Starting phenix.real_space_refine (version: dev) on Mon Feb 27 14:32:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m79_30128/02_2023/6m79_30128_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m79_30128/02_2023/6m79_30128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m79_30128/02_2023/6m79_30128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m79_30128/02_2023/6m79_30128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m79_30128/02_2023/6m79_30128_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m79_30128/02_2023/6m79_30128_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15296 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "B ARG 16": "NH1" <-> "NH2" Residue "B PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B ASP 406": "OD1" <-> "OD2" Residue "C ARG 16": "NH1" <-> "NH2" Residue "C PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "C PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C GLU 282": "OE1" <-> "OE2" Residue "C PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 335": "NH1" <-> "NH2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C ASP 406": "OD1" <-> "OD2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 41": "OE1" <-> "OE2" Residue "D PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ARG 208": "NH1" <-> "NH2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D GLU 347": "OE1" <-> "OE2" Residue "D ASP 406": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 15324 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3750 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 460, 3734 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 432} Chain breaks: 2 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 Conformer: "B" Number of residues, atoms: 460, 3734 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 432} Chain breaks: 2 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 bond proxies already assigned to first conformer: 3828 Chain: "B" Number of atoms: 3760 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 461, 3752 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 27, 'TRANS': 433} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 461, 3752 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 27, 'TRANS': 433} Chain breaks: 3 bond proxies already assigned to first conformer: 3854 Chain: "C" Number of atoms: 3750 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 460, 3734 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 432} Chain breaks: 2 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 Conformer: "B" Number of residues, atoms: 460, 3734 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 432} Chain breaks: 2 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 bond proxies already assigned to first conformer: 3828 Chain: "D" Number of atoms: 3760 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 461, 3752 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 27, 'TRANS': 433} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 461, 3752 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 27, 'TRANS': 433} Chain breaks: 3 bond proxies already assigned to first conformer: 3854 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'FAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'FAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'FAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'FAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AASN A 356 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 356 " occ=0.50 residue: pdb=" N AASP A 473 " occ=0.49 ... (14 atoms not shown) pdb=" OD2BASP A 473 " occ=0.51 residue: pdb=" N AASN B 356 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 356 " occ=0.50 residue: pdb=" N AASN C 356 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 356 " occ=0.50 residue: pdb=" N AASP C 473 " occ=0.49 ... (14 atoms not shown) pdb=" OD2BASP C 473 " occ=0.51 residue: pdb=" N AASN D 356 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN D 356 " occ=0.50 Time building chain proxies: 16.07, per 1000 atoms: 1.05 Number of scatterers: 15324 At special positions: 0 Unit cell: (136.53, 109.89, 119.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 12 15.00 O 2780 8.00 N 2610 7.00 C 9858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.59 Conformation dependent library (CDL) restraints added in 4.0 seconds 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3476 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 4 sheets defined 54.0% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 21 through 29 Processing helix chain 'A' and resid 40 through 43 No H-bonds generated for 'chain 'A' and resid 40 through 43' Processing helix chain 'A' and resid 50 through 70 removed outlier: 3.625A pdb=" N TRP A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 106 through 122 removed outlier: 4.472A pdb=" N ARG A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 200 through 208 removed outlier: 4.140A pdb=" N LEU A 205 " --> pdb=" O PRO A 201 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N THR A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ARG A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 227 removed outlier: 3.653A pdb=" N LYS A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 5.025A pdb=" N ALA A 233 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN A 235 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER A 236 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 237 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 258 through 274 Processing helix chain 'A' and resid 278 through 303 removed outlier: 4.019A pdb=" N ARG A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.598A pdb=" N ALA A 350 " --> pdb=" O ARG A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 368 Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 390 through 401 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 428 through 433 removed outlier: 3.584A pdb=" N TRP A 433 " --> pdb=" O TYR A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 474 through 483 Processing helix chain 'B' and resid 21 through 29 Processing helix chain 'B' and resid 40 through 43 No H-bonds generated for 'chain 'B' and resid 40 through 43' Processing helix chain 'B' and resid 50 through 70 removed outlier: 3.625A pdb=" N TRP B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 106 through 122 removed outlier: 4.472A pdb=" N ARG B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.140A pdb=" N LEU B 205 " --> pdb=" O PRO B 201 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU B 206 " --> pdb=" O SER B 202 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR B 207 " --> pdb=" O ASN B 203 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ARG B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 227 removed outlier: 3.653A pdb=" N LYS B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 removed outlier: 5.025A pdb=" N ALA B 233 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 235 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER B 236 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS B 237 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 258 through 274 Processing helix chain 'B' and resid 278 through 303 removed outlier: 4.019A pdb=" N ARG B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 333 Processing helix chain 'B' and resid 339 through 351 removed outlier: 3.597A pdb=" N ALA B 350 " --> pdb=" O ARG B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 368 Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 390 through 401 Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.585A pdb=" N TRP B 433 " --> pdb=" O TYR B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 453 through 458 Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'C' and resid 21 through 29 Processing helix chain 'C' and resid 40 through 43 No H-bonds generated for 'chain 'C' and resid 40 through 43' Processing helix chain 'C' and resid 50 through 70 removed outlier: 3.625A pdb=" N TRP C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 106 through 122 removed outlier: 4.473A pdb=" N ARG C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 200 through 208 removed outlier: 4.140A pdb=" N LEU C 205 " --> pdb=" O PRO C 201 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU C 206 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N THR C 207 " --> pdb=" O ASN C 203 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ARG C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 227 removed outlier: 3.654A pdb=" N LYS C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 237 removed outlier: 5.025A pdb=" N ALA C 233 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 235 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER C 236 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS C 237 " --> pdb=" O LYS C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 252 Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 278 through 303 removed outlier: 4.019A pdb=" N ARG C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 333 Processing helix chain 'C' and resid 339 through 351 removed outlier: 3.597A pdb=" N ALA C 350 " --> pdb=" O ARG C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 368 Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 390 through 401 Processing helix chain 'C' and resid 416 through 423 Processing helix chain 'C' and resid 428 through 433 removed outlier: 3.584A pdb=" N TRP C 433 " --> pdb=" O TYR C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 437 No H-bonds generated for 'chain 'C' and resid 435 through 437' Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 453 through 458 Processing helix chain 'C' and resid 474 through 483 Processing helix chain 'D' and resid 21 through 29 Processing helix chain 'D' and resid 40 through 43 No H-bonds generated for 'chain 'D' and resid 40 through 43' Processing helix chain 'D' and resid 50 through 70 removed outlier: 3.625A pdb=" N TRP D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'D' and resid 106 through 122 removed outlier: 4.473A pdb=" N ARG D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 160 Processing helix chain 'D' and resid 200 through 208 removed outlier: 4.140A pdb=" N LEU D 205 " --> pdb=" O PRO D 201 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU D 206 " --> pdb=" O SER D 202 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N THR D 207 " --> pdb=" O ASN D 203 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ARG D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 227 removed outlier: 3.653A pdb=" N LYS D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 237 removed outlier: 5.026A pdb=" N ALA D 233 " --> pdb=" O ILE D 230 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN D 235 " --> pdb=" O TYR D 232 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER D 236 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS D 237 " --> pdb=" O LYS D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 258 through 274 Processing helix chain 'D' and resid 278 through 303 removed outlier: 4.018A pdb=" N ARG D 294 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 333 Processing helix chain 'D' and resid 339 through 351 removed outlier: 3.597A pdb=" N ALA D 350 " --> pdb=" O ARG D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 368 Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 390 through 401 Processing helix chain 'D' and resid 416 through 423 Processing helix chain 'D' and resid 428 through 433 removed outlier: 3.585A pdb=" N TRP D 433 " --> pdb=" O TYR D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 437 No H-bonds generated for 'chain 'D' and resid 435 through 437' Processing helix chain 'D' and resid 448 through 450 No H-bonds generated for 'chain 'D' and resid 448 through 450' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 474 through 486 Processing sheet with id= A, first strand: chain 'A' and resid 125 through 129 removed outlier: 5.019A pdb=" N ASN A 101 " --> pdb=" O TRP A 10 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER A 31 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL A 9 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE A 33 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE A 11 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A 35 " --> pdb=" O PHE A 11 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 125 through 129 removed outlier: 5.019A pdb=" N ASN B 101 " --> pdb=" O TRP B 10 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER B 31 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL B 9 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE B 33 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE B 11 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 35 " --> pdb=" O PHE B 11 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 125 through 129 removed outlier: 5.019A pdb=" N ASN C 101 " --> pdb=" O TRP C 10 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER C 31 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL C 9 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE C 33 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE C 11 " --> pdb=" O PHE C 33 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C 35 " --> pdb=" O PHE C 11 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 125 through 129 removed outlier: 5.019A pdb=" N ASN D 101 " --> pdb=" O TRP D 10 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER D 31 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL D 9 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE D 33 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE D 11 " --> pdb=" O PHE D 33 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL D 35 " --> pdb=" O PHE D 11 " (cutoff:3.500A) 618 hydrogen bonds defined for protein. 1818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.39 Time building geometry restraints manager: 7.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4817 1.34 - 1.46: 2806 1.46 - 1.57: 8077 1.57 - 1.69: 8 1.69 - 1.81: 96 Bond restraints: 15804 Sorted by residual: bond pdb=" O3P FAD D 702 " pdb=" P FAD D 702 " ideal model delta sigma weight residual 1.660 1.564 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" O3P FAD C 702 " pdb=" P FAD C 702 " ideal model delta sigma weight residual 1.660 1.564 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" O3P FAD A 702 " pdb=" P FAD A 702 " ideal model delta sigma weight residual 1.660 1.564 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" O3P FAD B 702 " pdb=" P FAD B 702 " ideal model delta sigma weight residual 1.660 1.565 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" O5B FAD B 702 " pdb=" PA FAD B 702 " ideal model delta sigma weight residual 1.634 1.541 0.093 2.00e-02 2.50e+03 2.14e+01 ... (remaining 15799 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.95: 663 106.95 - 114.18: 8987 114.18 - 121.41: 8169 121.41 - 128.64: 3485 128.64 - 135.87: 250 Bond angle restraints: 21554 Sorted by residual: angle pdb=" C ASN A 303 " pdb=" N PHE A 304 " pdb=" CA PHE A 304 " ideal model delta sigma weight residual 123.16 119.78 3.38 1.23e+00 6.61e-01 7.53e+00 angle pdb=" O1P FAD A 702 " pdb=" P FAD A 702 " pdb=" O2P FAD A 702 " ideal model delta sigma weight residual 122.50 114.27 8.23 3.00e+00 1.11e-01 7.53e+00 angle pdb=" O1P FAD D 702 " pdb=" P FAD D 702 " pdb=" O2P FAD D 702 " ideal model delta sigma weight residual 122.50 114.29 8.21 3.00e+00 1.11e-01 7.49e+00 angle pdb=" O1P FAD C 702 " pdb=" P FAD C 702 " pdb=" O2P FAD C 702 " ideal model delta sigma weight residual 122.50 114.30 8.20 3.00e+00 1.11e-01 7.48e+00 angle pdb=" O1P FAD B 702 " pdb=" P FAD B 702 " pdb=" O2P FAD B 702 " ideal model delta sigma weight residual 122.50 114.33 8.17 3.00e+00 1.11e-01 7.42e+00 ... (remaining 21549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.26: 8526 20.26 - 40.51: 490 40.51 - 60.76: 96 60.76 - 81.02: 24 81.02 - 101.27: 18 Dihedral angle restraints: 9154 sinusoidal: 3774 harmonic: 5380 Sorted by residual: dihedral pdb=" C5' AMP B 701 " pdb=" O5' AMP B 701 " pdb=" P AMP B 701 " pdb=" O3P AMP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 41.28 -101.27 1 2.00e+01 2.50e-03 2.87e+01 dihedral pdb=" C5' AMP D 701 " pdb=" O5' AMP D 701 " pdb=" P AMP D 701 " pdb=" O3P AMP D 701 " ideal model delta sinusoidal sigma weight residual -60.00 41.26 -101.26 1 2.00e+01 2.50e-03 2.87e+01 dihedral pdb=" CB GLU C 282 " pdb=" CG GLU C 282 " pdb=" CD GLU C 282 " pdb=" OE1 GLU C 282 " ideal model delta sinusoidal sigma weight residual 0.00 88.08 -88.08 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 9151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1147 0.032 - 0.064: 730 0.064 - 0.096: 271 0.096 - 0.127: 87 0.127 - 0.159: 31 Chirality restraints: 2266 Sorted by residual: chirality pdb=" CA PRO C 339 " pdb=" N PRO C 339 " pdb=" C PRO C 339 " pdb=" CB PRO C 339 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA PRO B 339 " pdb=" N PRO B 339 " pdb=" C PRO B 339 " pdb=" CB PRO B 339 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA PRO D 339 " pdb=" N PRO D 339 " pdb=" C PRO D 339 " pdb=" CB PRO D 339 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 2263 not shown) Planarity restraints: 2672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 338 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO A 339 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 338 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO B 339 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 338 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO C 339 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 339 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 339 " 0.022 5.00e-02 4.00e+02 ... (remaining 2669 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 178 2.63 - 3.20: 13344 3.20 - 3.77: 21865 3.77 - 4.33: 29643 4.33 - 4.90: 50785 Nonbonded interactions: 115815 Sorted by model distance: nonbonded pdb=" O TYR D 232 " pdb=" OG SER D 236 " model vdw 2.067 2.440 nonbonded pdb=" O TYR A 232 " pdb=" OG SER A 236 " model vdw 2.067 2.440 nonbonded pdb=" O TYR C 232 " pdb=" OG SER C 236 " model vdw 2.067 2.440 nonbonded pdb=" O TYR B 232 " pdb=" OG SER B 236 " model vdw 2.067 2.440 nonbonded pdb=" O ARG D 359 " pdb=" OG SER D 363 " model vdw 2.119 2.440 ... (remaining 115810 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 5 through 142 or resid 146 through 355 or resid 357 throug \ h 472 or resid 474 through 484 or resid 701 through 702)) selection = (chain 'B' and (resid 5 through 355 or resid 357 through 472 or resid 474 throug \ h 484 or resid 701 through 702)) selection = (chain 'C' and (resid 5 through 142 or resid 146 through 355 or resid 357 throug \ h 472 or resid 474 through 484 or resid 701 through 702)) selection = (chain 'D' and (resid 5 through 355 or resid 357 through 472 or resid 474 throug \ h 484 or resid 701 through 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 64 5.16 5 C 9858 2.51 5 N 2610 2.21 5 O 2780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.220 Construct map_model_manager: 0.010 Extract box with map and model: 4.340 Check model and map are aligned: 0.210 Process input model: 50.280 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.008 0.096 15804 Z= 0.518 Angle : 0.753 8.231 21554 Z= 0.413 Chirality : 0.048 0.159 2266 Planarity : 0.004 0.040 2672 Dihedral : 14.664 101.273 5678 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 3.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.19), residues: 1832 helix: 0.81 (0.16), residues: 1024 sheet: -0.02 (0.46), residues: 132 loop : -1.91 (0.22), residues: 676 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 221 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 28 residues processed: 275 average time/residue: 0.2987 time to fit residues: 118.0319 Evaluate side-chains 185 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 157 time to evaluate : 1.876 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1397 time to fit residues: 10.0393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 0.0070 chunk 74 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 HIS D 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 15804 Z= 0.146 Angle : 0.547 7.549 21554 Z= 0.272 Chirality : 0.040 0.136 2266 Planarity : 0.004 0.033 2672 Dihedral : 7.604 69.141 2058 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 1832 helix: 1.35 (0.16), residues: 1050 sheet: -0.17 (0.46), residues: 136 loop : -1.58 (0.22), residues: 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 1.939 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 191 average time/residue: 0.3227 time to fit residues: 88.5897 Evaluate side-chains 156 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 151 time to evaluate : 1.888 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2148 time to fit residues: 4.1613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 HIS D 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 15804 Z= 0.403 Angle : 0.703 8.710 21554 Z= 0.351 Chirality : 0.047 0.163 2266 Planarity : 0.005 0.039 2672 Dihedral : 7.723 84.731 2058 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 1832 helix: 0.87 (0.16), residues: 1034 sheet: 0.11 (0.46), residues: 132 loop : -1.96 (0.21), residues: 666 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 159 time to evaluate : 1.997 Fit side-chains outliers start: 28 outliers final: 13 residues processed: 181 average time/residue: 0.2769 time to fit residues: 75.8500 Evaluate side-chains 167 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 154 time to evaluate : 1.812 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1601 time to fit residues: 6.1449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 167 optimal weight: 10.0000 chunk 177 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 HIS D 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 15804 Z= 0.141 Angle : 0.533 6.812 21554 Z= 0.260 Chirality : 0.040 0.131 2266 Planarity : 0.003 0.031 2672 Dihedral : 7.299 78.837 2058 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.19), residues: 1832 helix: 1.29 (0.16), residues: 1042 sheet: -0.10 (0.47), residues: 136 loop : -1.53 (0.22), residues: 654 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 172 time to evaluate : 1.776 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 175 average time/residue: 0.2854 time to fit residues: 74.7090 Evaluate side-chains 160 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.778 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1710 time to fit residues: 2.7341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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: 0.8011 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 15804 Z= 0.367 Angle : 0.673 9.112 21554 Z= 0.332 Chirality : 0.046 0.159 2266 Planarity : 0.005 0.037 2672 Dihedral : 7.592 84.157 2058 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 1832 helix: 1.01 (0.16), residues: 1030 sheet: 0.14 (0.47), residues: 132 loop : -1.82 (0.21), residues: 670 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 165 time to evaluate : 1.703 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 169 average time/residue: 0.2661 time to fit residues: 70.4987 Evaluate side-chains 163 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 158 time to evaluate : 1.777 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2188 time to fit residues: 4.2043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.0060 chunk 160 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- 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: 0.7988 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 15804 Z= 0.266 Angle : 0.613 9.283 21554 Z= 0.301 Chirality : 0.043 0.141 2266 Planarity : 0.004 0.036 2672 Dihedral : 7.498 82.729 2058 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.19), residues: 1832 helix: 1.03 (0.16), residues: 1034 sheet: -0.02 (0.47), residues: 134 loop : -1.73 (0.22), residues: 664 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 1.747 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 156 average time/residue: 0.2712 time to fit residues: 65.6808 Evaluate side-chains 151 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 2.035 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1314 time to fit residues: 2.7220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 108 optimal weight: 0.0980 chunk 81 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7916 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 15804 Z= 0.141 Angle : 0.525 7.437 21554 Z= 0.254 Chirality : 0.040 0.129 2266 Planarity : 0.003 0.032 2672 Dihedral : 7.169 75.088 2058 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.20), residues: 1832 helix: 1.44 (0.16), residues: 1036 sheet: -0.22 (0.46), residues: 136 loop : -1.44 (0.22), residues: 660 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 166 time to evaluate : 1.912 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 170 average time/residue: 0.2641 time to fit residues: 70.1141 Evaluate side-chains 166 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1342 time to fit residues: 3.9036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN D 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 15804 Z= 0.166 Angle : 0.539 7.699 21554 Z= 0.261 Chirality : 0.040 0.140 2266 Planarity : 0.004 0.032 2672 Dihedral : 7.149 72.634 2058 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1832 helix: 1.53 (0.16), residues: 1036 sheet: -0.15 (0.47), residues: 136 loop : -1.37 (0.22), residues: 660 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.818 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.2662 time to fit residues: 66.7336 Evaluate side-chains 155 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.883 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 5.9990 chunk 155 optimal weight: 0.0470 chunk 165 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 129 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 156 optimal weight: 8.9990 chunk 164 optimal weight: 6.9990 chunk 108 optimal weight: 0.0980 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN D 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 15804 Z= 0.130 Angle : 0.509 7.100 21554 Z= 0.245 Chirality : 0.039 0.135 2266 Planarity : 0.003 0.031 2672 Dihedral : 7.001 66.850 2058 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1832 helix: 1.72 (0.16), residues: 1034 sheet: -0.15 (0.47), residues: 136 loop : -1.21 (0.23), residues: 662 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.840 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2694 time to fit residues: 65.0733 Evaluate side-chains 153 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.897 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 4.9990 chunk 106 optimal weight: 0.0050 chunk 82 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 168 optimal weight: 0.0470 chunk 145 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 112 optimal weight: 0.0970 chunk 89 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.6092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN D 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 15804 Z= 0.124 Angle : 0.496 6.511 21554 Z= 0.237 Chirality : 0.038 0.131 2266 Planarity : 0.003 0.031 2672 Dihedral : 6.836 59.004 2058 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 1832 helix: 1.95 (0.17), residues: 1034 sheet: -0.17 (0.47), residues: 136 loop : -1.03 (0.23), residues: 662 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 1.820 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 168 average time/residue: 0.2532 time to fit residues: 65.7431 Evaluate side-chains 157 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 1.753 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1370 time to fit residues: 2.9393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 18 optimal weight: 0.0040 chunk 26 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 overall best weight: 2.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN D 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.148911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118323 restraints weight = 58634.419| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 4.04 r_work: 0.3132 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 15804 Z= 0.299 Angle : 0.624 8.751 21554 Z= 0.306 Chirality : 0.044 0.151 2266 Planarity : 0.004 0.030 2672 Dihedral : 7.281 74.053 2058 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1832 helix: 1.48 (0.16), residues: 1040 sheet: 0.02 (0.47), residues: 134 loop : -1.33 (0.22), residues: 658 =============================================================================== Job complete usr+sys time: 2796.32 seconds wall clock time: 52 minutes 19.70 seconds (3139.70 seconds total)