Starting phenix.real_space_refine on Fri Feb 16 04:57:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1s_22629/02_2024/7k1s_22629.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1s_22629/02_2024/7k1s_22629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1s_22629/02_2024/7k1s_22629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1s_22629/02_2024/7k1s_22629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1s_22629/02_2024/7k1s_22629.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1s_22629/02_2024/7k1s_22629.pdb" } resolution = 3.9 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 9087 2.51 5 N 2478 2.21 5 O 2778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A GLU 716": "OE1" <-> "OE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B GLU 384": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B GLU 586": "OE1" <-> "OE2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B GLU 694": "OE1" <-> "OE2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "B GLU 716": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 384": "OE1" <-> "OE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C GLU 586": "OE1" <-> "OE2" Residue "C GLU 663": "OE1" <-> "OE2" Residue "C GLU 694": "OE1" <-> "OE2" Residue "C GLU 705": "OE1" <-> "OE2" Residue "C GLU 716": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14409 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4717 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4717 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 4717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4717 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.79, per 1000 atoms: 0.54 Number of scatterers: 14409 At special positions: 0 Unit cell: (90.1, 96.46, 178.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2778 8.00 N 2478 7.00 C 9087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 584 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 540 " distance=2.02 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 417 " distance=2.04 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 540 " distance=2.02 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 277 " distance=2.04 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 584 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 540 " distance=2.02 Simple disulfide: pdb=" SG CYS C 213 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 369 " - pdb=" SG CYS C 417 " distance=2.04 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 645 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN D 3 " - " MAN D 6 " " MAN D 4 " - " MAN D 5 " " MAN E 3 " - " MAN E 6 " " MAN E 4 " - " MAN E 5 " " MAN F 3 " - " MAN F 6 " " MAN F 4 " - " MAN F 5 " ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG E 2 " - " MAN E 3 " " NAG F 2 " - " MAN F 3 " ALPHA1-6 " MAN D 3 " - " MAN D 4 " " MAN E 3 " - " MAN E 4 " " MAN F 3 " - " MAN F 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1001 " - " ASN A 686 " " NAG B1001 " - " ASN B 686 " " NAG C1001 " - " ASN C 686 " " NAG D 1 " - " ASN A 257 " " NAG E 1 " - " ASN B 257 " " NAG F 1 " - " ASN C 257 " Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 2.8 seconds 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3330 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 33 sheets defined 22.3% alpha, 42.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 199 through 211 removed outlier: 5.488A pdb=" N ASP A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LYS A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 363 through 368 removed outlier: 3.720A pdb=" N GLU A 367 " --> pdb=" O PRO A 363 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 363 through 368' Processing helix chain 'A' and resid 408 through 412 removed outlier: 3.681A pdb=" N ILE A 412 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 434 removed outlier: 4.441A pdb=" N LYS A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU A 420 " --> pdb=" O GLN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 554 removed outlier: 4.159A pdb=" N ALA A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 566 removed outlier: 3.650A pdb=" N LEU A 561 " --> pdb=" O ASN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 676 No H-bonds generated for 'chain 'A' and resid 674 through 676' Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 723 through 729 Processing helix chain 'B' and resid 199 through 211 removed outlier: 5.488A pdb=" N ASP B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS B 209 " --> pdb=" O ASP B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.720A pdb=" N GLU B 367 " --> pdb=" O PRO B 363 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 363 through 368' Processing helix chain 'B' and resid 408 through 412 removed outlier: 3.682A pdb=" N ILE B 412 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 434 removed outlier: 4.441A pdb=" N LYS B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 554 removed outlier: 3.872A pdb=" N GLN B 518 " --> pdb=" O PHE B 514 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA B 548 " --> pdb=" O ASN B 544 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 566 removed outlier: 3.650A pdb=" N LEU B 561 " --> pdb=" O ASN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 676 No H-bonds generated for 'chain 'B' and resid 674 through 676' Processing helix chain 'B' and resid 702 through 707 Processing helix chain 'B' and resid 713 through 722 Processing helix chain 'B' and resid 723 through 729 Processing helix chain 'C' and resid 199 through 211 removed outlier: 5.488A pdb=" N ASP C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LYS C 209 " --> pdb=" O ASP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 233 No H-bonds generated for 'chain 'C' and resid 231 through 233' Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 363 through 368 removed outlier: 3.720A pdb=" N GLU C 367 " --> pdb=" O PRO C 363 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 363 through 368' Processing helix chain 'C' and resid 408 through 412 removed outlier: 3.681A pdb=" N ILE C 412 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 434 removed outlier: 4.441A pdb=" N LYS C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU C 420 " --> pdb=" O GLN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 554 removed outlier: 4.158A pdb=" N ALA C 548 " --> pdb=" O ASN C 544 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 549 " --> pdb=" O ARG C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 566 removed outlier: 3.650A pdb=" N LEU C 561 " --> pdb=" O ASN C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 676 No H-bonds generated for 'chain 'C' and resid 674 through 676' Processing helix chain 'C' and resid 702 through 707 Processing helix chain 'C' and resid 713 through 722 Processing helix chain 'C' and resid 723 through 729 Processing sheet with id=AA1, first strand: chain 'A' and resid 570 through 574 removed outlier: 4.371A pdb=" N THR A 129 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 130 " --> pdb=" O GLY C 677 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE C 679 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ARG A 132 " --> pdb=" O ILE C 679 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 403 removed outlier: 6.092A pdb=" N TRP A 374 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS A 157 " --> pdb=" O TRP A 374 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU A 376 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 155 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU A 378 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA A 153 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU A 150 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 398 through 403 removed outlier: 6.092A pdb=" N TRP A 374 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS A 157 " --> pdb=" O TRP A 374 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU A 376 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 155 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU A 378 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA A 153 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU A 150 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 197 removed outlier: 6.476A pdb=" N THR A 178 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG A 191 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL A 176 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA A 193 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A 174 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG A 195 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS A 172 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N TYR A 170 " --> pdb=" O PRO A 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 197 removed outlier: 6.476A pdb=" N THR A 178 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG A 191 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL A 176 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA A 193 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A 174 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG A 195 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS A 172 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N TYR A 170 " --> pdb=" O PRO A 197 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LYS A 166 " --> pdb=" O ASN A 360 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASN A 360 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 212 through 214 Processing sheet with id=AA7, first strand: chain 'A' and resid 216 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA9, first strand: chain 'A' and resid 591 through 595 removed outlier: 3.863A pdb=" N GLN A 628 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 636 " --> pdb=" O GLN A 628 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 607 through 609 Processing sheet with id=AB2, first strand: chain 'A' and resid 650 through 655 removed outlier: 5.727A pdb=" N GLU A 663 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TYR A 667 " --> pdb=" O GLU A 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 677 through 679 removed outlier: 3.828A pdb=" N GLY A 677 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR B 129 " --> pdb=" O VAL B 581 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 398 through 403 removed outlier: 6.091A pdb=" N TRP B 374 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS B 157 " --> pdb=" O TRP B 374 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU B 376 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 155 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU B 378 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA B 153 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLU B 150 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 398 through 403 removed outlier: 6.091A pdb=" N TRP B 374 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS B 157 " --> pdb=" O TRP B 374 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU B 376 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 155 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU B 378 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA B 153 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLU B 150 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 186 through 197 removed outlier: 6.476A pdb=" N THR B 178 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG B 191 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 176 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA B 193 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 174 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG B 195 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 172 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N TYR B 170 " --> pdb=" O PRO B 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 186 through 197 removed outlier: 6.476A pdb=" N THR B 178 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG B 191 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 176 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA B 193 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 174 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG B 195 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 172 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N TYR B 170 " --> pdb=" O PRO B 197 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LYS B 166 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASN B 360 " --> pdb=" O LYS B 166 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 212 through 214 Processing sheet with id=AB9, first strand: chain 'B' and resid 216 through 221 Processing sheet with id=AC1, first strand: chain 'B' and resid 293 through 294 Processing sheet with id=AC2, first strand: chain 'B' and resid 591 through 595 removed outlier: 3.862A pdb=" N GLN B 628 " --> pdb=" O ILE B 636 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 636 " --> pdb=" O GLN B 628 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 607 through 609 Processing sheet with id=AC4, first strand: chain 'B' and resid 650 through 655 removed outlier: 5.727A pdb=" N GLU B 663 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TYR B 667 " --> pdb=" O GLU B 663 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 677 through 679 removed outlier: 3.750A pdb=" N GLY B 677 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR C 129 " --> pdb=" O VAL C 581 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 398 through 403 removed outlier: 6.091A pdb=" N TRP C 374 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS C 157 " --> pdb=" O TRP C 374 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU C 376 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C 155 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU C 378 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA C 153 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU C 150 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 398 through 403 removed outlier: 6.091A pdb=" N TRP C 374 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS C 157 " --> pdb=" O TRP C 374 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU C 376 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C 155 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU C 378 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA C 153 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU C 150 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 186 through 197 removed outlier: 6.476A pdb=" N THR C 178 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG C 191 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 176 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA C 193 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL C 174 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ARG C 195 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS C 172 " --> pdb=" O ARG C 195 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N TYR C 170 " --> pdb=" O PRO C 197 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 186 through 197 removed outlier: 6.476A pdb=" N THR C 178 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG C 191 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 176 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA C 193 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL C 174 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ARG C 195 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS C 172 " --> pdb=" O ARG C 195 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N TYR C 170 " --> pdb=" O PRO C 197 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LYS C 166 " --> pdb=" O ASN C 360 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASN C 360 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 212 through 214 Processing sheet with id=AD2, first strand: chain 'C' and resid 216 through 221 Processing sheet with id=AD3, first strand: chain 'C' and resid 293 through 294 Processing sheet with id=AD4, first strand: chain 'C' and resid 591 through 595 removed outlier: 3.862A pdb=" N GLN C 628 " --> pdb=" O ILE C 636 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 636 " --> pdb=" O GLN C 628 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 607 through 609 Processing sheet with id=AD6, first strand: chain 'C' and resid 650 through 655 removed outlier: 5.727A pdb=" N GLU C 663 " --> pdb=" O TYR C 667 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TYR C 667 " --> pdb=" O GLU C 663 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1719 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: 5.06 Time building geometry restraints manager: 6.06 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: 4680 1.34 - 1.46: 3625 1.46 - 1.58: 6332 1.58 - 1.70: 0 1.70 - 1.83: 102 Bond restraints: 14739 Sorted by residual: bond pdb=" N ILE B 679 " pdb=" CA ILE B 679 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.19e-02 7.06e+03 8.98e+00 bond pdb=" N ILE C 679 " pdb=" CA ILE C 679 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.19e-02 7.06e+03 8.84e+00 bond pdb=" N VAL C 512 " pdb=" CA VAL C 512 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.59e+00 bond pdb=" N ILE A 679 " pdb=" CA ILE A 679 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.19e-02 7.06e+03 8.40e+00 bond pdb=" N MET B 678 " pdb=" CA MET B 678 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.19e-02 7.06e+03 8.33e+00 ... (remaining 14734 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.23: 363 106.23 - 113.17: 8173 113.17 - 120.12: 5055 120.12 - 127.06: 6266 127.06 - 134.01: 159 Bond angle restraints: 20016 Sorted by residual: angle pdb=" N VAL A 512 " pdb=" CA VAL A 512 " pdb=" C VAL A 512 " ideal model delta sigma weight residual 113.07 107.60 5.47 1.37e+00 5.33e-01 1.59e+01 angle pdb=" N PHE A 514 " pdb=" CA PHE A 514 " pdb=" C PHE A 514 " ideal model delta sigma weight residual 111.71 107.77 3.94 1.15e+00 7.56e-01 1.17e+01 angle pdb=" N PHE C 514 " pdb=" CA PHE C 514 " pdb=" C PHE C 514 " ideal model delta sigma weight residual 112.34 107.98 4.36 1.30e+00 5.92e-01 1.13e+01 angle pdb=" N PHE B 514 " pdb=" CA PHE B 514 " pdb=" C PHE B 514 " ideal model delta sigma weight residual 112.34 108.14 4.20 1.30e+00 5.92e-01 1.04e+01 angle pdb=" C THR B 509 " pdb=" N SER B 510 " pdb=" CA SER B 510 " ideal model delta sigma weight residual 122.83 118.18 4.65 1.54e+00 4.22e-01 9.10e+00 ... (remaining 20011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.24: 8554 23.24 - 46.48: 464 46.48 - 69.72: 48 69.72 - 92.96: 42 92.96 - 116.20: 6 Dihedral angle restraints: 9114 sinusoidal: 3939 harmonic: 5175 Sorted by residual: dihedral pdb=" CB CYS B 608 " pdb=" SG CYS B 608 " pdb=" SG CYS B 645 " pdb=" CB CYS B 645 " ideal model delta sinusoidal sigma weight residual -86.00 -164.35 78.35 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CB CYS A 608 " pdb=" SG CYS A 608 " pdb=" SG CYS A 645 " pdb=" CB CYS A 645 " ideal model delta sinusoidal sigma weight residual -86.00 -164.35 78.35 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CB CYS C 608 " pdb=" SG CYS C 608 " pdb=" SG CYS C 645 " pdb=" CB CYS C 645 " ideal model delta sinusoidal sigma weight residual -86.00 -164.34 78.34 1 1.00e+01 1.00e-02 7.66e+01 ... (remaining 9111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 2268 0.184 - 0.368: 15 0.368 - 0.552: 0 0.552 - 0.735: 0 0.735 - 0.919: 3 Chirality restraints: 2286 Sorted by residual: chirality pdb=" C1 MAN F 4 " pdb=" O6 MAN F 3 " pdb=" C2 MAN F 4 " pdb=" O5 MAN F 4 " both_signs ideal model delta sigma weight residual False 2.40 1.48 0.92 2.00e-02 2.50e+03 2.11e+03 chirality pdb=" C1 MAN D 4 " pdb=" O6 MAN D 3 " pdb=" C2 MAN D 4 " pdb=" O5 MAN D 4 " both_signs ideal model delta sigma weight residual False 2.40 1.53 0.87 2.00e-02 2.50e+03 1.90e+03 chirality pdb=" C1 MAN E 4 " pdb=" O6 MAN E 3 " pdb=" C2 MAN E 4 " pdb=" O5 MAN E 4 " both_signs ideal model delta sigma weight residual False 2.40 1.56 0.84 2.00e-02 2.50e+03 1.76e+03 ... (remaining 2283 not shown) Planarity restraints: 2547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.266 2.00e-02 2.50e+03 2.22e-01 6.17e+02 pdb=" C7 NAG F 2 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.373 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.262 2.00e-02 2.50e+03 2.18e-01 5.96e+02 pdb=" C7 NAG E 2 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.365 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.187 2.00e-02 2.50e+03 1.54e-01 2.97e+02 pdb=" C7 NAG D 2 " 0.051 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.136 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.250 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.022 2.00e-02 2.50e+03 ... (remaining 2544 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 37 2.30 - 2.95: 6792 2.95 - 3.60: 19460 3.60 - 4.25: 32642 4.25 - 4.90: 55457 Nonbonded interactions: 114388 Sorted by model distance: nonbonded pdb=" OE2 GLU A 513 " pdb=" OE2 GLU B 513 " model vdw 1.647 3.040 nonbonded pdb=" CD2 LEU A 698 " pdb=" CG1 VAL C 512 " model vdw 1.722 3.880 nonbonded pdb=" OE1 GLU A 513 " pdb=" OE1 GLU B 513 " model vdw 1.767 3.040 nonbonded pdb=" OE2 GLU A 513 " pdb=" CD GLU B 513 " model vdw 1.903 3.270 nonbonded pdb=" CD1 LEU A 517 " pdb=" OE2 GLU B 513 " model vdw 2.121 3.460 ... (remaining 114383 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.090 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 40.050 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.090 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 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 : 0.006 0.064 14739 Z= 0.413 Angle : 0.894 7.983 20016 Z= 0.504 Chirality : 0.064 0.919 2286 Planarity : 0.009 0.222 2541 Dihedral : 14.988 116.195 5739 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.38 % Allowed : 3.05 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.61 (0.18), residues: 1740 helix: -0.57 (0.28), residues: 303 sheet: -2.12 (0.21), residues: 471 loop : -1.91 (0.17), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 253 HIS 0.011 0.002 HIS C 527 PHE 0.033 0.003 PHE A 453 TYR 0.031 0.003 TYR A 302 ARG 0.005 0.001 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 306 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8022 (tttt) cc_final: 0.7766 (ttpt) REVERT: A 246 ASN cc_start: 0.5972 (m-40) cc_final: 0.5106 (p0) REVERT: A 393 MET cc_start: 0.8555 (mtt) cc_final: 0.8081 (mtm) REVERT: A 401 ILE cc_start: 0.8350 (tt) cc_final: 0.8068 (tt) REVERT: A 657 HIS cc_start: 0.6975 (m-70) cc_final: 0.6485 (t-170) REVERT: B 246 ASN cc_start: 0.6085 (m-40) cc_final: 0.5385 (p0) REVERT: B 393 MET cc_start: 0.8650 (mtt) cc_final: 0.8411 (mtt) REVERT: B 531 MET cc_start: 0.6997 (mmp) cc_final: 0.6760 (mmm) REVERT: B 657 HIS cc_start: 0.7096 (m-70) cc_final: 0.6647 (t-90) REVERT: C 216 LYS cc_start: 0.8099 (tttt) cc_final: 0.7814 (ttpt) REVERT: C 246 ASN cc_start: 0.6356 (m-40) cc_final: 0.5458 (p0) REVERT: C 406 GLU cc_start: 0.7748 (mm-30) cc_final: 0.6719 (tp30) REVERT: C 531 MET cc_start: 0.6818 (mmp) cc_final: 0.6517 (mmm) outliers start: 6 outliers final: 0 residues processed: 312 average time/residue: 0.3310 time to fit residues: 140.8646 Evaluate side-chains 166 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.0980 chunk 131 optimal weight: 0.0870 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 101 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN A 405 ASN A 411 GLN A 525 GLN A 543 GLN A 628 GLN A 724 HIS B 223 ASN B 411 GLN B 543 GLN B 583 ASN B 628 GLN B 649 HIS B 724 HIS C 223 ASN C 411 GLN C 543 GLN C 583 ASN C 628 GLN C 649 HIS C 724 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14739 Z= 0.203 Angle : 0.634 8.952 20016 Z= 0.327 Chirality : 0.046 0.169 2286 Planarity : 0.004 0.037 2541 Dihedral : 8.822 88.346 2391 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.61 % Allowed : 10.75 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.37 (0.19), residues: 1740 helix: 0.64 (0.30), residues: 288 sheet: -1.24 (0.23), residues: 459 loop : -1.20 (0.18), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 359 HIS 0.007 0.001 HIS B 649 PHE 0.024 0.002 PHE C 148 TYR 0.028 0.002 TYR A 314 ARG 0.008 0.001 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 193 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ILE cc_start: 0.8814 (mt) cc_final: 0.8502 (mt) REVERT: A 215 SER cc_start: 0.7992 (t) cc_final: 0.7715 (t) REVERT: A 216 LYS cc_start: 0.8056 (tttt) cc_final: 0.7727 (ttpt) REVERT: A 401 ILE cc_start: 0.8161 (tt) cc_final: 0.7863 (tt) REVERT: A 678 MET cc_start: 0.8160 (tpp) cc_final: 0.7925 (tpp) REVERT: A 719 ARG cc_start: 0.7197 (mtm110) cc_final: 0.6975 (ttm110) REVERT: B 198 ILE cc_start: 0.8776 (mt) cc_final: 0.8440 (mt) REVERT: B 215 SER cc_start: 0.7987 (t) cc_final: 0.7611 (t) REVERT: B 246 ASN cc_start: 0.5806 (m-40) cc_final: 0.5275 (p0) REVERT: B 393 MET cc_start: 0.8517 (mtt) cc_final: 0.8237 (mtt) REVERT: B 401 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7960 (tt) REVERT: B 678 MET cc_start: 0.7997 (tpp) cc_final: 0.7778 (tpp) REVERT: B 723 MET cc_start: 0.7400 (mtm) cc_final: 0.7066 (mtm) REVERT: C 198 ILE cc_start: 0.8772 (mt) cc_final: 0.8442 (mt) REVERT: C 215 SER cc_start: 0.8033 (t) cc_final: 0.7640 (t) REVERT: C 216 LYS cc_start: 0.8095 (tttt) cc_final: 0.7797 (ttpt) REVERT: C 246 ASN cc_start: 0.6262 (m-40) cc_final: 0.5465 (p0) REVERT: C 302 TYR cc_start: 0.7890 (m-80) cc_final: 0.6710 (m-80) REVERT: C 406 GLU cc_start: 0.7732 (mm-30) cc_final: 0.6818 (tp30) REVERT: C 579 ILE cc_start: 0.8397 (mm) cc_final: 0.8186 (mm) outliers start: 41 outliers final: 22 residues processed: 224 average time/residue: 0.2823 time to fit residues: 92.1134 Evaluate side-chains 177 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 713 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 158 optimal weight: 0.9980 chunk 171 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS A 458 GLN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 HIS A 724 HIS B 254 HIS B 458 GLN B 541 GLN ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN B 674 HIS B 724 HIS C 254 HIS C 458 GLN ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 ASN C 724 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14739 Z= 0.282 Angle : 0.633 8.178 20016 Z= 0.327 Chirality : 0.046 0.192 2286 Planarity : 0.004 0.037 2541 Dihedral : 8.236 77.854 2391 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.18 % Allowed : 14.38 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.98 (0.19), residues: 1740 helix: 1.43 (0.32), residues: 270 sheet: -0.99 (0.23), residues: 459 loop : -1.06 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 359 HIS 0.017 0.002 HIS B 657 PHE 0.021 0.002 PHE C 148 TYR 0.024 0.002 TYR C 260 ARG 0.011 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 156 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8104 (tttt) cc_final: 0.7815 (ttpt) REVERT: A 401 ILE cc_start: 0.8076 (tt) cc_final: 0.7856 (tt) REVERT: A 678 MET cc_start: 0.8033 (tpp) cc_final: 0.7798 (tpp) REVERT: B 215 SER cc_start: 0.8256 (t) cc_final: 0.7893 (t) REVERT: B 401 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.8020 (tt) REVERT: B 678 MET cc_start: 0.8034 (tpp) cc_final: 0.7831 (tpp) REVERT: C 215 SER cc_start: 0.8042 (t) cc_final: 0.7734 (t) REVERT: C 531 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6535 (mmp) REVERT: C 657 HIS cc_start: 0.7213 (m-70) cc_final: 0.6815 (t-170) outliers start: 50 outliers final: 30 residues processed: 194 average time/residue: 0.2522 time to fit residues: 73.7323 Evaluate side-chains 177 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 145 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 531 MET Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 713 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.2980 chunk 119 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 168 optimal weight: 0.5980 chunk 150 optimal weight: 0.5980 chunk 45 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 HIS A 724 HIS ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 HIS B 724 HIS ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 724 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14739 Z= 0.185 Angle : 0.562 8.514 20016 Z= 0.288 Chirality : 0.044 0.182 2286 Planarity : 0.004 0.038 2541 Dihedral : 7.632 71.527 2391 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.67 % Allowed : 17.56 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.65 (0.20), residues: 1740 helix: 1.79 (0.32), residues: 273 sheet: -0.73 (0.23), residues: 456 loop : -0.90 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 180 HIS 0.011 0.001 HIS B 657 PHE 0.018 0.001 PHE B 148 TYR 0.019 0.002 TYR B 260 ARG 0.006 0.000 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 159 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.7438 (mt) cc_final: 0.7119 (mm) REVERT: A 216 LYS cc_start: 0.8068 (tttt) cc_final: 0.7751 (ttpt) REVERT: A 401 ILE cc_start: 0.8105 (tt) cc_final: 0.7870 (tt) REVERT: A 579 ILE cc_start: 0.8649 (mm) cc_final: 0.8384 (mm) REVERT: A 678 MET cc_start: 0.8004 (tpp) cc_final: 0.7756 (tpp) REVERT: B 198 ILE cc_start: 0.8700 (mt) cc_final: 0.8432 (mt) REVERT: B 401 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7905 (tt) REVERT: B 678 MET cc_start: 0.8014 (tpp) cc_final: 0.7786 (tpp) REVERT: B 719 ARG cc_start: 0.7165 (mtm110) cc_final: 0.6788 (ttp-110) REVERT: C 215 SER cc_start: 0.8002 (t) cc_final: 0.7613 (t) REVERT: C 657 HIS cc_start: 0.7033 (m-70) cc_final: 0.6779 (t-170) outliers start: 42 outliers final: 25 residues processed: 193 average time/residue: 0.2534 time to fit residues: 72.7936 Evaluate side-chains 171 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 713 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 125 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 ASN ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14739 Z= 0.181 Angle : 0.552 8.628 20016 Z= 0.281 Chirality : 0.043 0.167 2286 Planarity : 0.003 0.035 2541 Dihedral : 7.135 65.266 2391 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.80 % Allowed : 17.88 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.50 (0.20), residues: 1740 helix: 2.01 (0.32), residues: 273 sheet: -0.68 (0.23), residues: 462 loop : -0.80 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 180 HIS 0.005 0.001 HIS C 527 PHE 0.015 0.001 PHE B 148 TYR 0.020 0.001 TYR B 260 ARG 0.006 0.000 ARG C 611 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 159 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8062 (tttt) cc_final: 0.7748 (ttpt) REVERT: A 401 ILE cc_start: 0.8091 (tt) cc_final: 0.7846 (tt) REVERT: A 586 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8226 (tm-30) REVERT: A 678 MET cc_start: 0.7995 (tpp) cc_final: 0.7752 (tpp) REVERT: B 215 SER cc_start: 0.8107 (t) cc_final: 0.7743 (t) REVERT: B 401 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7906 (tt) REVERT: B 599 MET cc_start: 0.4183 (mmt) cc_final: 0.3637 (mmt) REVERT: B 678 MET cc_start: 0.8006 (tpp) cc_final: 0.7760 (tpp) REVERT: B 705 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: B 719 ARG cc_start: 0.7175 (mtm110) cc_final: 0.6808 (ttp-110) REVERT: C 215 SER cc_start: 0.8155 (t) cc_final: 0.7777 (t) REVERT: C 586 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: C 657 HIS cc_start: 0.7051 (m-70) cc_final: 0.6848 (t-170) outliers start: 44 outliers final: 35 residues processed: 192 average time/residue: 0.2581 time to fit residues: 73.5118 Evaluate side-chains 183 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 144 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 713 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 721 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14739 Z= 0.377 Angle : 0.699 10.226 20016 Z= 0.356 Chirality : 0.048 0.232 2286 Planarity : 0.004 0.039 2541 Dihedral : 6.748 54.609 2391 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.07 % Allowed : 18.58 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.80 (0.19), residues: 1740 helix: 1.67 (0.32), residues: 270 sheet: -0.56 (0.23), residues: 462 loop : -1.15 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 359 HIS 0.006 0.001 HIS A 254 PHE 0.022 0.003 PHE C 293 TYR 0.027 0.003 TYR A 260 ARG 0.011 0.001 ARG C 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 139 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8170 (tttt) cc_final: 0.7906 (ttpt) REVERT: A 401 ILE cc_start: 0.8125 (tt) cc_final: 0.7865 (tt) REVERT: A 531 MET cc_start: 0.7498 (mmp) cc_final: 0.7145 (mmp) REVERT: A 554 PHE cc_start: 0.6712 (OUTLIER) cc_final: 0.5538 (t80) REVERT: A 586 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8220 (tm-30) REVERT: A 599 MET cc_start: 0.4249 (mmt) cc_final: 0.3965 (mmt) REVERT: A 678 MET cc_start: 0.8026 (tpp) cc_final: 0.7787 (tpp) REVERT: B 401 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7943 (tt) REVERT: B 513 GLU cc_start: 0.6814 (mp0) cc_final: 0.6575 (mt-10) REVERT: B 531 MET cc_start: 0.7488 (mmp) cc_final: 0.7277 (mmp) REVERT: B 678 MET cc_start: 0.8031 (tpp) cc_final: 0.7790 (tpp) REVERT: C 215 SER cc_start: 0.8276 (t) cc_final: 0.7979 (t) REVERT: C 554 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6186 (t80) REVERT: C 586 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8190 (tm-30) outliers start: 64 outliers final: 48 residues processed: 189 average time/residue: 0.2571 time to fit residues: 72.7317 Evaluate side-chains 190 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 137 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 713 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 167 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 0.0570 chunk 103 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 HIS C 674 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14739 Z= 0.228 Angle : 0.595 8.730 20016 Z= 0.301 Chirality : 0.044 0.209 2286 Planarity : 0.004 0.038 2541 Dihedral : 6.238 51.622 2391 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.50 % Allowed : 20.42 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.70 (0.19), residues: 1740 helix: 1.82 (0.32), residues: 270 sheet: -0.40 (0.23), residues: 483 loop : -1.17 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 180 HIS 0.023 0.001 HIS C 657 PHE 0.015 0.002 PHE B 148 TYR 0.024 0.002 TYR C 260 ARG 0.007 0.001 ARG C 611 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 135 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8128 (tttt) cc_final: 0.7889 (ttpt) REVERT: A 401 ILE cc_start: 0.8132 (tt) cc_final: 0.7896 (tt) REVERT: A 531 MET cc_start: 0.7371 (mmp) cc_final: 0.7079 (mmp) REVERT: A 586 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8217 (tm-30) REVERT: A 599 MET cc_start: 0.4361 (mmt) cc_final: 0.3938 (mmt) REVERT: A 678 MET cc_start: 0.7994 (tpp) cc_final: 0.7754 (tpp) REVERT: B 303 MET cc_start: 0.7737 (ttp) cc_final: 0.7528 (ttt) REVERT: B 401 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7973 (tt) REVERT: B 531 MET cc_start: 0.7373 (mmp) cc_final: 0.7147 (mmp) REVERT: B 599 MET cc_start: 0.4136 (mmt) cc_final: 0.3757 (mmt) REVERT: B 678 MET cc_start: 0.8020 (tpp) cc_final: 0.7782 (tpp) REVERT: B 719 ARG cc_start: 0.7212 (mtm110) cc_final: 0.6871 (ttp-110) REVERT: C 215 SER cc_start: 0.8234 (t) cc_final: 0.7907 (t) REVERT: C 554 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6056 (t80) REVERT: C 586 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8174 (tm-30) outliers start: 55 outliers final: 43 residues processed: 178 average time/residue: 0.2444 time to fit residues: 66.0457 Evaluate side-chains 177 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 130 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 713 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 114 optimal weight: 0.1980 chunk 82 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 131 optimal weight: 0.3980 chunk 152 optimal weight: 1.9990 chunk 160 optimal weight: 0.0570 chunk 146 optimal weight: 0.7980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14739 Z= 0.155 Angle : 0.550 11.662 20016 Z= 0.275 Chirality : 0.043 0.181 2286 Planarity : 0.003 0.037 2541 Dihedral : 5.577 48.071 2391 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.56 % Allowed : 19.91 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.45 (0.20), residues: 1740 helix: 2.13 (0.32), residues: 270 sheet: -0.33 (0.23), residues: 480 loop : -0.97 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 180 HIS 0.005 0.001 HIS B 527 PHE 0.014 0.001 PHE B 148 TYR 0.031 0.001 TYR C 260 ARG 0.008 0.000 ARG C 611 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 146 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ILE cc_start: 0.8697 (mt) cc_final: 0.8399 (mt) REVERT: A 216 LYS cc_start: 0.8078 (tttt) cc_final: 0.7823 (ttpt) REVERT: A 401 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7948 (tt) REVERT: A 531 MET cc_start: 0.7289 (mmp) cc_final: 0.7026 (mmp) REVERT: A 554 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.5763 (t80) REVERT: A 586 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: A 678 MET cc_start: 0.7970 (tpp) cc_final: 0.7711 (tpp) REVERT: A 723 MET cc_start: 0.7217 (mtm) cc_final: 0.6990 (mtm) REVERT: B 401 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7908 (tt) REVERT: B 531 MET cc_start: 0.7362 (mmp) cc_final: 0.7123 (mmp) REVERT: B 599 MET cc_start: 0.4108 (mmt) cc_final: 0.3717 (mmt) REVERT: B 611 ARG cc_start: 0.8248 (mtp85) cc_final: 0.7840 (mmm-85) REVERT: B 678 MET cc_start: 0.7930 (tpp) cc_final: 0.7699 (tpp) REVERT: B 719 ARG cc_start: 0.7136 (mtm110) cc_final: 0.6866 (ttp-110) REVERT: C 215 SER cc_start: 0.8154 (t) cc_final: 0.7812 (t) REVERT: C 554 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6261 (t80) REVERT: C 586 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: C 599 MET cc_start: 0.3980 (mmt) cc_final: 0.3666 (mmt) outliers start: 56 outliers final: 39 residues processed: 187 average time/residue: 0.2480 time to fit residues: 70.1334 Evaluate side-chains 180 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 135 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 713 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 1.9990 chunk 160 optimal weight: 0.0170 chunk 94 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 overall best weight: 1.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14739 Z= 0.272 Angle : 0.606 9.390 20016 Z= 0.306 Chirality : 0.045 0.251 2286 Planarity : 0.004 0.038 2541 Dihedral : 5.380 42.142 2391 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.50 % Allowed : 20.42 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.54 (0.20), residues: 1740 helix: 2.00 (0.32), residues: 270 sheet: -0.28 (0.23), residues: 477 loop : -1.09 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 359 HIS 0.005 0.001 HIS C 527 PHE 0.016 0.002 PHE B 293 TYR 0.028 0.002 TYR C 260 ARG 0.008 0.001 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 129 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8186 (tttt) cc_final: 0.7944 (ttpt) REVERT: A 401 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7987 (tt) REVERT: A 531 MET cc_start: 0.7387 (mmp) cc_final: 0.7132 (mmp) REVERT: A 554 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6086 (t80) REVERT: A 586 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8175 (tm-30) REVERT: A 678 MET cc_start: 0.7981 (tpp) cc_final: 0.7751 (tpp) REVERT: B 303 MET cc_start: 0.7817 (tmm) cc_final: 0.7412 (tmm) REVERT: B 401 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7966 (tt) REVERT: B 531 MET cc_start: 0.7474 (mmp) cc_final: 0.7257 (mmp) REVERT: B 554 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.5562 (t80) REVERT: B 599 MET cc_start: 0.4144 (mmt) cc_final: 0.3749 (mmt) REVERT: B 678 MET cc_start: 0.8003 (tpp) cc_final: 0.7773 (tpp) REVERT: B 719 ARG cc_start: 0.7116 (mtm110) cc_final: 0.6892 (ttp-110) REVERT: B 724 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.7249 (t-170) REVERT: C 215 SER cc_start: 0.8182 (t) cc_final: 0.7876 (t) REVERT: C 554 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6332 (t80) REVERT: C 586 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8111 (tm-30) REVERT: C 599 MET cc_start: 0.3948 (mmt) cc_final: 0.3578 (mmt) outliers start: 55 outliers final: 43 residues processed: 169 average time/residue: 0.2518 time to fit residues: 64.0037 Evaluate side-chains 177 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 126 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 724 HIS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 713 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 159 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14739 Z= 0.357 Angle : 0.671 10.020 20016 Z= 0.343 Chirality : 0.047 0.273 2286 Planarity : 0.004 0.039 2541 Dihedral : 5.383 33.911 2391 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.82 % Allowed : 20.23 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.91 (0.19), residues: 1740 helix: 1.58 (0.32), residues: 270 sheet: -0.46 (0.23), residues: 516 loop : -1.35 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 359 HIS 0.006 0.002 HIS C 254 PHE 0.019 0.003 PHE B 293 TYR 0.037 0.002 TYR C 260 ARG 0.007 0.001 ARG C 611 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 132 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 ILE cc_start: 0.8168 (tt) cc_final: 0.7932 (tt) REVERT: A 531 MET cc_start: 0.7563 (mmp) cc_final: 0.7222 (mmp) REVERT: A 554 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6296 (t80) REVERT: A 586 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8148 (tm-30) REVERT: A 678 MET cc_start: 0.8022 (tpp) cc_final: 0.7818 (tpp) REVERT: B 401 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7983 (tt) REVERT: B 531 MET cc_start: 0.7618 (mmp) cc_final: 0.7217 (mmp) REVERT: B 554 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6138 (t80) REVERT: B 599 MET cc_start: 0.4169 (mmt) cc_final: 0.3805 (mmt) REVERT: B 611 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7702 (mmm-85) REVERT: B 678 MET cc_start: 0.8017 (tpp) cc_final: 0.7790 (tpp) REVERT: B 719 ARG cc_start: 0.7112 (mtm110) cc_final: 0.6783 (mtm110) REVERT: B 724 HIS cc_start: 0.7800 (OUTLIER) cc_final: 0.7310 (t-170) REVERT: C 554 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.6559 (t80) REVERT: C 586 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8101 (tm-30) REVERT: C 599 MET cc_start: 0.4069 (mmt) cc_final: 0.3722 (mmt) outliers start: 60 outliers final: 43 residues processed: 175 average time/residue: 0.2406 time to fit residues: 63.7947 Evaluate side-chains 171 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 121 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 724 HIS Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 713 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.152841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.119386 restraints weight = 18529.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.122999 restraints weight = 11376.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.125539 restraints weight = 8011.634| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14739 Z= 0.212 Angle : 0.586 10.821 20016 Z= 0.296 Chirality : 0.045 0.299 2286 Planarity : 0.004 0.038 2541 Dihedral : 5.064 33.480 2391 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.31 % Allowed : 20.99 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.70 (0.20), residues: 1740 helix: 1.91 (0.32), residues: 270 sheet: -0.37 (0.23), residues: 516 loop : -1.23 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 180 HIS 0.005 0.001 HIS A 143 PHE 0.013 0.002 PHE B 148 TYR 0.028 0.002 TYR B 260 ARG 0.007 0.000 ARG A 611 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2784.00 seconds wall clock time: 51 minutes 57.49 seconds (3117.49 seconds total)