Starting phenix.real_space_refine on Sun Feb 18 13:25:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0j_11968/02_2024/7b0j_11968_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0j_11968/02_2024/7b0j_11968.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0j_11968/02_2024/7b0j_11968_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0j_11968/02_2024/7b0j_11968_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0j_11968/02_2024/7b0j_11968_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0j_11968/02_2024/7b0j_11968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0j_11968/02_2024/7b0j_11968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0j_11968/02_2024/7b0j_11968_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0j_11968/02_2024/7b0j_11968_updated.pdb" } resolution = 2.85 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 108 5.16 5 C 14477 2.51 5 N 3644 2.21 5 O 3865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A ARG 260": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 393": "OD1" <-> "OD2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A ASP 629": "OD1" <-> "OD2" Residue "A ASP 632": "OD1" <-> "OD2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A ARG 710": "NH1" <-> "NH2" Residue "A TYR 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 105": "NH1" <-> "NH2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 393": "OD1" <-> "OD2" Residue "B ARG 394": "NH1" <-> "NH2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B GLU 478": "OE1" <-> "OE2" Residue "B TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 566": "OE1" <-> "OE2" Residue "B ASP 629": "OD1" <-> "OD2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B ARG 700": "NH1" <-> "NH2" Residue "B GLU 707": "OE1" <-> "OE2" Residue "B ARG 710": "NH1" <-> "NH2" Residue "B TYR 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ASP 44": "OD1" <-> "OD2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C ARG 260": "NH1" <-> "NH2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C GLU 264": "OE1" <-> "OE2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 393": "OD1" <-> "OD2" Residue "C ARG 394": "NH1" <-> "NH2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C GLU 478": "OE1" <-> "OE2" Residue "C TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 566": "OE1" <-> "OE2" Residue "C ASP 629": "OD1" <-> "OD2" Residue "C ASP 632": "OD1" <-> "OD2" Residue "C GLU 634": "OE1" <-> "OE2" Residue "C GLU 648": "OE1" <-> "OE2" Residue "C ARG 700": "NH1" <-> "NH2" Residue "C GLU 707": "OE1" <-> "OE2" Residue "C ARG 710": "NH1" <-> "NH2" Residue "C TYR 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D GLU 229": "OE1" <-> "OE2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D GLU 242": "OE1" <-> "OE2" Residue "D ARG 260": "NH1" <-> "NH2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D GLU 264": "OE1" <-> "OE2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "D PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 393": "OD1" <-> "OD2" Residue "D ARG 394": "NH1" <-> "NH2" Residue "D GLU 417": "OE1" <-> "OE2" Residue "D TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D GLU 478": "OE1" <-> "OE2" Residue "D TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 566": "OE1" <-> "OE2" Residue "D ASP 629": "OD1" <-> "OD2" Residue "D ASP 632": "OD1" <-> "OD2" Residue "D GLU 634": "OE1" <-> "OE2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "D ARG 700": "NH1" <-> "NH2" Residue "D GLU 707": "OE1" <-> "OE2" Residue "D ARG 710": "NH1" <-> "NH2" Residue "D TYR 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 748": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22102 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5480 Classifications: {'peptide': 682} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 25, 'TRANS': 656} Chain breaks: 4 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 5480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5480 Classifications: {'peptide': 682} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 25, 'TRANS': 656} Chain breaks: 4 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5482 Classifications: {'peptide': 682} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 25, 'TRANS': 656} Chain breaks: 4 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 5480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5480 Classifications: {'peptide': 682} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 25, 'TRANS': 656} Chain breaks: 4 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' CA': 1, 'LPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' CA': 1, 'LPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' CA': 1, 'LPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' CA': 1, 'LPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.64, per 1000 atoms: 0.53 Number of scatterers: 22102 At special positions: 0 Unit cell: (131.75, 131.75, 133.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 108 16.00 P 4 15.00 O 3865 8.00 N 3644 7.00 C 14477 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.26 Conformation dependent library (CDL) restraints added in 4.4 seconds 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5248 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 0 sheets defined 66.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain 'A' and resid 31 through 42 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 99 through 105 Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 145 through 152 Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.826A pdb=" N LYS A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 203 Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'A' and resid 216 through 233 removed outlier: 3.619A pdb=" N LYS A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 256 Processing helix chain 'A' and resid 262 through 269 Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 304 through 315 Processing helix chain 'A' and resid 326 through 338 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 362 through 384 removed outlier: 3.843A pdb=" N SER A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 422 Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 427 through 431 Processing helix chain 'A' and resid 433 through 458 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 473 through 492 removed outlier: 3.989A pdb=" N LEU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 503 through 541 removed outlier: 3.721A pdb=" N LEU A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU A 514 " --> pdb=" O GLY A 510 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASP A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR A 540 " --> pdb=" O GLN A 536 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 576 removed outlier: 4.005A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE A 576 " --> pdb=" O PHE A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 584 removed outlier: 3.665A pdb=" N THR A 584 " --> pdb=" O LEU A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 584' Processing helix chain 'A' and resid 591 through 609 Processing helix chain 'A' and resid 612 through 627 removed outlier: 3.660A pdb=" N HIS A 626 " --> pdb=" O ASN A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 646 removed outlier: 3.757A pdb=" N TYR A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 658 No H-bonds generated for 'chain 'A' and resid 655 through 658' Processing helix chain 'A' and resid 667 through 673 removed outlier: 3.593A pdb=" N TRP A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 720 Processing helix chain 'A' and resid 723 through 726 No H-bonds generated for 'chain 'A' and resid 723 through 726' Processing helix chain 'A' and resid 732 through 751 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 73 through 79 Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 145 through 152 Processing helix chain 'B' and resid 155 through 164 removed outlier: 3.827A pdb=" N LYS B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 203 Processing helix chain 'B' and resid 206 through 211 Processing helix chain 'B' and resid 216 through 233 removed outlier: 3.619A pdb=" N LYS B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 256 Processing helix chain 'B' and resid 262 through 269 Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 298 through 301 No H-bonds generated for 'chain 'B' and resid 298 through 301' Processing helix chain 'B' and resid 304 through 315 Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'B' and resid 362 through 384 removed outlier: 3.842A pdb=" N SER B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 422 Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 427 through 431 Processing helix chain 'B' and resid 433 through 458 Processing helix chain 'B' and resid 465 through 467 No H-bonds generated for 'chain 'B' and resid 465 through 467' Processing helix chain 'B' and resid 473 through 492 removed outlier: 3.990A pdb=" N LEU B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 503 through 541 removed outlier: 3.720A pdb=" N LEU B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU B 514 " --> pdb=" O GLY B 510 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASP B 515 " --> pdb=" O ARG B 511 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR B 540 " --> pdb=" O GLN B 536 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 576 removed outlier: 4.006A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 584 removed outlier: 3.664A pdb=" N THR B 584 " --> pdb=" O LEU B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 584' Processing helix chain 'B' and resid 591 through 609 Processing helix chain 'B' and resid 612 through 627 removed outlier: 3.661A pdb=" N HIS B 626 " --> pdb=" O ASN B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 646 removed outlier: 3.756A pdb=" N TYR B 646 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 658 No H-bonds generated for 'chain 'B' and resid 655 through 658' Processing helix chain 'B' and resid 667 through 673 removed outlier: 3.593A pdb=" N TRP B 672 " --> pdb=" O TYR B 668 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 720 Processing helix chain 'B' and resid 723 through 726 No H-bonds generated for 'chain 'B' and resid 723 through 726' Processing helix chain 'B' and resid 732 through 751 Processing helix chain 'C' and resid 31 through 42 Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 73 through 79 Processing helix chain 'C' and resid 83 through 91 Processing helix chain 'C' and resid 99 through 105 Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 145 through 152 Processing helix chain 'C' and resid 155 through 164 removed outlier: 3.826A pdb=" N LYS C 164 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 216 through 233 removed outlier: 3.618A pdb=" N LYS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 256 Processing helix chain 'C' and resid 262 through 269 Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 298 through 301 No H-bonds generated for 'chain 'C' and resid 298 through 301' Processing helix chain 'C' and resid 304 through 315 Processing helix chain 'C' and resid 326 through 338 Processing helix chain 'C' and resid 340 through 349 Processing helix chain 'C' and resid 362 through 384 removed outlier: 3.843A pdb=" N SER C 384 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 422 Proline residue: C 408 - end of helix Processing helix chain 'C' and resid 427 through 431 Processing helix chain 'C' and resid 433 through 458 Processing helix chain 'C' and resid 465 through 467 No H-bonds generated for 'chain 'C' and resid 465 through 467' Processing helix chain 'C' and resid 473 through 492 removed outlier: 3.989A pdb=" N LEU C 492 " --> pdb=" O SER C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 503 through 541 removed outlier: 3.720A pdb=" N LEU C 513 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU C 514 " --> pdb=" O GLY C 510 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASP C 515 " --> pdb=" O ARG C 511 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR C 540 " --> pdb=" O GLN C 536 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 576 removed outlier: 4.005A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE C 576 " --> pdb=" O PHE C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 584 removed outlier: 3.664A pdb=" N THR C 584 " --> pdb=" O LEU C 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 581 through 584' Processing helix chain 'C' and resid 591 through 609 Processing helix chain 'C' and resid 612 through 627 removed outlier: 3.659A pdb=" N HIS C 626 " --> pdb=" O ASN C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 646 removed outlier: 3.757A pdb=" N TYR C 646 " --> pdb=" O LEU C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 658 No H-bonds generated for 'chain 'C' and resid 655 through 658' Processing helix chain 'C' and resid 667 through 673 removed outlier: 3.593A pdb=" N TRP C 672 " --> pdb=" O TYR C 668 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 720 Processing helix chain 'C' and resid 723 through 726 No H-bonds generated for 'chain 'C' and resid 723 through 726' Processing helix chain 'C' and resid 732 through 751 Processing helix chain 'D' and resid 31 through 42 Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 73 through 79 Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'D' and resid 99 through 105 Processing helix chain 'D' and resid 109 through 115 Processing helix chain 'D' and resid 145 through 152 Processing helix chain 'D' and resid 155 through 164 removed outlier: 3.827A pdb=" N LYS D 164 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 203 Processing helix chain 'D' and resid 206 through 211 Processing helix chain 'D' and resid 216 through 233 removed outlier: 3.617A pdb=" N LYS D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 256 Processing helix chain 'D' and resid 262 through 269 Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 298 through 301 No H-bonds generated for 'chain 'D' and resid 298 through 301' Processing helix chain 'D' and resid 304 through 315 Processing helix chain 'D' and resid 326 through 338 Processing helix chain 'D' and resid 340 through 349 Processing helix chain 'D' and resid 362 through 384 removed outlier: 3.842A pdb=" N SER D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 422 Proline residue: D 408 - end of helix Processing helix chain 'D' and resid 427 through 431 Processing helix chain 'D' and resid 433 through 458 Processing helix chain 'D' and resid 465 through 467 No H-bonds generated for 'chain 'D' and resid 465 through 467' Processing helix chain 'D' and resid 473 through 492 removed outlier: 3.989A pdb=" N LEU D 492 " --> pdb=" O SER D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 496 No H-bonds generated for 'chain 'D' and resid 494 through 496' Processing helix chain 'D' and resid 503 through 541 removed outlier: 3.721A pdb=" N LEU D 513 " --> pdb=" O LEU D 509 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU D 514 " --> pdb=" O GLY D 510 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASP D 515 " --> pdb=" O ARG D 511 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR D 540 " --> pdb=" O GLN D 536 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 576 removed outlier: 4.006A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE D 576 " --> pdb=" O PHE D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 584 removed outlier: 3.664A pdb=" N THR D 584 " --> pdb=" O LEU D 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 581 through 584' Processing helix chain 'D' and resid 591 through 609 Processing helix chain 'D' and resid 612 through 627 removed outlier: 3.661A pdb=" N HIS D 626 " --> pdb=" O ASN D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 646 removed outlier: 3.756A pdb=" N TYR D 646 " --> pdb=" O LEU D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 658 No H-bonds generated for 'chain 'D' and resid 655 through 658' Processing helix chain 'D' and resid 667 through 673 removed outlier: 3.593A pdb=" N TRP D 672 " --> pdb=" O TYR D 668 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 720 Processing helix chain 'D' and resid 723 through 726 No H-bonds generated for 'chain 'D' and resid 723 through 726' Processing helix chain 'D' and resid 732 through 751 1168 hydrogen bonds defined for protein. 3504 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: 6.87 Time building geometry restraints manager: 9.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3437 1.30 - 1.43: 6291 1.43 - 1.56: 12722 1.56 - 1.68: 20 1.68 - 1.81: 176 Bond restraints: 22646 Sorted by residual: bond pdb=" CG LEU A 380 " pdb=" CD1 LEU A 380 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.96e+00 bond pdb=" CG LEU C 380 " pdb=" CD1 LEU C 380 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.89e+00 bond pdb=" CG LEU B 380 " pdb=" CD1 LEU B 380 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.83e+00 bond pdb=" CG LEU D 380 " pdb=" CD1 LEU D 380 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.83e+00 bond pdb=" C18 LPP C1001 " pdb=" C19 LPP C1001 " ideal model delta sigma weight residual 1.527 1.570 -0.043 2.00e-02 2.50e+03 4.55e+00 ... (remaining 22641 not shown) Histogram of bond angle deviations from ideal: 98.81 - 105.88: 432 105.88 - 112.95: 12315 112.95 - 120.02: 8103 120.02 - 127.09: 9554 127.09 - 134.16: 299 Bond angle restraints: 30703 Sorted by residual: angle pdb=" CA GLU A 727 " pdb=" CB GLU A 727 " pdb=" CG GLU A 727 " ideal model delta sigma weight residual 114.10 123.33 -9.23 2.00e+00 2.50e-01 2.13e+01 angle pdb=" CA GLU B 727 " pdb=" CB GLU B 727 " pdb=" CG GLU B 727 " ideal model delta sigma weight residual 114.10 123.32 -9.22 2.00e+00 2.50e-01 2.13e+01 angle pdb=" CA GLU C 727 " pdb=" CB GLU C 727 " pdb=" CG GLU C 727 " ideal model delta sigma weight residual 114.10 123.32 -9.22 2.00e+00 2.50e-01 2.13e+01 angle pdb=" CA GLU D 727 " pdb=" CB GLU D 727 " pdb=" CG GLU D 727 " ideal model delta sigma weight residual 114.10 123.27 -9.17 2.00e+00 2.50e-01 2.10e+01 angle pdb=" CB GLU A 727 " pdb=" CG GLU A 727 " pdb=" CD GLU A 727 " ideal model delta sigma weight residual 112.60 120.18 -7.58 1.70e+00 3.46e-01 1.99e+01 ... (remaining 30698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11725 17.95 - 35.90: 1288 35.90 - 53.85: 308 53.85 - 71.79: 68 71.79 - 89.74: 28 Dihedral angle restraints: 13417 sinusoidal: 5349 harmonic: 8068 Sorted by residual: dihedral pdb=" CA ASN A 558 " pdb=" C ASN A 558 " pdb=" N ASN A 559 " pdb=" CA ASN A 559 " ideal model delta harmonic sigma weight residual -180.00 -161.90 -18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASN D 558 " pdb=" C ASN D 558 " pdb=" N ASN D 559 " pdb=" CA ASN D 559 " ideal model delta harmonic sigma weight residual 180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ASN B 558 " pdb=" C ASN B 558 " pdb=" N ASN B 559 " pdb=" CA ASN B 559 " ideal model delta harmonic sigma weight residual -180.00 -161.98 -18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 13414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2061 0.040 - 0.081: 1124 0.081 - 0.121: 197 0.121 - 0.161: 63 0.161 - 0.201: 8 Chirality restraints: 3453 Sorted by residual: chirality pdb=" CA PRO A 399 " pdb=" N PRO A 399 " pdb=" C PRO A 399 " pdb=" CB PRO A 399 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA PRO B 399 " pdb=" N PRO B 399 " pdb=" C PRO B 399 " pdb=" CB PRO B 399 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA PRO C 399 " pdb=" N PRO C 399 " pdb=" C PRO C 399 " pdb=" CB PRO C 399 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 3450 not shown) Planarity restraints: 3804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 398 " 0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO A 399 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 399 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 399 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 398 " 0.056 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO B 399 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 399 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 399 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 398 " -0.056 5.00e-02 4.00e+02 8.61e-02 1.19e+01 pdb=" N PRO C 399 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 399 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 399 " -0.046 5.00e-02 4.00e+02 ... (remaining 3801 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5556 2.79 - 3.32: 22376 3.32 - 3.85: 37428 3.85 - 4.37: 44897 4.37 - 4.90: 75897 Nonbonded interactions: 186154 Sorted by model distance: nonbonded pdb=" O LEU C 29 " pdb=" NZ LYS C 34 " model vdw 2.265 2.520 nonbonded pdb=" O LEU D 29 " pdb=" NZ LYS D 34 " model vdw 2.265 2.520 nonbonded pdb=" O LEU B 29 " pdb=" NZ LYS B 34 " model vdw 2.266 2.520 nonbonded pdb=" O LEU A 29 " pdb=" NZ LYS A 34 " model vdw 2.266 2.520 nonbonded pdb=" NH1 ARG B 491 " pdb=" OG SER B 494 " model vdw 2.306 2.520 ... (remaining 186149 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' and (resid 17 through 670 or (resid 671 and (name N or name CA or nam \ e C or name O or name CB )) or resid 672 through 753 or resid 1001 through 1002) \ ) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.140 Check model and map are aligned: 0.350 Set scattering table: 0.200 Process input model: 61.410 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 22646 Z= 0.510 Angle : 0.801 9.542 30703 Z= 0.427 Chirality : 0.048 0.201 3453 Planarity : 0.006 0.086 3804 Dihedral : 16.504 89.742 8169 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.03 % Allowed : 0.51 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2688 helix: 0.90 (0.12), residues: 1908 sheet: None (None), residues: 0 loop : -2.45 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 326 HIS 0.008 0.002 HIS B 250 PHE 0.030 0.003 PHE A 340 TYR 0.028 0.003 TYR D 155 ARG 0.009 0.001 ARG D 491 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 432 time to evaluate : 2.490 Fit side-chains REVERT: A 79 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7235 (mt-10) REVERT: A 98 ASP cc_start: 0.7502 (m-30) cc_final: 0.7292 (m-30) REVERT: A 676 HIS cc_start: 0.2274 (OUTLIER) cc_final: 0.1259 (p-80) REVERT: B 79 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7238 (mt-10) REVERT: B 98 ASP cc_start: 0.7499 (m-30) cc_final: 0.7282 (m-30) REVERT: B 676 HIS cc_start: 0.2311 (OUTLIER) cc_final: 0.1274 (p-80) REVERT: C 79 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7240 (mt-10) REVERT: C 98 ASP cc_start: 0.7486 (m-30) cc_final: 0.7275 (m-30) REVERT: C 676 HIS cc_start: 0.2387 (OUTLIER) cc_final: 0.1358 (p-80) REVERT: D 79 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7227 (mt-10) REVERT: D 98 ASP cc_start: 0.7500 (m-30) cc_final: 0.7285 (m-30) REVERT: D 676 HIS cc_start: 0.2272 (OUTLIER) cc_final: 0.1261 (p-80) outliers start: 24 outliers final: 4 residues processed: 448 average time/residue: 1.3707 time to fit residues: 695.4114 Evaluate side-chains 402 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 394 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 727 GLU Chi-restraints excluded: chain C residue 676 HIS Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain D residue 676 HIS Chi-restraints excluded: chain D residue 727 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 0.6980 chunk 206 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 213 optimal weight: 6.9990 chunk 82 optimal weight: 0.0670 chunk 129 optimal weight: 20.0000 chunk 158 optimal weight: 0.9990 chunk 247 optimal weight: 0.8980 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN A 585 ASN B 308 GLN B 585 ASN C 308 GLN C 585 ASN D 308 GLN D 585 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 22646 Z= 0.166 Angle : 0.515 6.723 30703 Z= 0.269 Chirality : 0.037 0.151 3453 Planarity : 0.004 0.055 3804 Dihedral : 9.392 84.340 3088 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.89 % Allowed : 10.42 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.17), residues: 2688 helix: 1.65 (0.12), residues: 1928 sheet: None (None), residues: 0 loop : -2.26 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 635 HIS 0.002 0.000 HIS C 250 PHE 0.017 0.002 PHE A 335 TYR 0.013 0.001 TYR C 459 ARG 0.004 0.000 ARG D 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 425 time to evaluate : 2.847 Fit side-chains REVERT: A 44 ASP cc_start: 0.7753 (t0) cc_final: 0.7333 (t0) REVERT: A 79 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7291 (mt-10) REVERT: A 98 ASP cc_start: 0.7364 (m-30) cc_final: 0.7156 (m-30) REVERT: A 228 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7340 (tm-30) REVERT: A 266 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6834 (tm-30) REVERT: A 615 MET cc_start: 0.7903 (mtt) cc_final: 0.7465 (mtt) REVERT: B 44 ASP cc_start: 0.7752 (t0) cc_final: 0.7331 (t0) REVERT: B 79 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7259 (mt-10) REVERT: B 98 ASP cc_start: 0.7369 (m-30) cc_final: 0.7158 (m-30) REVERT: B 228 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: B 266 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: B 615 MET cc_start: 0.7909 (mtt) cc_final: 0.7472 (mtt) REVERT: C 44 ASP cc_start: 0.7755 (t0) cc_final: 0.7330 (t0) REVERT: C 79 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7265 (mt-10) REVERT: C 98 ASP cc_start: 0.7315 (m-30) cc_final: 0.7109 (m-30) REVERT: C 228 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7344 (tm-30) REVERT: C 266 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6836 (tm-30) REVERT: C 615 MET cc_start: 0.7895 (mtt) cc_final: 0.7474 (mtt) REVERT: D 44 ASP cc_start: 0.7747 (t0) cc_final: 0.7326 (t0) REVERT: D 79 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7260 (mt-10) REVERT: D 98 ASP cc_start: 0.7366 (m-30) cc_final: 0.7157 (m-30) REVERT: D 228 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: D 266 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6829 (tm-30) REVERT: D 615 MET cc_start: 0.7901 (mtt) cc_final: 0.7465 (mtt) outliers start: 44 outliers final: 0 residues processed: 437 average time/residue: 1.2371 time to fit residues: 621.3814 Evaluate side-chains 398 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 390 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 266 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 205 optimal weight: 8.9990 chunk 168 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 247 optimal weight: 0.5980 chunk 267 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN A 559 ASN B 559 ASN C 559 ASN D 559 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22646 Z= 0.278 Angle : 0.547 7.690 30703 Z= 0.284 Chirality : 0.039 0.192 3453 Planarity : 0.004 0.050 3804 Dihedral : 8.758 59.172 3068 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.14 % Allowed : 14.87 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.17), residues: 2688 helix: 1.72 (0.12), residues: 1920 sheet: None (None), residues: 0 loop : -2.08 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 314 HIS 0.002 0.001 HIS C 501 PHE 0.017 0.002 PHE B 300 TYR 0.021 0.002 TYR A 624 ARG 0.003 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 380 time to evaluate : 2.617 Fit side-chains REVERT: A 79 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7244 (mt-10) REVERT: A 98 ASP cc_start: 0.7460 (m-30) cc_final: 0.7211 (m-30) REVERT: A 228 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: A 266 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6959 (tm-30) REVERT: A 589 ASP cc_start: 0.7930 (t0) cc_final: 0.7597 (t0) REVERT: B 79 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7243 (mt-10) REVERT: B 98 ASP cc_start: 0.7462 (m-30) cc_final: 0.7212 (m-30) REVERT: B 228 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: B 266 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: B 589 ASP cc_start: 0.7937 (t0) cc_final: 0.7575 (t0) REVERT: C 79 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7243 (mt-10) REVERT: C 98 ASP cc_start: 0.7465 (m-30) cc_final: 0.7214 (m-30) REVERT: C 228 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: C 242 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7214 (mt-10) REVERT: C 266 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6960 (tm-30) REVERT: C 589 ASP cc_start: 0.7908 (t0) cc_final: 0.7575 (t0) REVERT: D 79 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7242 (mt-10) REVERT: D 98 ASP cc_start: 0.7458 (m-30) cc_final: 0.7249 (m-30) REVERT: D 228 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: D 266 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: D 589 ASP cc_start: 0.7921 (t0) cc_final: 0.7604 (t0) outliers start: 50 outliers final: 4 residues processed: 399 average time/residue: 1.3039 time to fit residues: 594.3816 Evaluate side-chains 388 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 376 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 712 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN A 559 ASN B 308 GLN B 559 ASN C 308 GLN C 559 ASN D 308 GLN D 559 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22646 Z= 0.308 Angle : 0.551 8.320 30703 Z= 0.285 Chirality : 0.039 0.158 3453 Planarity : 0.004 0.052 3804 Dihedral : 8.706 59.540 3068 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.49 % Allowed : 17.19 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.17), residues: 2688 helix: 1.67 (0.12), residues: 1924 sheet: None (None), residues: 0 loop : -2.11 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 635 HIS 0.002 0.001 HIS B 630 PHE 0.019 0.002 PHE B 300 TYR 0.017 0.002 TYR B 523 ARG 0.003 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 385 time to evaluate : 2.582 Fit side-chains REVERT: A 79 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7248 (mt-10) REVERT: A 228 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: A 242 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7203 (mt-10) REVERT: A 589 ASP cc_start: 0.7893 (t0) cc_final: 0.7557 (t0) REVERT: B 79 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7246 (mt-10) REVERT: B 228 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: B 242 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7203 (mt-10) REVERT: B 589 ASP cc_start: 0.7901 (t0) cc_final: 0.7561 (t0) REVERT: C 79 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7248 (mt-10) REVERT: C 228 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7357 (tm-30) REVERT: C 242 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7204 (mt-10) REVERT: C 437 MET cc_start: 0.7623 (ttp) cc_final: 0.7419 (ttm) REVERT: C 589 ASP cc_start: 0.7901 (t0) cc_final: 0.7582 (t0) REVERT: D 79 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7246 (mt-10) REVERT: D 228 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: D 242 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7206 (mt-10) REVERT: D 589 ASP cc_start: 0.7923 (t0) cc_final: 0.7598 (t0) outliers start: 58 outliers final: 11 residues processed: 409 average time/residue: 1.2795 time to fit residues: 601.7090 Evaluate side-chains 395 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 380 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 712 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 195 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN A 559 ASN A 605 ASN B 308 GLN B 559 ASN C 308 GLN C 559 ASN C 605 ASN D 308 GLN D 559 ASN D 605 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22646 Z= 0.344 Angle : 0.572 8.447 30703 Z= 0.295 Chirality : 0.040 0.160 3453 Planarity : 0.004 0.047 3804 Dihedral : 8.528 58.381 3068 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.57 % Allowed : 18.77 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.16), residues: 2688 helix: 1.60 (0.12), residues: 1924 sheet: None (None), residues: 0 loop : -2.12 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 314 HIS 0.003 0.001 HIS C 626 PHE 0.020 0.002 PHE D 300 TYR 0.018 0.002 TYR B 523 ARG 0.003 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 395 time to evaluate : 2.578 Fit side-chains REVERT: A 79 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7272 (mt-10) REVERT: A 228 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: A 242 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7162 (mt-10) REVERT: A 266 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: A 589 ASP cc_start: 0.7915 (t0) cc_final: 0.7580 (t0) REVERT: B 79 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7267 (mt-10) REVERT: B 228 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: B 242 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7161 (mt-10) REVERT: B 266 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: B 589 ASP cc_start: 0.7920 (t0) cc_final: 0.7586 (t0) REVERT: C 79 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7270 (mt-10) REVERT: C 228 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: C 242 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7145 (mt-10) REVERT: C 266 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7073 (tm-30) REVERT: C 589 ASP cc_start: 0.7916 (t0) cc_final: 0.7582 (t0) REVERT: D 79 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7271 (mt-10) REVERT: D 228 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: D 242 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7144 (mt-10) REVERT: D 266 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7072 (tm-30) REVERT: D 589 ASP cc_start: 0.7955 (t0) cc_final: 0.7600 (t0) outliers start: 60 outliers final: 14 residues processed: 424 average time/residue: 1.2866 time to fit residues: 622.5689 Evaluate side-chains 409 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 387 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 712 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 263 optimal weight: 0.9990 chunk 218 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 87 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN A 559 ASN B 308 GLN C 308 GLN D 308 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 22646 Z= 0.164 Angle : 0.485 7.527 30703 Z= 0.251 Chirality : 0.036 0.151 3453 Planarity : 0.004 0.042 3804 Dihedral : 8.030 58.080 3068 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.86 % Allowed : 21.17 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.17), residues: 2688 helix: 1.88 (0.12), residues: 1928 sheet: None (None), residues: 0 loop : -1.86 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 635 HIS 0.002 0.000 HIS B 626 PHE 0.015 0.001 PHE A 335 TYR 0.012 0.001 TYR A 200 ARG 0.003 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 398 time to evaluate : 2.486 Fit side-chains REVERT: A 44 ASP cc_start: 0.7720 (t0) cc_final: 0.7277 (t0) REVERT: A 228 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7367 (tm-30) REVERT: A 242 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7127 (mt-10) REVERT: A 589 ASP cc_start: 0.7862 (t0) cc_final: 0.7534 (t0) REVERT: B 44 ASP cc_start: 0.7719 (t0) cc_final: 0.7277 (t0) REVERT: B 228 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: B 242 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7130 (mt-10) REVERT: B 589 ASP cc_start: 0.7877 (t0) cc_final: 0.7521 (t0) REVERT: C 44 ASP cc_start: 0.7713 (t0) cc_final: 0.7272 (t0) REVERT: C 79 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7254 (mt-10) REVERT: C 228 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: C 242 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7127 (mt-10) REVERT: C 589 ASP cc_start: 0.7912 (t0) cc_final: 0.7558 (t0) REVERT: D 44 ASP cc_start: 0.7721 (t0) cc_final: 0.7273 (t0) REVERT: D 228 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: D 242 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7132 (mt-10) REVERT: D 589 ASP cc_start: 0.7902 (t0) cc_final: 0.7598 (t0) outliers start: 20 outliers final: 3 residues processed: 406 average time/residue: 1.2795 time to fit residues: 594.7789 Evaluate side-chains 391 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 384 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 559 ASN Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 559 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 0.0970 chunk 29 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 221 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 262 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN A 420 GLN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN B 420 GLN B 559 ASN C 308 GLN C 420 GLN C 559 ASN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 GLN D 420 GLN D 559 ASN ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22646 Z= 0.212 Angle : 0.500 7.474 30703 Z= 0.257 Chirality : 0.037 0.150 3453 Planarity : 0.004 0.042 3804 Dihedral : 7.869 58.706 3068 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.71 % Allowed : 20.40 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.17), residues: 2688 helix: 1.85 (0.12), residues: 1932 sheet: None (None), residues: 0 loop : -1.91 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 635 HIS 0.002 0.001 HIS B 630 PHE 0.015 0.001 PHE B 340 TYR 0.012 0.001 TYR D 523 ARG 0.002 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 381 time to evaluate : 3.002 Fit side-chains REVERT: A 228 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: A 266 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: A 437 MET cc_start: 0.7509 (ttp) cc_final: 0.7190 (ttm) REVERT: A 589 ASP cc_start: 0.7854 (t0) cc_final: 0.7566 (t0) REVERT: B 228 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: B 266 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.7017 (tm-30) REVERT: B 437 MET cc_start: 0.7511 (ttp) cc_final: 0.7189 (ttm) REVERT: B 589 ASP cc_start: 0.7870 (t0) cc_final: 0.7539 (t0) REVERT: C 79 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7255 (mt-10) REVERT: C 228 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: C 266 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7017 (tm-30) REVERT: C 437 MET cc_start: 0.7520 (ttp) cc_final: 0.7197 (ttm) REVERT: C 589 ASP cc_start: 0.7889 (t0) cc_final: 0.7609 (t0) REVERT: D 228 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: D 266 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: D 437 MET cc_start: 0.7510 (ttp) cc_final: 0.7190 (ttm) REVERT: D 589 ASP cc_start: 0.7897 (t0) cc_final: 0.7604 (t0) outliers start: 40 outliers final: 6 residues processed: 401 average time/residue: 1.2335 time to fit residues: 568.4724 Evaluate side-chains 389 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 375 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 610 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 129 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN B 308 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 GLN C 559 ASN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 GLN ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22646 Z= 0.228 Angle : 0.508 7.734 30703 Z= 0.261 Chirality : 0.038 0.151 3453 Planarity : 0.004 0.042 3804 Dihedral : 7.677 59.142 3068 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.71 % Allowed : 20.62 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.17), residues: 2688 helix: 1.87 (0.12), residues: 1928 sheet: None (None), residues: 0 loop : -1.82 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 635 HIS 0.002 0.001 HIS B 703 PHE 0.015 0.002 PHE D 300 TYR 0.013 0.001 TYR C 523 ARG 0.002 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 371 time to evaluate : 2.794 Fit side-chains REVERT: A 228 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: A 266 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: A 589 ASP cc_start: 0.7863 (t0) cc_final: 0.7582 (t0) REVERT: B 228 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: B 266 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.7029 (tm-30) REVERT: B 589 ASP cc_start: 0.7870 (t0) cc_final: 0.7581 (t0) REVERT: C 228 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: C 266 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.7029 (tm-30) REVERT: C 437 MET cc_start: 0.7618 (ttp) cc_final: 0.7339 (ttm) REVERT: C 589 ASP cc_start: 0.7890 (t0) cc_final: 0.7599 (t0) REVERT: D 228 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: D 266 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: D 589 ASP cc_start: 0.7907 (t0) cc_final: 0.7626 (t0) outliers start: 40 outliers final: 15 residues processed: 393 average time/residue: 1.3294 time to fit residues: 598.2676 Evaluate side-chains 388 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 365 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 559 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 610 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 0.8980 chunk 251 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 220 optimal weight: 0.0000 chunk 231 optimal weight: 4.9990 chunk 243 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN B 308 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22646 Z= 0.173 Angle : 0.482 8.220 30703 Z= 0.249 Chirality : 0.037 0.148 3453 Planarity : 0.004 0.042 3804 Dihedral : 7.389 59.073 3068 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.33 % Allowed : 21.09 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.17), residues: 2688 helix: 1.97 (0.12), residues: 1928 sheet: None (None), residues: 0 loop : -1.74 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 635 HIS 0.002 0.000 HIS D 626 PHE 0.016 0.001 PHE C 335 TYR 0.011 0.001 TYR B 200 ARG 0.002 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 391 time to evaluate : 2.734 Fit side-chains REVERT: A 228 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: A 266 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: A 589 ASP cc_start: 0.7835 (t0) cc_final: 0.7603 (t0) REVERT: B 228 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7358 (tm-30) REVERT: B 266 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: B 589 ASP cc_start: 0.7857 (t0) cc_final: 0.7577 (t0) REVERT: C 228 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: C 266 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6999 (tm-30) REVERT: C 437 MET cc_start: 0.7579 (ttp) cc_final: 0.7351 (ttm) REVERT: C 589 ASP cc_start: 0.7860 (t0) cc_final: 0.7563 (t0) REVERT: D 228 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: D 266 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.7000 (tm-30) REVERT: D 589 ASP cc_start: 0.7873 (t0) cc_final: 0.7607 (t0) outliers start: 31 outliers final: 10 residues processed: 406 average time/residue: 1.3028 time to fit residues: 605.0157 Evaluate side-chains 395 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 377 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 559 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 610 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 1.9990 chunk 258 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 179 optimal weight: 0.2980 chunk 270 optimal weight: 4.9990 chunk 249 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN B 308 GLN B 559 ASN C 308 GLN C 559 ASN D 308 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22646 Z= 0.201 Angle : 0.497 8.172 30703 Z= 0.256 Chirality : 0.037 0.149 3453 Planarity : 0.004 0.042 3804 Dihedral : 7.385 59.730 3068 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.11 % Allowed : 21.95 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.17), residues: 2688 helix: 1.92 (0.12), residues: 1928 sheet: None (None), residues: 0 loop : -1.71 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 635 HIS 0.002 0.000 HIS B 703 PHE 0.015 0.001 PHE C 340 TYR 0.013 0.001 TYR D 523 ARG 0.003 0.000 ARG D 360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 382 time to evaluate : 2.530 Fit side-chains REVERT: A 228 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: A 266 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.7009 (tm-30) REVERT: A 589 ASP cc_start: 0.7869 (t0) cc_final: 0.7643 (t0) REVERT: B 79 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7270 (mt-10) REVERT: B 228 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: B 266 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: B 589 ASP cc_start: 0.7877 (t0) cc_final: 0.7645 (t0) REVERT: C 79 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7277 (mt-10) REVERT: C 228 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7371 (tm-30) REVERT: C 266 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.7019 (tm-30) REVERT: C 437 MET cc_start: 0.7592 (ttp) cc_final: 0.7365 (ttm) REVERT: C 589 ASP cc_start: 0.7901 (t0) cc_final: 0.7670 (t0) REVERT: D 228 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: D 266 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.7029 (tm-30) REVERT: D 589 ASP cc_start: 0.7904 (t0) cc_final: 0.7684 (t0) outliers start: 26 outliers final: 10 residues processed: 394 average time/residue: 1.2916 time to fit residues: 580.9638 Evaluate side-chains 398 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 380 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain D residue 228 GLN Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 610 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 0.7980 chunk 229 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 198 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 216 optimal weight: 0.6980 chunk 90 optimal weight: 0.0980 chunk 221 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** 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 = 0.3739 r_free = 0.3739 target = 0.156693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.124785 restraints weight = 24027.022| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.63 r_work: 0.3163 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22646 Z= 0.142 Angle : 0.467 8.375 30703 Z= 0.240 Chirality : 0.036 0.144 3453 Planarity : 0.004 0.042 3804 Dihedral : 6.922 58.099 3068 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.94 % Allowed : 22.07 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.17), residues: 2688 helix: 2.15 (0.12), residues: 1904 sheet: None (None), residues: 0 loop : -1.59 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 635 HIS 0.002 0.000 HIS C 626 PHE 0.014 0.001 PHE C 340 TYR 0.012 0.001 TYR C 459 ARG 0.004 0.000 ARG C 360 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9108.83 seconds wall clock time: 162 minutes 19.83 seconds (9739.83 seconds total)