29 POV A 609 " 0.035 2.00e-02 2.50e+03 pdb="C210 POV A 609 " 0.034 2.00e-02 2.50e+03 pdb="C211 POV A 609 " -0.034 2.00e-02 2.50e+03 ... (remaining 5030 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.24: 3719 2.24 - 2.83: 76661 2.83 - 3.42: 91440 3.42 - 4.01: 132133 4.01 - 4.60: 199501 Nonbonded interactions: 503454 Sorted by model distance: nonbonded pdb=" O THR D 237 " pdb=" H ILE D 242 " model vdw 1.655 1.850 nonbonded pdb=" H GLY D 63 " pdb=" O THR D 73 " model vdw 1.675 1.850 nonbonded pdb=" O SER D 267 " pdb=" HG1 THR D 271 " model vdw 1.684 1.850 nonbonded pdb=" H ARG C 163 " pdb=" O GLU C 208 " model vdw 1.688 1.850 nonbonded pdb=" O PHE B 475 " pdb="HD22 ASN B 479 " model vdw 1.689 1.850 ... (remaining 503449 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 418 or resid 601 or resid 604 or resid 608)) selection = (chain 'C' and (resid 9 through 418 or resid 601 or resid 604 or resid 608)) } ncs_group { reference = (chain 'B' and (resid 6 through 308 or (resid 459 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name HB \ 2 or name HB3)) or resid 460 through 487 or resid 506 or resid 509)) selection = (chain 'E' and (resid 6 through 487 or resid 509 or resid 512)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'M' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = (chain 'K' and (resid 1 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 39 through 105)) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.510 Extract box with map and model: 11.640 Check model and map are aligned: 0.520 Set scattering table: 0.300 Process input model: 116.600 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.240 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.213 18696 Z= 0.439 Angle : 0.925 20.068 25241 Z= 0.380 Chirality : 0.050 0.425 2897 Planarity : 0.007 0.310 3001 Dihedral : 14.535 158.165 7121 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.97 % Allowed : 7.52 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.25 % 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: -0.08 (0.19), residues: 2092 helix: 1.00 (0.22), residues: 545 sheet: -0.69 (0.21), residues: 629 loop : -0.04 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 316 HIS 0.003 0.001 HIS D 122 PHE 0.017 0.001 PHE D 158 TYR 0.015 0.001 TYR E 143 ARG 0.005 0.000 ARG E 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 410 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Evaluate side-chains 366 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 329 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 17 residues processed: 358 average time/residue: 2.6203 time to fit residues: 1060.4605 Evaluate side-chains 240 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 223 time to evaluate : 3.161 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 3 average time/residue: 0.4514 time to fit residues: 6.0689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 187 optimal weight: 0.0980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 6 GLN L 6 GLN L 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18696 Z= 0.203 Angle : 0.551 5.946 25241 Z= 0.284 Chirality : 0.042 0.205 2897 Planarity : 0.004 0.060 3001 Dihedral : 13.633 164.312 3224 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.13 % Allowed : 14.67 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.25 % 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: 0.24 (0.19), residues: 2092 helix: 1.61 (0.21), residues: 545 sheet: -0.58 (0.20), residues: 637 loop : -0.02 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 316 HIS 0.003 0.001 HIS B 267 PHE 0.019 0.001 PHE E 470 TYR 0.019 0.001 TYR E 299 ARG 0.006 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 410 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Evaluate side-chains 274 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 234 time to evaluate : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 24 residues processed: 264 average time/residue: 2.3606 time to fit residues: 715.6822 Evaluate side-chains 237 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 213 time to evaluate : 2.885 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 4 average time/residue: 1.1946 time to fit residues: 9.5471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 186 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN D 40 ASN D 426 ASN E 119 HIS J 81 HIS K 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 18696 Z= 0.478 Angle : 0.613 6.392 25241 Z= 0.314 Chirality : 0.045 0.204 2897 Planarity : 0.005 0.071 3001 Dihedral : 13.138 162.147 3224 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.83 % Allowed : 15.47 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.25 % 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: 0.06 (0.18), residues: 2092 helix: 1.56 (0.21), residues: 553 sheet: -0.73 (0.19), residues: 669 loop : -0.15 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 316 HIS 0.005 0.001 HIS E 119 PHE 0.017 0.002 PHE E 470 TYR 0.021 0.002 TYR B 157 ARG 0.011 0.001 ARG H 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 410 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 225 time to evaluate : 3.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 30 residues processed: 268 average time/residue: 2.4339 time to fit residues: 747.9429 Evaluate side-chains 240 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 210 time to evaluate : 3.110 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 26 residues processed: 4 average time/residue: 1.3832 time to fit residues: 10.5531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 188 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN K 6 GLN K 87 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18696 Z= 0.168 Angle : 0.521 5.141 25241 Z= 0.265 Chirality : 0.041 0.210 2897 Planarity : 0.004 0.074 3001 Dihedral : 12.009 104.581 3224 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.24 % Allowed : 16.59 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.25 % 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: 0.30 (0.19), residues: 2092 helix: 1.86 (0.21), residues: 553 sheet: -0.64 (0.19), residues: 661 loop : -0.04 (0.22), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 316 HIS 0.002 0.001 HIS B 267 PHE 0.017 0.001 PHE E 470 TYR 0.021 0.001 TYR E 299 ARG 0.009 0.000 ARG H 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 410 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 224 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 27 residues processed: 260 average time/residue: 2.3927 time to fit residues: 713.4149 Evaluate side-chains 240 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 213 time to evaluate : 2.737 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 25 residues processed: 2 average time/residue: 1.2285 time to fit residues: 6.3023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 148 optimal weight: 0.0970 chunk 82 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 18696 Z= 0.337 Angle : 0.552 5.223 25241 Z= 0.281 Chirality : 0.042 0.190 2897 Planarity : 0.004 0.055 3001 Dihedral : 11.792 107.023 3224 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.29 % Allowed : 17.23 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.25 % 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: 0.24 (0.19), residues: 2092 helix: 1.80 (0.21), residues: 553 sheet: -0.67 (0.19), residues: 667 loop : -0.06 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 316 HIS 0.003 0.001 HIS C 109 PHE 0.017 0.001 PHE E 470 TYR 0.018 0.001 TYR D 235 ARG 0.007 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 410 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 219 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 30 residues processed: 258 average time/residue: 2.3282 time to fit residues: 693.4174 Evaluate side-chains 240 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 210 time to evaluate : 2.698 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 28 residues processed: 2 average time/residue: 0.4338 time to fit residues: 4.7923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 18696 Z= 0.264 Angle : 0.534 5.129 25241 Z= 0.271 Chirality : 0.042 0.196 2897 Planarity : 0.004 0.057 3001 Dihedral : 11.526 107.422 3224 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.29 % Allowed : 17.39 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.25 % 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: 0.31 (0.19), residues: 2092 helix: 1.92 (0.21), residues: 553 sheet: -0.66 (0.19), residues: 667 loop : -0.04 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 316 HIS 0.003 0.001 HIS C 109 PHE 0.019 0.001 PHE D 425 TYR 0.019 0.001 TYR B 299 ARG 0.008 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 410 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 220 time to evaluate : 3.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 34 residues processed: 258 average time/residue: 2.4105 time to fit residues: 715.6372 Evaluate side-chains 245 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 211 time to evaluate : 2.917 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 32 residues processed: 3 average time/residue: 1.0872 time to fit residues: 7.7779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 146 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18696 Z= 0.211 Angle : 0.519 5.230 25241 Z= 0.262 Chirality : 0.041 0.199 2897 Planarity : 0.004 0.056 3001 Dihedral : 11.155 106.092 3224 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.29 % Allowed : 17.44 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.25 % 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: 0.41 (0.19), residues: 2092 helix: 2.02 (0.21), residues: 553 sheet: -0.61 (0.19), residues: 661 loop : -0.00 (0.22), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 237 HIS 0.002 0.001 HIS C 109 PHE 0.025 0.001 PHE D 425 TYR 0.020 0.001 TYR B 299 ARG 0.009 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 410 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 223 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 33 residues processed: 262 average time/residue: 2.4450 time to fit residues: 742.6893 Evaluate side-chains 246 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 213 time to evaluate : 3.024 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 32 residues processed: 1 average time/residue: 0.4967 time to fit residues: 4.5546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18696 Z= 0.199 Angle : 0.515 5.558 25241 Z= 0.261 Chirality : 0.041 0.204 2897 Planarity : 0.004 0.058 3001 Dihedral : 10.859 104.289 3224 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.19 % Allowed : 17.71 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 2092 helix: 2.09 (0.21), residues: 553 sheet: -0.55 (0.19), residues: 659 loop : 0.03 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 237 HIS 0.003 0.001 HIS C 109 PHE 0.030 0.001 PHE D 425 TYR 0.020 0.001 TYR B 299 ARG 0.010 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 410 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 218 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 34 residues processed: 255 average time/residue: 2.4485 time to fit residues: 714.0986 Evaluate side-chains 249 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 215 time to evaluate : 2.860 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 31 residues processed: 3 average time/residue: 0.8869 time to fit residues: 7.1240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18696 Z= 0.211 Angle : 0.520 8.281 25241 Z= 0.263 Chirality : 0.041 0.212 2897 Planarity : 0.004 0.060 3001 Dihedral : 10.648 102.624 3224 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.81 % Allowed : 18.03 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.25 % 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: 0.52 (0.19), residues: 2092 helix: 2.11 (0.21), residues: 553 sheet: -0.51 (0.20), residues: 659 loop : 0.04 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 237 HIS 0.003 0.001 HIS C 109 PHE 0.034 0.001 PHE D 425 TYR 0.019 0.001 TYR B 299 ARG 0.012 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 410 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Evaluate side-chains 254 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 220 time to evaluate : 3.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 32 residues processed: 252 average time/residue: 2.3809 time to fit residues: 686.9891 Evaluate side-chains 244 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 212 time to evaluate : 2.788 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 31 residues processed: 1 average time/residue: 0.3547 time to fit residues: 3.7972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 126 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 0.028 18696 Z= 0.198 Angle : 0.521 8.044 25241 Z= 0.263 Chirality : 0.041 0.217 2897 Planarity : 0.004 0.062 3001 Dihedral : 10.377 100.533 3224 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.87 % Allowed : 18.03 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.25 % 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: 0.55 (0.19), residues: 2092 helix: 2.14 (0.22), residues: 553 sheet: -0.48 (0.20), residues: 659 loop : 0.05 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 237 HIS 0.002 0.000 HIS C 109 PHE 0.041 0.001 PHE D 425 TYR 0.020 0.001 TYR B 299 ARG 0.013 0.000 ARG K 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 410 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 214 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 31 residues processed: 247 average time/residue: 2.4405 time to fit residues: 692.4309 Evaluate side-chains 243 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 212 time to evaluate : 3.069 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 30 residues processed: 2 average time/residue: 0.5577 time to fit residues: 5.5434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 68 optimal weight: 0.0570 chunk 168 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.9104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.103329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.076682 restraints weight = 98076.807| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.64 r_work: 0.3030 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2970 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: