Starting phenix.real_space_refine on Wed Feb 21 11:37:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m79_30128/02_2024/6m79_30128_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m79_30128/02_2024/6m79_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_2024/6m79_30128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m79_30128/02_2024/6m79_30128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m79_30128/02_2024/6m79_30128_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m79_30128/02_2024/6m79_30128_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 15.41, per 1000 atoms: 1.01 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: 5.84 Conformation dependent library (CDL) restraints added in 5.4 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: 2.77 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: 3.95 Time building geometry restraints manager: 6.34 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: 8582 20.26 - 40.51: 534 40.51 - 60.76: 136 60.76 - 81.02: 56 81.02 - 101.27: 18 Dihedral angle restraints: 9326 sinusoidal: 3946 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 9323 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 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.010 Extract box with map and model: 3.960 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 51.340 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 : 16.068 101.273 5850 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 % Allowed : 7.47 % Favored : 88.54 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 214 HIS 0.007 0.002 HIS A 355 PHE 0.013 0.002 PHE D 100 TYR 0.018 0.002 TYR B 299 ARG 0.004 0.001 ARG D 91 *********************** 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 : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ILE cc_start: 0.7925 (mt) cc_final: 0.7661 (mt) REVERT: A 345 MET cc_start: 0.8449 (mmm) cc_final: 0.8128 (mmm) REVERT: A 474 ILE cc_start: 0.5722 (OUTLIER) cc_final: 0.5329 (tt) REVERT: B 28 HIS cc_start: 0.7583 (t-90) cc_final: 0.7272 (t-90) REVERT: B 345 MET cc_start: 0.8587 (mmm) cc_final: 0.8178 (mmp) REVERT: B 422 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8037 (ttpt) REVERT: B 479 GLU cc_start: 0.5572 (OUTLIER) cc_final: 0.5023 (tp30) REVERT: C 86 ILE cc_start: 0.7943 (mt) cc_final: 0.7694 (mt) REVERT: C 345 MET cc_start: 0.8453 (mmm) cc_final: 0.8136 (mmm) REVERT: C 474 ILE cc_start: 0.5707 (OUTLIER) cc_final: 0.5322 (tt) REVERT: D 28 HIS cc_start: 0.7571 (t-90) cc_final: 0.7252 (t-90) REVERT: D 345 MET cc_start: 0.8589 (mmm) cc_final: 0.8191 (mmp) REVERT: D 422 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8024 (ttpt) REVERT: D 479 GLU cc_start: 0.5576 (OUTLIER) cc_final: 0.5017 (tp30) outliers start: 60 outliers final: 28 residues processed: 275 average time/residue: 0.2944 time to fit residues: 115.8952 Evaluate side-chains 191 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 157 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 422 LYS Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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: 0.7755 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15804 Z= 0.210 Angle : 0.595 7.370 21554 Z= 0.296 Chirality : 0.043 0.143 2266 Planarity : 0.004 0.036 2672 Dihedral : 11.042 79.217 2284 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.18 % Allowed : 11.77 % Favored : 86.05 % 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: 0.18 (0.19), residues: 1832 helix: 1.22 (0.16), residues: 1040 sheet: -0.02 (0.46), residues: 134 loop : -1.67 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 214 HIS 0.004 0.001 HIS C 447 PHE 0.010 0.001 PHE B 100 TYR 0.010 0.001 TYR C 47 ARG 0.003 0.000 ARG A 332 *********************** 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 196 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 165 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8139 (t) REVERT: A 86 ILE cc_start: 0.7834 (mt) cc_final: 0.7632 (mt) REVERT: A 345 MET cc_start: 0.8405 (mmm) cc_final: 0.8141 (mmm) REVERT: B 345 MET cc_start: 0.8594 (mmm) cc_final: 0.8233 (mmp) REVERT: B 479 GLU cc_start: 0.5373 (OUTLIER) cc_final: 0.4960 (tp30) REVERT: C 79 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8133 (t) REVERT: C 86 ILE cc_start: 0.7853 (mt) cc_final: 0.7649 (mt) REVERT: C 345 MET cc_start: 0.8401 (mmm) cc_final: 0.8147 (mmm) REVERT: D 345 MET cc_start: 0.8600 (mmm) cc_final: 0.8236 (mmp) REVERT: D 479 GLU cc_start: 0.5383 (OUTLIER) cc_final: 0.4954 (tp30) outliers start: 31 outliers final: 17 residues processed: 186 average time/residue: 0.2876 time to fit residues: 77.8277 Evaluate side-chains 172 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 266 ARG Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 266 ARG Chi-restraints excluded: chain D residue 479 GLU 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: 0.9980 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: 10.0000 chunk 149 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 134 optimal weight: 0.0970 overall best weight: 2.8184 ------------------------------------------------------------------------------- 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: 0.7796 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15804 Z= 0.292 Angle : 0.638 8.408 21554 Z= 0.315 Chirality : 0.044 0.145 2266 Planarity : 0.004 0.037 2672 Dihedral : 10.234 78.667 2258 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.68 % Allowed : 12.14 % Favored : 85.18 % 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: 0.07 (0.19), residues: 1832 helix: 1.11 (0.16), residues: 1036 sheet: 0.13 (0.47), residues: 132 loop : -1.71 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 214 HIS 0.006 0.002 HIS C 355 PHE 0.013 0.002 PHE D 100 TYR 0.024 0.002 TYR B 299 ARG 0.003 0.000 ARG C 12 *********************** 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 205 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 166 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ILE cc_start: 0.7860 (mt) cc_final: 0.7656 (mt) REVERT: A 345 MET cc_start: 0.8463 (mmm) cc_final: 0.8250 (mmm) REVERT: B 345 MET cc_start: 0.8628 (mmm) cc_final: 0.8416 (mmm) REVERT: B 479 GLU cc_start: 0.5396 (OUTLIER) cc_final: 0.4914 (tp30) REVERT: C 86 ILE cc_start: 0.7874 (mt) cc_final: 0.7673 (mt) REVERT: C 345 MET cc_start: 0.8463 (mmm) cc_final: 0.8258 (mmm) REVERT: D 345 MET cc_start: 0.8635 (mmm) cc_final: 0.8409 (mmm) REVERT: D 479 GLU cc_start: 0.5398 (OUTLIER) cc_final: 0.4916 (tp30) outliers start: 39 outliers final: 26 residues processed: 197 average time/residue: 0.2722 time to fit residues: 79.5454 Evaluate side-chains 188 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 266 ARG Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 266 ARG Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 167 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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: 0.7766 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15804 Z= 0.206 Angle : 0.574 7.773 21554 Z= 0.281 Chirality : 0.042 0.133 2266 Planarity : 0.004 0.034 2672 Dihedral : 9.589 75.165 2252 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.99 % Allowed : 13.51 % Favored : 84.50 % 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: 0.20 (0.19), residues: 1832 helix: 1.24 (0.16), residues: 1042 sheet: -0.05 (0.47), residues: 136 loop : -1.66 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 214 HIS 0.005 0.001 HIS C 355 PHE 0.011 0.001 PHE D 100 TYR 0.021 0.001 TYR D 299 ARG 0.002 0.000 ARG C 332 *********************** 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 191 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 163 time to evaluate : 1.837 Fit side-chains REVERT: A 119 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7842 (tp) REVERT: A 345 MET cc_start: 0.8411 (mmm) cc_final: 0.8187 (mmm) REVERT: B 28 HIS cc_start: 0.7446 (t-90) cc_final: 0.7209 (t-90) REVERT: B 345 MET cc_start: 0.8635 (mmm) cc_final: 0.8398 (mmm) REVERT: B 479 GLU cc_start: 0.5453 (OUTLIER) cc_final: 0.4902 (tp30) REVERT: C 119 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7841 (tp) REVERT: C 345 MET cc_start: 0.8417 (mmm) cc_final: 0.8203 (mmm) REVERT: D 28 HIS cc_start: 0.7435 (t-90) cc_final: 0.7193 (t-90) REVERT: D 345 MET cc_start: 0.8642 (mmm) cc_final: 0.8390 (mmm) REVERT: D 479 GLU cc_start: 0.5448 (OUTLIER) cc_final: 0.4895 (tp30) outliers start: 28 outliers final: 17 residues processed: 185 average time/residue: 0.2704 time to fit residues: 74.5134 Evaluate side-chains 180 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 132 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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: 0.7844 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 15804 Z= 0.449 Angle : 0.730 10.005 21554 Z= 0.363 Chirality : 0.049 0.174 2266 Planarity : 0.005 0.042 2672 Dihedral : 10.325 80.492 2248 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.24 % Allowed : 12.89 % Favored : 84.87 % 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: 0.86 (0.16), residues: 1028 sheet: 0.12 (0.47), residues: 132 loop : -1.92 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 214 HIS 0.009 0.002 HIS C 355 PHE 0.019 0.002 PHE B 100 TYR 0.021 0.002 TYR B 299 ARG 0.004 0.001 ARG A 12 *********************** 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 186 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 1.965 Fit side-chains REVERT: A 119 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7903 (tp) REVERT: B 345 MET cc_start: 0.8705 (mmm) cc_final: 0.8470 (mmm) REVERT: B 479 GLU cc_start: 0.5572 (OUTLIER) cc_final: 0.4694 (tp30) REVERT: C 119 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7898 (tp) REVERT: D 345 MET cc_start: 0.8718 (mmm) cc_final: 0.8478 (mmm) REVERT: D 479 GLU cc_start: 0.5573 (OUTLIER) cc_final: 0.4691 (tp30) outliers start: 32 outliers final: 27 residues processed: 182 average time/residue: 0.2639 time to fit residues: 72.4377 Evaluate side-chains 183 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 152 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.1980 chunk 160 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.7746 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15804 Z= 0.159 Angle : 0.546 8.024 21554 Z= 0.266 Chirality : 0.040 0.132 2266 Planarity : 0.004 0.034 2672 Dihedral : 9.351 73.676 2248 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.56 % Allowed : 14.07 % Favored : 84.37 % 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: 0.28 (0.19), residues: 1832 helix: 1.32 (0.16), residues: 1034 sheet: -0.20 (0.47), residues: 136 loop : -1.58 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 214 HIS 0.005 0.001 HIS A 447 PHE 0.008 0.001 PHE D 100 TYR 0.021 0.001 TYR D 299 ARG 0.003 0.000 ARG B 359 *********************** 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 185 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 164 time to evaluate : 1.711 Fit side-chains REVERT: B 345 MET cc_start: 0.8627 (mmm) cc_final: 0.8344 (mmm) REVERT: B 479 GLU cc_start: 0.5418 (OUTLIER) cc_final: 0.4926 (tp30) REVERT: D 345 MET cc_start: 0.8640 (mmm) cc_final: 0.8354 (mmm) REVERT: D 479 GLU cc_start: 0.5417 (OUTLIER) cc_final: 0.4914 (tp30) outliers start: 21 outliers final: 19 residues processed: 181 average time/residue: 0.2674 time to fit residues: 73.9759 Evaluate side-chains 174 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 7.9990 chunk 20 optimal weight: 0.0070 chunk 101 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 108 optimal weight: 0.0570 chunk 81 optimal weight: 4.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- 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: 0.7701 moved from start: 0.2450 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= 0.137 Angle : 0.511 6.972 21554 Z= 0.247 Chirality : 0.039 0.129 2266 Planarity : 0.003 0.033 2672 Dihedral : 8.955 72.398 2248 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.37 % Allowed : 14.51 % Favored : 84.12 % 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: 0.71 (0.20), residues: 1832 helix: 1.65 (0.16), residues: 1034 sheet: -0.17 (0.46), residues: 136 loop : -1.33 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 382 HIS 0.005 0.001 HIS A 447 PHE 0.010 0.001 PHE C 46 TYR 0.023 0.001 TYR B 299 ARG 0.002 0.000 ARG A 439 *********************** 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 181 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 1.834 Fit side-chains REVERT: B 479 GLU cc_start: 0.5236 (OUTLIER) cc_final: 0.4973 (tp30) REVERT: D 479 GLU cc_start: 0.5230 (OUTLIER) cc_final: 0.4960 (tp30) outliers start: 18 outliers final: 13 residues processed: 177 average time/residue: 0.2708 time to fit residues: 72.8989 Evaluate side-chains 165 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 112 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 139 optimal weight: 6.9990 chunk 161 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7699 moved from start: 0.2544 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= 0.136 Angle : 0.508 6.456 21554 Z= 0.245 Chirality : 0.039 0.128 2266 Planarity : 0.003 0.031 2672 Dihedral : 8.858 68.552 2246 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.12 % Allowed : 14.82 % Favored : 84.06 % 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: 0.84 (0.20), residues: 1832 helix: 1.71 (0.16), residues: 1040 sheet: -0.11 (0.47), residues: 136 loop : -1.19 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 214 HIS 0.004 0.001 HIS A 447 PHE 0.009 0.001 PHE C 46 TYR 0.022 0.001 TYR A 154 ARG 0.001 0.000 ARG A 439 *********************** 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 174 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 1.773 Fit side-chains REVERT: B 345 MET cc_start: 0.8428 (mmm) cc_final: 0.8141 (mmp) REVERT: D 345 MET cc_start: 0.8429 (mmm) cc_final: 0.8159 (mmp) outliers start: 14 outliers final: 11 residues processed: 172 average time/residue: 0.2463 time to fit residues: 65.4779 Evaluate side-chains 164 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 363 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 4.9990 chunk 155 optimal weight: 0.1980 chunk 165 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15804 Z= 0.336 Angle : 0.652 8.780 21554 Z= 0.322 Chirality : 0.045 0.154 2266 Planarity : 0.004 0.036 2672 Dihedral : 9.101 67.803 2234 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.62 % Allowed : 14.63 % Favored : 83.75 % 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: 0.22 (0.20), residues: 1832 helix: 1.25 (0.16), residues: 1042 sheet: 0.03 (0.47), residues: 134 loop : -1.65 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 214 HIS 0.007 0.002 HIS A 355 PHE 0.014 0.002 PHE B 100 TYR 0.022 0.002 TYR D 299 ARG 0.003 0.000 ARG A 208 *********************** 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 176 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 1.724 Fit side-chains REVERT: A 345 MET cc_start: 0.8015 (mmm) cc_final: 0.7492 (mmm) REVERT: B 345 MET cc_start: 0.8617 (mmm) cc_final: 0.8345 (mmp) REVERT: C 345 MET cc_start: 0.8018 (mmm) cc_final: 0.7510 (mmm) REVERT: D 345 MET cc_start: 0.8625 (mmm) cc_final: 0.8353 (mmp) outliers start: 22 outliers final: 18 residues processed: 171 average time/residue: 0.2559 time to fit residues: 66.5721 Evaluate side-chains 165 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 363 SER 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: 0.0980 chunk 82 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 89 optimal weight: 0.1980 chunk 115 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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: 0.7750 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15804 Z= 0.179 Angle : 0.549 8.093 21554 Z= 0.268 Chirality : 0.041 0.131 2266 Planarity : 0.004 0.031 2672 Dihedral : 8.797 68.721 2234 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.12 % Allowed : 15.38 % Favored : 83.50 % 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: 0.48 (0.20), residues: 1832 helix: 1.43 (0.16), residues: 1042 sheet: -0.04 (0.47), residues: 134 loop : -1.45 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 214 HIS 0.005 0.001 HIS A 447 PHE 0.010 0.001 PHE D 100 TYR 0.023 0.001 TYR B 299 ARG 0.002 0.000 ARG C 332 ********************** 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 166 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 152 time to evaluate : 1.719 Fit side-chains REVERT: B 345 MET cc_start: 0.8521 (mmm) cc_final: 0.8263 (mmp) REVERT: D 345 MET cc_start: 0.8521 (mmm) cc_final: 0.8265 (mmp) outliers start: 14 outliers final: 13 residues processed: 164 average time/residue: 0.2433 time to fit residues: 61.8097 Evaluate side-chains 164 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 363 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 134 optimal weight: 0.1980 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 0.0770 chunk 128 optimal weight: 4.9990 overall best weight: 2.2544 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.149404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118813 restraints weight = 58652.809| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 4.03 r_work: 0.3153 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15804 Z= 0.235 Angle : 0.581 8.672 21554 Z= 0.284 Chirality : 0.042 0.136 2266 Planarity : 0.004 0.031 2672 Dihedral : 8.901 67.942 2234 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.31 % Allowed : 15.26 % Favored : 83.44 % 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: 0.39 (0.20), residues: 1832 helix: 1.37 (0.16), residues: 1042 sheet: -0.09 (0.47), residues: 134 loop : -1.51 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 214 HIS 0.005 0.001 HIS A 355 PHE 0.011 0.002 PHE B 100 TYR 0.023 0.001 TYR D 299 ARG 0.002 0.000 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2947.88 seconds wall clock time: 54 minutes 22.73 seconds (3262.73 seconds total)