Starting phenix.real_space_refine on Sun Mar 17 09:25:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/03_2024/7l2j_23130_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/03_2024/7l2j_23130.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/03_2024/7l2j_23130_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/03_2024/7l2j_23130_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/03_2024/7l2j_23130_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/03_2024/7l2j_23130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/03_2024/7l2j_23130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/03_2024/7l2j_23130_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2j_23130/03_2024/7l2j_23130_updated.pdb" } resolution = 3.66 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= 0.004 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 C 11360 2.51 5 N 2780 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 280": "NH1" <-> "NH2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B GLU 651": "OE1" <-> "OE2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "C GLU 651": "OE1" <-> "OE2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "D GLU 651": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17336 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4294 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 529, 4285 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 529, 4285 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 4377 Chain: "B" Number of atoms: 4294 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 529, 4285 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 529, 4285 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 4377 Chain: "C" Number of atoms: 4294 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 529, 4285 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 529, 4285 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 4377 Chain: "D" Number of atoms: 4294 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 529, 4285 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 529, 4285 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 514} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 4377 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AGLU A 648 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 648 " occ=0.50 residue: pdb=" N AGLU B 648 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU B 648 " occ=0.50 residue: pdb=" N AGLU C 648 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU C 648 " occ=0.50 residue: pdb=" N AGLU D 648 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU D 648 " occ=0.50 Time building chain proxies: 17.21, per 1000 atoms: 0.99 Number of scatterers: 17336 At special positions: 0 Unit cell: (125.35, 125.35, 112.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 4 15.00 O 3092 8.00 N 2780 7.00 C 11360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.04 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.04 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.04 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.04 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: 6.33 Conformation dependent library (CDL) restraints added in 5.8 seconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4008 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 4 sheets defined 57.4% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.87 Creating SS restraints... Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 214 through 222 Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 354 removed outlier: 4.014A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 416 through 428 removed outlier: 3.747A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 470 through 497 Processing helix chain 'A' and resid 503 through 506 No H-bonds generated for 'chain 'A' and resid 503 through 506' Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 537 through 556 removed outlier: 4.468A pdb=" N LEU A 553 " --> pdb=" O TRP A 549 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR A 555 " --> pdb=" O ASN A 551 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 598 removed outlier: 3.924A pdb=" N ASP A 576 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 4.130A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 674 through 711 removed outlier: 3.783A pdb=" N ALA A 690 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 261 through 268 removed outlier: 3.597A pdb=" N LEU B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 354 removed outlier: 3.985A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 416 through 428 Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 470 through 497 Processing helix chain 'B' and resid 503 through 506 No H-bonds generated for 'chain 'B' and resid 503 through 506' Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 537 through 556 removed outlier: 3.709A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU B 553 " --> pdb=" O TRP B 549 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR B 555 " --> pdb=" O ASN B 551 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR B 556 " --> pdb=" O MET B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 598 removed outlier: 4.086A pdb=" N ASP B 576 " --> pdb=" O MET B 572 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 removed outlier: 4.057A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 674 through 711 removed outlier: 3.756A pdb=" N ALA B 690 " --> pdb=" O VAL B 686 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 214 through 223 Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 266 Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.506A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 428 removed outlier: 3.788A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 470 through 497 Processing helix chain 'C' and resid 503 through 506 No H-bonds generated for 'chain 'C' and resid 503 through 506' Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 537 through 556 removed outlier: 3.587A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 550 " --> pdb=" O ALA C 546 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU C 553 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR C 555 " --> pdb=" O ASN C 551 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR C 556 " --> pdb=" O MET C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 598 removed outlier: 4.207A pdb=" N ASP C 576 " --> pdb=" O MET C 572 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 4.215A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 674 through 711 removed outlier: 3.731A pdb=" N ALA C 690 " --> pdb=" O VAL C 686 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 214 through 223 Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 266 Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 354 removed outlier: 3.984A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 428 removed outlier: 3.798A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 470 through 497 Processing helix chain 'D' and resid 503 through 506 No H-bonds generated for 'chain 'D' and resid 503 through 506' Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 537 through 556 removed outlier: 4.474A pdb=" N LEU D 553 " --> pdb=" O TRP D 549 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N TYR D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR D 555 " --> pdb=" O ASN D 551 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR D 556 " --> pdb=" O MET D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 598 removed outlier: 4.056A pdb=" N ASP D 576 " --> pdb=" O MET D 572 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 4.104A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 674 through 688 removed outlier: 3.519A pdb=" N ILE D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 711 removed outlier: 3.626A pdb=" N LYS D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 742 through 747 removed outlier: 4.216A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 742 through 747 removed outlier: 4.041A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 742 through 747 removed outlier: 4.337A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 742 through 747 removed outlier: 4.258A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) 838 hydrogen bonds defined for protein. 2490 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.37 Time building geometry restraints manager: 6.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2680 1.31 - 1.43: 5009 1.43 - 1.56: 9885 1.56 - 1.69: 10 1.69 - 1.81: 164 Bond restraints: 17748 Sorted by residual: bond pdb=" C ASP C 654 " pdb=" N PHE C 655 " ideal model delta sigma weight residual 1.333 1.234 0.099 1.29e-02 6.01e+03 5.87e+01 bond pdb=" C ASP D 654 " pdb=" N PHE D 655 " ideal model delta sigma weight residual 1.333 1.433 -0.100 1.42e-02 4.96e+03 4.99e+01 bond pdb=" C ASP B 654 " pdb=" N PHE B 655 " ideal model delta sigma weight residual 1.333 1.259 0.073 1.29e-02 6.01e+03 3.23e+01 bond pdb=" C TYR B 511 " pdb=" N SER B 512 " ideal model delta sigma weight residual 1.335 1.269 0.066 1.31e-02 5.83e+03 2.57e+01 bond pdb=" CA THR D 650 " pdb=" C THR D 650 " ideal model delta sigma weight residual 1.521 1.570 -0.049 1.24e-02 6.50e+03 1.56e+01 ... (remaining 17743 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.93: 263 105.93 - 112.96: 9408 112.96 - 119.99: 6745 119.99 - 127.02: 7451 127.02 - 134.05: 153 Bond angle restraints: 24020 Sorted by residual: angle pdb=" N ILE D 573 " pdb=" CA ILE D 573 " pdb=" C ILE D 573 " ideal model delta sigma weight residual 110.82 106.53 4.29 9.70e-01 1.06e+00 1.96e+01 angle pdb=" N GLU D 651 " pdb=" CA GLU D 651 " pdb=" C GLU D 651 " ideal model delta sigma weight residual 109.06 116.34 -7.28 1.70e+00 3.46e-01 1.84e+01 angle pdb=" C TYR C 511 " pdb=" N SER C 512 " pdb=" CA SER C 512 " ideal model delta sigma weight residual 120.82 127.01 -6.19 1.50e+00 4.44e-01 1.70e+01 angle pdb=" N GLU B 651 " pdb=" CA GLU B 651 " pdb=" C GLU B 651 " ideal model delta sigma weight residual 109.23 114.83 -5.60 1.55e+00 4.16e-01 1.30e+01 angle pdb=" N GLU C 651 " pdb=" CA GLU C 651 " pdb=" C GLU C 651 " ideal model delta sigma weight residual 109.23 114.68 -5.45 1.55e+00 4.16e-01 1.24e+01 ... (remaining 24015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 10348 35.86 - 71.71: 100 71.71 - 107.57: 15 107.57 - 143.42: 0 143.42 - 179.28: 1 Dihedral angle restraints: 10464 sinusoidal: 4220 harmonic: 6244 Sorted by residual: dihedral pdb=" CB BGLU D 648 " pdb=" CG BGLU D 648 " pdb=" CD BGLU D 648 " pdb=" OE1BGLU D 648 " ideal model delta sinusoidal sigma weight residual 0.00 179.28 -179.28 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB CYS D 386 " pdb=" SG CYS D 386 " pdb=" SG CYS D 390 " pdb=" CB CYS D 390 " ideal model delta sinusoidal sigma weight residual 93.00 59.93 33.07 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" CB CYS B 386 " pdb=" SG CYS B 386 " pdb=" SG CYS B 390 " pdb=" CB CYS B 390 " ideal model delta sinusoidal sigma weight residual 93.00 59.94 33.06 1 1.00e+01 1.00e-02 1.55e+01 ... (remaining 10461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.008: 2700 1.008 - 2.015: 0 2.015 - 3.023: 0 3.023 - 4.031: 0 4.031 - 5.038: 8 Chirality restraints: 2708 Sorted by residual: chirality pdb=" C3 XJ7 D 901 " pdb=" C2 XJ7 D 901 " pdb=" C24 XJ7 D 901 " pdb=" O3 XJ7 D 901 " both_signs ideal model delta sigma weight residual False -2.50 2.54 -5.04 2.00e-01 2.50e+01 6.35e+02 chirality pdb=" C3 XJ7 A 901 " pdb=" C2 XJ7 A 901 " pdb=" C24 XJ7 A 901 " pdb=" O3 XJ7 A 901 " both_signs ideal model delta sigma weight residual False -2.50 2.53 -5.04 2.00e-01 2.50e+01 6.34e+02 chirality pdb=" C3 XJ7 C 901 " pdb=" C2 XJ7 C 901 " pdb=" C24 XJ7 C 901 " pdb=" O3 XJ7 C 901 " both_signs ideal model delta sigma weight residual False -2.50 2.53 -5.04 2.00e-01 2.50e+01 6.34e+02 ... (remaining 2705 not shown) Planarity restraints: 2964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 649 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.71e+00 pdb=" C PHE D 649 " 0.054 2.00e-02 2.50e+03 pdb=" O PHE D 649 " -0.020 2.00e-02 2.50e+03 pdb=" N THR D 650 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 649 " -0.012 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C PHE B 649 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE B 649 " -0.017 2.00e-02 2.50e+03 pdb=" N THR B 650 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 548 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C GLY B 548 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY B 548 " -0.015 2.00e-02 2.50e+03 pdb=" N TRP B 549 " -0.013 2.00e-02 2.50e+03 ... (remaining 2961 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 184 2.64 - 3.20: 16845 3.20 - 3.77: 26004 3.77 - 4.33: 35647 4.33 - 4.90: 58920 Nonbonded interactions: 137600 Sorted by model distance: nonbonded pdb=" OG SER B 722 " pdb=" O CYS B 741 " model vdw 2.074 2.440 nonbonded pdb=" O ILE A 672 " pdb=" ND2 ASN A 676 " model vdw 2.173 2.520 nonbonded pdb=" O ILE C 672 " pdb=" ND2 ASN C 676 " model vdw 2.174 2.520 nonbonded pdb=" O ILE B 672 " pdb=" ND2 ASN B 676 " model vdw 2.205 2.520 nonbonded pdb=" NZ LYS B 425 " pdb=" OE1 GLU B 709 " model vdw 2.216 2.520 ... (remaining 137595 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 198 through 647 or resid 649 through 749 or resid 901)) selection = (chain 'B' and (resid 198 through 647 or resid 649 through 749 or resid 901)) selection = (chain 'C' and (resid 198 through 647 or resid 649 through 749 or resid 901)) selection = (chain 'D' and (resid 198 through 647 or resid 649 through 749 or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.550 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 57.680 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.130 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 17748 Z= 0.438 Angle : 0.705 7.283 24020 Z= 0.399 Chirality : 0.276 5.038 2708 Planarity : 0.004 0.031 2964 Dihedral : 11.794 179.276 6444 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.16 % Allowed : 1.45 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.68 (0.18), residues: 2112 helix: 1.72 (0.14), residues: 1224 sheet: -0.22 (0.54), residues: 56 loop : -1.51 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 697 HIS 0.004 0.001 HIS B 364 PHE 0.016 0.002 PHE C 236 TYR 0.017 0.002 TYR C 565 ARG 0.004 0.001 ARG A 721 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 724 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 HIS cc_start: 0.8737 (m90) cc_final: 0.8379 (m90) REVERT: A 304 PHE cc_start: 0.7473 (m-80) cc_final: 0.6952 (m-80) REVERT: A 352 ILE cc_start: 0.8626 (mt) cc_final: 0.8413 (mt) REVERT: A 359 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6983 (mt-10) REVERT: A 383 ASP cc_start: 0.8166 (p0) cc_final: 0.7799 (t0) REVERT: A 384 LEU cc_start: 0.8583 (mt) cc_final: 0.8271 (mt) REVERT: A 560 GLN cc_start: 0.8263 (tp40) cc_final: 0.7834 (tp-100) REVERT: A 739 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7795 (mmm-85) REVERT: B 254 LEU cc_start: 0.8561 (mt) cc_final: 0.8216 (mt) REVERT: B 331 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7146 (mtp85) REVERT: B 332 LYS cc_start: 0.9238 (mttt) cc_final: 0.8678 (mtmt) REVERT: B 345 LYS cc_start: 0.8946 (mmtt) cc_final: 0.8274 (mmtt) REVERT: B 391 GLU cc_start: 0.6248 (mm-30) cc_final: 0.6026 (tt0) REVERT: B 557 ARG cc_start: 0.8553 (ptp-170) cc_final: 0.7888 (ptp-110) REVERT: B 739 ARG cc_start: 0.8439 (mtp85) cc_final: 0.8018 (mmm-85) REVERT: B 743 ARG cc_start: 0.8398 (ttm110) cc_final: 0.7960 (ttm-80) REVERT: C 331 ARG cc_start: 0.7643 (ttm-80) cc_final: 0.7392 (mtp180) REVERT: C 391 GLU cc_start: 0.6435 (mm-30) cc_final: 0.6221 (tt0) REVERT: C 419 ASN cc_start: 0.8720 (t0) cc_final: 0.8326 (t0) REVERT: C 423 GLN cc_start: 0.8628 (tp40) cc_final: 0.8371 (tp40) REVERT: C 560 GLN cc_start: 0.8228 (tp40) cc_final: 0.7955 (tp40) REVERT: C 671 TYR cc_start: 0.9056 (t80) cc_final: 0.8819 (t80) REVERT: D 261 LEU cc_start: 0.8753 (mt) cc_final: 0.8179 (mt) REVERT: D 265 LYS cc_start: 0.8945 (mttt) cc_final: 0.8418 (tptp) REVERT: D 289 HIS cc_start: 0.8911 (m90) cc_final: 0.8557 (m-70) REVERT: D 332 LYS cc_start: 0.9208 (mttt) cc_final: 0.8960 (mtmm) REVERT: D 345 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8412 (mmtt) REVERT: D 383 ASP cc_start: 0.7917 (p0) cc_final: 0.7476 (t0) REVERT: D 384 LEU cc_start: 0.8347 (mt) cc_final: 0.8049 (mt) REVERT: D 552 MET cc_start: 0.8994 (tpp) cc_final: 0.8737 (tpp) REVERT: D 562 MET cc_start: 0.8713 (mmm) cc_final: 0.8486 (mmt) REVERT: D 677 MET cc_start: 0.7650 (ttm) cc_final: 0.6653 (ttm) REVERT: D 700 GLN cc_start: 0.8812 (mt0) cc_final: 0.8540 (mt0) REVERT: D 739 ARG cc_start: 0.8080 (mtp85) cc_final: 0.7815 (mmm-85) REVERT: D 743 ARG cc_start: 0.7904 (ttm110) cc_final: 0.7653 (ttm-80) outliers start: 3 outliers final: 0 residues processed: 725 average time/residue: 0.3277 time to fit residues: 338.1684 Evaluate side-chains 454 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 454 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 53 optimal weight: 0.1980 chunk 106 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 121 optimal weight: 10.0000 chunk 188 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN B 270 ASN B 364 HIS ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 GLN C 270 ASN C 289 HIS C 494 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 GLN D 533 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17748 Z= 0.187 Angle : 0.622 9.712 24020 Z= 0.321 Chirality : 0.040 0.205 2708 Planarity : 0.004 0.058 2964 Dihedral : 8.222 68.958 2432 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.31 % Allowed : 13.41 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.69 (0.19), residues: 2112 helix: 1.83 (0.15), residues: 1248 sheet: -0.07 (0.55), residues: 56 loop : -1.81 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 697 HIS 0.008 0.001 HIS A 364 PHE 0.054 0.002 PHE C 304 TYR 0.017 0.001 TYR C 351 ARG 0.010 0.001 ARG D 701 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 486 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 HIS cc_start: 0.8733 (m90) cc_final: 0.8364 (m90) REVERT: A 304 PHE cc_start: 0.7303 (m-80) cc_final: 0.7053 (m-80) REVERT: A 359 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7095 (mt-10) REVERT: A 365 LEU cc_start: 0.8473 (mt) cc_final: 0.8004 (pp) REVERT: A 577 LEU cc_start: 0.8239 (mt) cc_final: 0.8001 (tp) REVERT: A 636 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7667 (mm-30) REVERT: A 692 GLU cc_start: 0.7865 (mp0) cc_final: 0.7408 (mp0) REVERT: A 698 LYS cc_start: 0.8892 (mttt) cc_final: 0.8619 (mtpt) REVERT: B 331 ARG cc_start: 0.7712 (ttm-80) cc_final: 0.7272 (mtp180) REVERT: B 353 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.8981 (mm) REVERT: B 592 SER cc_start: 0.8960 (t) cc_final: 0.8749 (t) REVERT: C 331 ARG cc_start: 0.7762 (ttm-80) cc_final: 0.7380 (mtp-110) REVERT: C 391 GLU cc_start: 0.6580 (mm-30) cc_final: 0.6380 (tt0) REVERT: C 423 GLN cc_start: 0.8681 (tp40) cc_final: 0.8462 (tp40) REVERT: C 535 LYS cc_start: 0.7822 (mptt) cc_final: 0.7371 (mptt) REVERT: C 637 LEU cc_start: 0.9190 (mt) cc_final: 0.8663 (mp) REVERT: D 254 LEU cc_start: 0.8224 (mt) cc_final: 0.7940 (mt) REVERT: D 289 HIS cc_start: 0.8581 (m90) cc_final: 0.8271 (m90) REVERT: D 332 LYS cc_start: 0.9226 (mttt) cc_final: 0.8993 (mtmm) REVERT: D 345 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8318 (mmtt) REVERT: D 701 ARG cc_start: 0.8265 (tpp80) cc_final: 0.7980 (tpp80) outliers start: 43 outliers final: 26 residues processed: 512 average time/residue: 0.2820 time to fit residues: 217.9335 Evaluate side-chains 441 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 414 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 742 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 52 optimal weight: 30.0000 chunk 189 optimal weight: 0.8980 chunk 204 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 chunk 64 optimal weight: 0.0060 chunk 151 optimal weight: 0.7980 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN B 289 HIS ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 GLN C 206 HIS C 289 HIS C 408 ASN C 419 ASN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17748 Z= 0.190 Angle : 0.627 18.100 24020 Z= 0.311 Chirality : 0.040 0.279 2708 Planarity : 0.003 0.046 2964 Dihedral : 7.501 59.154 2432 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.54 % Allowed : 15.93 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.67 (0.19), residues: 2112 helix: 1.80 (0.15), residues: 1252 sheet: 0.08 (0.54), residues: 56 loop : -1.81 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 697 HIS 0.006 0.001 HIS C 289 PHE 0.033 0.001 PHE C 304 TYR 0.017 0.001 TYR C 495 ARG 0.007 0.001 ARG C 701 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 437 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.7369 (m-80) cc_final: 0.7104 (m-80) REVERT: A 308 MET cc_start: 0.8551 (tpt) cc_final: 0.8230 (tpt) REVERT: A 359 GLU cc_start: 0.7305 (mt-10) cc_final: 0.7075 (mt-10) REVERT: A 365 LEU cc_start: 0.8551 (mt) cc_final: 0.8191 (pp) REVERT: A 636 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7691 (mm-30) REVERT: A 692 GLU cc_start: 0.7938 (mp0) cc_final: 0.7479 (mp0) REVERT: A 698 LYS cc_start: 0.8950 (mttt) cc_final: 0.8708 (mtpt) REVERT: B 289 HIS cc_start: 0.8693 (m90) cc_final: 0.8187 (m90) REVERT: B 331 ARG cc_start: 0.7834 (ttm-80) cc_final: 0.7472 (mmp-170) REVERT: B 332 LYS cc_start: 0.9386 (mttt) cc_final: 0.9066 (mtmt) REVERT: B 353 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8875 (mm) REVERT: B 445 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8794 (tpp) REVERT: B 592 SER cc_start: 0.9000 (t) cc_final: 0.8796 (t) REVERT: B 692 GLU cc_start: 0.7629 (mp0) cc_final: 0.7211 (mp0) REVERT: C 285 ASN cc_start: 0.7695 (OUTLIER) cc_final: 0.7374 (p0) REVERT: C 303 LYS cc_start: 0.8418 (mmmt) cc_final: 0.8115 (ptmt) REVERT: C 331 ARG cc_start: 0.7610 (ttm-80) cc_final: 0.7298 (mtp-110) REVERT: C 391 GLU cc_start: 0.6692 (mm-30) cc_final: 0.6423 (tt0) REVERT: C 419 ASN cc_start: 0.8533 (t0) cc_final: 0.8326 (t0) REVERT: C 423 GLN cc_start: 0.8724 (tp40) cc_final: 0.8492 (tp40) REVERT: C 535 LYS cc_start: 0.7704 (mptt) cc_final: 0.7333 (mptt) REVERT: C 636 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7585 (mm-30) REVERT: D 254 LEU cc_start: 0.8160 (mt) cc_final: 0.7878 (mt) REVERT: D 326 GLU cc_start: 0.8395 (tt0) cc_final: 0.8127 (tt0) REVERT: D 636 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7831 (mm-30) REVERT: D 701 ARG cc_start: 0.8312 (tpp80) cc_final: 0.8033 (tpp80) outliers start: 66 outliers final: 43 residues processed: 466 average time/residue: 0.2873 time to fit residues: 201.7194 Evaluate side-chains 453 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 407 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 693 SER Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 445 MET Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 742 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 0.0770 chunk 142 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 HIS A 289 HIS A 494 GLN B 206 HIS ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN C 289 HIS ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17748 Z= 0.184 Angle : 0.598 15.001 24020 Z= 0.301 Chirality : 0.040 0.318 2708 Planarity : 0.003 0.038 2964 Dihedral : 7.078 56.494 2432 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.43 % Allowed : 16.52 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.49 (0.18), residues: 2112 helix: 1.63 (0.15), residues: 1260 sheet: 0.19 (0.56), residues: 56 loop : -1.90 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 697 HIS 0.004 0.001 HIS A 364 PHE 0.046 0.001 PHE B 304 TYR 0.018 0.001 TYR D 351 ARG 0.007 0.000 ARG C 701 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 438 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.7249 (m-80) cc_final: 0.7026 (m-80) REVERT: A 359 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6921 (mt-10) REVERT: A 365 LEU cc_start: 0.8600 (mt) cc_final: 0.8301 (pp) REVERT: A 460 LEU cc_start: 0.8324 (mt) cc_final: 0.7888 (mp) REVERT: A 636 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7734 (mm-30) REVERT: A 692 GLU cc_start: 0.7995 (mp0) cc_final: 0.7549 (mp0) REVERT: A 698 LYS cc_start: 0.8951 (mttt) cc_final: 0.8728 (mtmt) REVERT: B 289 HIS cc_start: 0.8700 (m90) cc_final: 0.8057 (m90) REVERT: B 331 ARG cc_start: 0.7869 (ttm-80) cc_final: 0.7478 (mmp-170) REVERT: B 332 LYS cc_start: 0.9311 (mttt) cc_final: 0.9054 (mtmm) REVERT: B 353 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8865 (mm) REVERT: B 637 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8893 (mt) REVERT: B 692 GLU cc_start: 0.7743 (mp0) cc_final: 0.7400 (mp0) REVERT: B 698 LYS cc_start: 0.8844 (mttp) cc_final: 0.8430 (mtmm) REVERT: C 331 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7202 (mtp-110) REVERT: C 419 ASN cc_start: 0.8568 (t0) cc_final: 0.8356 (t0) REVERT: C 535 LYS cc_start: 0.7711 (mptt) cc_final: 0.7236 (mptt) REVERT: C 636 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7541 (mm-30) REVERT: C 692 GLU cc_start: 0.7805 (mp0) cc_final: 0.7342 (mp0) REVERT: D 289 HIS cc_start: 0.8769 (m90) cc_final: 0.8441 (m90) REVERT: D 636 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7784 (mm-30) outliers start: 64 outliers final: 45 residues processed: 468 average time/residue: 0.2951 time to fit residues: 206.5121 Evaluate side-chains 469 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 422 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 693 SER Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 445 MET Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 674 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 149 optimal weight: 0.5980 chunk 82 optimal weight: 0.0040 chunk 171 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS A 494 GLN B 232 ASN B 560 GLN C 289 HIS ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17748 Z= 0.238 Angle : 0.607 15.439 24020 Z= 0.306 Chirality : 0.040 0.246 2708 Planarity : 0.003 0.036 2964 Dihedral : 6.846 55.228 2432 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.81 % Allowed : 16.36 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.44 (0.18), residues: 2112 helix: 1.57 (0.14), residues: 1260 sheet: 0.44 (0.57), residues: 56 loop : -1.92 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 697 HIS 0.004 0.001 HIS A 364 PHE 0.038 0.001 PHE B 304 TYR 0.015 0.001 TYR D 351 ARG 0.006 0.000 ARG C 701 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 429 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 HIS cc_start: 0.8518 (m90) cc_final: 0.8268 (m90) REVERT: A 359 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6984 (mt-10) REVERT: A 460 LEU cc_start: 0.8325 (mt) cc_final: 0.7888 (mp) REVERT: A 592 SER cc_start: 0.9042 (t) cc_final: 0.8704 (t) REVERT: A 636 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7919 (mm-30) REVERT: A 692 GLU cc_start: 0.8044 (mp0) cc_final: 0.7592 (mp0) REVERT: A 698 LYS cc_start: 0.8976 (mttt) cc_final: 0.8739 (mtmt) REVERT: B 289 HIS cc_start: 0.8368 (m90) cc_final: 0.8040 (m90) REVERT: B 331 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7460 (mmp-170) REVERT: B 332 LYS cc_start: 0.9312 (mttt) cc_final: 0.9102 (mtmm) REVERT: B 353 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8895 (mm) REVERT: B 692 GLU cc_start: 0.7786 (mp0) cc_final: 0.7440 (mp0) REVERT: B 698 LYS cc_start: 0.8873 (mttp) cc_final: 0.8495 (mtmm) REVERT: C 285 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7543 (p0) REVERT: C 303 LYS cc_start: 0.8537 (mmmt) cc_final: 0.8048 (ptmt) REVERT: C 331 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.7290 (mtp180) REVERT: C 419 ASN cc_start: 0.8587 (t0) cc_final: 0.8367 (t0) REVERT: D 289 HIS cc_start: 0.8832 (m90) cc_final: 0.8305 (m90) REVERT: D 345 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8547 (mmtp) REVERT: D 636 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7820 (mm-30) REVERT: D 694 LYS cc_start: 0.9054 (tppt) cc_final: 0.8843 (tptp) outliers start: 71 outliers final: 53 residues processed: 455 average time/residue: 0.2905 time to fit residues: 201.7124 Evaluate side-chains 470 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 415 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 445 MET Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 742 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 201 optimal weight: 0.6980 chunk 167 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 105 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN B 408 ASN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 HIS ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17748 Z= 0.172 Angle : 0.590 15.488 24020 Z= 0.299 Chirality : 0.039 0.236 2708 Planarity : 0.003 0.035 2964 Dihedral : 6.644 55.833 2432 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.27 % Allowed : 17.06 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.67 (0.19), residues: 2112 helix: 1.74 (0.15), residues: 1232 sheet: 0.45 (0.59), residues: 56 loop : -1.65 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 697 HIS 0.003 0.001 HIS A 364 PHE 0.036 0.001 PHE B 304 TYR 0.027 0.001 TYR D 351 ARG 0.006 0.000 ARG D 499 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 442 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 HIS cc_start: 0.8459 (m90) cc_final: 0.8087 (m90) REVERT: A 308 MET cc_start: 0.8604 (tpt) cc_final: 0.8380 (tpt) REVERT: A 359 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6928 (mt-10) REVERT: A 460 LEU cc_start: 0.8255 (mt) cc_final: 0.7836 (mp) REVERT: A 592 SER cc_start: 0.8993 (t) cc_final: 0.8692 (t) REVERT: A 636 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7881 (mm-30) REVERT: A 692 GLU cc_start: 0.8012 (mp0) cc_final: 0.7577 (mp0) REVERT: A 698 LYS cc_start: 0.8954 (mttt) cc_final: 0.8701 (mtpt) REVERT: B 289 HIS cc_start: 0.8413 (m90) cc_final: 0.7901 (m90) REVERT: B 331 ARG cc_start: 0.7893 (ttm-80) cc_final: 0.7443 (mmp-170) REVERT: B 353 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8888 (mm) REVERT: B 445 MET cc_start: 0.9343 (tpp) cc_final: 0.8918 (tpp) REVERT: B 692 GLU cc_start: 0.7741 (mp0) cc_final: 0.7405 (mp0) REVERT: B 698 LYS cc_start: 0.8842 (mttp) cc_final: 0.8421 (mtmm) REVERT: C 289 HIS cc_start: 0.8064 (m90) cc_final: 0.7847 (m90) REVERT: C 331 ARG cc_start: 0.7632 (ttm-80) cc_final: 0.7261 (mtp180) REVERT: C 535 LYS cc_start: 0.7691 (mptt) cc_final: 0.7158 (mptt) REVERT: C 572 MET cc_start: 0.8351 (ttm) cc_final: 0.8029 (ttm) REVERT: C 636 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7551 (mm-30) REVERT: D 289 HIS cc_start: 0.8831 (m90) cc_final: 0.8288 (m90) REVERT: D 345 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8516 (mmtp) REVERT: D 636 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7781 (mm-30) outliers start: 61 outliers final: 48 residues processed: 463 average time/residue: 0.2754 time to fit residues: 193.3922 Evaluate side-chains 462 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 413 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 445 MET Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 742 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 169 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN D 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17748 Z= 0.190 Angle : 0.595 15.477 24020 Z= 0.300 Chirality : 0.039 0.228 2708 Planarity : 0.003 0.037 2964 Dihedral : 6.436 54.925 2432 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.27 % Allowed : 17.76 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.66 (0.19), residues: 2112 helix: 1.75 (0.15), residues: 1228 sheet: 0.56 (0.60), residues: 56 loop : -1.68 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 697 HIS 0.003 0.001 HIS A 364 PHE 0.032 0.001 PHE B 304 TYR 0.018 0.001 TYR B 666 ARG 0.006 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 429 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8595 (tpt) cc_final: 0.8344 (tpt) REVERT: A 359 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6911 (mt-10) REVERT: A 592 SER cc_start: 0.9004 (t) cc_final: 0.8679 (t) REVERT: A 636 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7841 (mm-30) REVERT: A 692 GLU cc_start: 0.8037 (mp0) cc_final: 0.7596 (mp0) REVERT: A 698 LYS cc_start: 0.8948 (mttt) cc_final: 0.8709 (mtpt) REVERT: B 285 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7504 (p0) REVERT: B 308 MET cc_start: 0.8587 (tpt) cc_final: 0.8254 (tpt) REVERT: B 331 ARG cc_start: 0.7911 (ttm-80) cc_final: 0.7443 (mmp-170) REVERT: B 445 MET cc_start: 0.9352 (tpp) cc_final: 0.9020 (tpp) REVERT: B 692 GLU cc_start: 0.7755 (mp0) cc_final: 0.7397 (mp0) REVERT: B 698 LYS cc_start: 0.8853 (mttp) cc_final: 0.8428 (mtmm) REVERT: C 289 HIS cc_start: 0.8132 (m90) cc_final: 0.7804 (m90) REVERT: C 303 LYS cc_start: 0.8437 (mmmt) cc_final: 0.8090 (ptmt) REVERT: C 331 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.7376 (mmp-170) REVERT: C 535 LYS cc_start: 0.7734 (mptt) cc_final: 0.7150 (mptt) REVERT: C 572 MET cc_start: 0.8159 (ttm) cc_final: 0.7893 (ttm) REVERT: C 636 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7566 (mm-30) REVERT: D 289 HIS cc_start: 0.8831 (m90) cc_final: 0.8242 (m90) REVERT: D 308 MET cc_start: 0.8546 (tpt) cc_final: 0.8280 (tpt) REVERT: D 345 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8609 (mmtp) REVERT: D 358 HIS cc_start: 0.7250 (OUTLIER) cc_final: 0.6623 (t-90) REVERT: D 460 LEU cc_start: 0.8491 (mt) cc_final: 0.7984 (mp) REVERT: D 636 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7785 (mm-30) REVERT: D 694 LYS cc_start: 0.8960 (tppt) cc_final: 0.8726 (tptm) REVERT: D 707 ASP cc_start: 0.8133 (t0) cc_final: 0.7888 (t0) outliers start: 61 outliers final: 46 residues processed: 454 average time/residue: 0.2679 time to fit residues: 183.4328 Evaluate side-chains 462 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 414 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 445 MET Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 735 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 127 optimal weight: 0.0980 chunk 136 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17748 Z= 0.169 Angle : 0.596 15.579 24020 Z= 0.300 Chirality : 0.038 0.220 2708 Planarity : 0.003 0.040 2964 Dihedral : 6.314 55.780 2432 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.11 % Allowed : 18.45 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.66 (0.19), residues: 2112 helix: 1.75 (0.15), residues: 1228 sheet: 0.54 (0.60), residues: 56 loop : -1.68 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 697 HIS 0.003 0.001 HIS A 364 PHE 0.032 0.001 PHE B 304 TYR 0.013 0.001 TYR B 246 ARG 0.019 0.001 ARG B 499 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 430 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8588 (tpt) cc_final: 0.8342 (tpt) REVERT: A 359 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6905 (mt-10) REVERT: A 592 SER cc_start: 0.8963 (t) cc_final: 0.8665 (t) REVERT: A 636 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7831 (mm-30) REVERT: A 692 GLU cc_start: 0.8020 (mp0) cc_final: 0.7580 (mp0) REVERT: A 698 LYS cc_start: 0.8940 (mttt) cc_final: 0.8675 (mtpt) REVERT: B 285 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7546 (p0) REVERT: B 308 MET cc_start: 0.8561 (tpt) cc_final: 0.7994 (tpt) REVERT: B 331 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7423 (mmp-170) REVERT: B 353 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8745 (mm) REVERT: B 445 MET cc_start: 0.9344 (tpp) cc_final: 0.9013 (tpp) REVERT: B 692 GLU cc_start: 0.7775 (mp0) cc_final: 0.7432 (mp0) REVERT: B 698 LYS cc_start: 0.8846 (mttp) cc_final: 0.8411 (mtmm) REVERT: C 289 HIS cc_start: 0.8195 (m90) cc_final: 0.7849 (m90) REVERT: C 331 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.7392 (mmp-170) REVERT: C 535 LYS cc_start: 0.7718 (mptt) cc_final: 0.7176 (mptt) REVERT: C 636 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7531 (mm-30) REVERT: D 289 HIS cc_start: 0.8860 (m90) cc_final: 0.8440 (m90) REVERT: D 308 MET cc_start: 0.8648 (tpt) cc_final: 0.8327 (tpt) REVERT: D 345 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8643 (mmtp) REVERT: D 358 HIS cc_start: 0.7214 (OUTLIER) cc_final: 0.6612 (t-90) REVERT: D 636 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7757 (mm-30) REVERT: D 707 ASP cc_start: 0.8141 (t0) cc_final: 0.7921 (t0) outliers start: 58 outliers final: 46 residues processed: 455 average time/residue: 0.2724 time to fit residues: 187.4886 Evaluate side-chains 464 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 415 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 445 MET Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 735 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 2.9990 chunk 192 optimal weight: 0.3980 chunk 175 optimal weight: 0.0070 chunk 186 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 overall best weight: 0.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN B 498 GLN ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS D 551 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17748 Z= 0.179 Angle : 0.612 15.514 24020 Z= 0.306 Chirality : 0.039 0.213 2708 Planarity : 0.003 0.037 2964 Dihedral : 6.247 56.730 2432 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.90 % Allowed : 19.21 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.66 (0.19), residues: 2112 helix: 1.75 (0.15), residues: 1228 sheet: 0.60 (0.60), residues: 56 loop : -1.68 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 697 HIS 0.003 0.001 HIS A 364 PHE 0.025 0.001 PHE B 304 TYR 0.017 0.001 TYR D 351 ARG 0.017 0.001 ARG D 499 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 427 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8594 (tpt) cc_final: 0.8347 (tpt) REVERT: A 359 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6922 (mt-10) REVERT: A 636 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7886 (mm-30) REVERT: A 692 GLU cc_start: 0.8023 (mp0) cc_final: 0.7640 (mp0) REVERT: A 698 LYS cc_start: 0.8902 (mttt) cc_final: 0.8663 (mtmt) REVERT: B 285 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7583 (p0) REVERT: B 308 MET cc_start: 0.8578 (tpt) cc_final: 0.8076 (tpt) REVERT: B 331 ARG cc_start: 0.7907 (ttm-80) cc_final: 0.7411 (mmp-170) REVERT: B 353 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8737 (mm) REVERT: B 445 MET cc_start: 0.9311 (tpp) cc_final: 0.8955 (tpp) REVERT: B 636 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7572 (mm-30) REVERT: B 692 GLU cc_start: 0.7784 (mp0) cc_final: 0.7434 (mp0) REVERT: B 698 LYS cc_start: 0.8846 (mttp) cc_final: 0.8426 (mtmm) REVERT: C 289 HIS cc_start: 0.8277 (m90) cc_final: 0.7886 (m90) REVERT: C 315 LEU cc_start: 0.8716 (mm) cc_final: 0.8320 (mm) REVERT: C 331 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.7347 (mmp-170) REVERT: C 535 LYS cc_start: 0.7692 (mptt) cc_final: 0.7132 (mptt) REVERT: C 636 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7523 (mm-30) REVERT: C 698 LYS cc_start: 0.8849 (mttp) cc_final: 0.8524 (mttm) REVERT: D 289 HIS cc_start: 0.8883 (m90) cc_final: 0.8366 (m90) REVERT: D 308 MET cc_start: 0.8651 (tpt) cc_final: 0.8343 (tpt) REVERT: D 358 HIS cc_start: 0.7123 (OUTLIER) cc_final: 0.6640 (t-90) REVERT: D 576 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6439 (t70) REVERT: D 636 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7766 (mm-30) REVERT: D 698 LYS cc_start: 0.8868 (mttp) cc_final: 0.8533 (mttm) REVERT: D 707 ASP cc_start: 0.8147 (t0) cc_final: 0.7946 (t0) REVERT: D 716 MET cc_start: 0.5589 (mmm) cc_final: 0.4768 (mmm) outliers start: 54 outliers final: 44 residues processed: 448 average time/residue: 0.2747 time to fit residues: 187.5714 Evaluate side-chains 462 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 414 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 445 MET Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 735 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 207 optimal weight: 0.0010 chunk 190 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 127 optimal weight: 0.8980 chunk 101 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17748 Z= 0.217 Angle : 0.633 15.560 24020 Z= 0.316 Chirality : 0.039 0.209 2708 Planarity : 0.003 0.052 2964 Dihedral : 6.258 55.926 2432 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.84 % Allowed : 19.42 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.59 (0.19), residues: 2112 helix: 1.69 (0.15), residues: 1228 sheet: 0.65 (0.60), residues: 56 loop : -1.71 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 740 HIS 0.003 0.001 HIS A 364 PHE 0.031 0.001 PHE B 304 TYR 0.016 0.001 TYR D 351 ARG 0.010 0.001 ARG D 499 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 415 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 LEU cc_start: 0.7477 (tp) cc_final: 0.7081 (tt) REVERT: A 308 MET cc_start: 0.8609 (tpt) cc_final: 0.8366 (tpt) REVERT: A 359 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6918 (mt-10) REVERT: A 592 SER cc_start: 0.8974 (t) cc_final: 0.8666 (t) REVERT: A 636 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7889 (mm-30) REVERT: A 692 GLU cc_start: 0.8047 (mp0) cc_final: 0.7631 (mp0) REVERT: A 698 LYS cc_start: 0.8923 (mttt) cc_final: 0.8663 (mtmt) REVERT: A 716 MET cc_start: 0.6492 (mmm) cc_final: 0.5413 (mmm) REVERT: B 285 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.7592 (p0) REVERT: B 308 MET cc_start: 0.8640 (tpt) cc_final: 0.8156 (tpt) REVERT: B 331 ARG cc_start: 0.7807 (ttm-80) cc_final: 0.7341 (mmp-170) REVERT: B 353 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8725 (mm) REVERT: B 445 MET cc_start: 0.9326 (tpp) cc_final: 0.9001 (tpp) REVERT: B 636 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7534 (mm-30) REVERT: B 692 GLU cc_start: 0.7826 (mp0) cc_final: 0.7501 (mp0) REVERT: B 698 LYS cc_start: 0.8860 (mttp) cc_final: 0.8436 (mtmm) REVERT: C 289 HIS cc_start: 0.8323 (m90) cc_final: 0.7909 (m90) REVERT: C 315 LEU cc_start: 0.8688 (mm) cc_final: 0.8321 (mm) REVERT: C 331 ARG cc_start: 0.7630 (ttm-80) cc_final: 0.7321 (mmp-170) REVERT: C 445 MET cc_start: 0.9371 (tpp) cc_final: 0.9072 (tpp) REVERT: C 535 LYS cc_start: 0.7709 (mptt) cc_final: 0.7097 (mptt) REVERT: C 636 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7589 (mm-30) REVERT: C 698 LYS cc_start: 0.8852 (mttp) cc_final: 0.8548 (mttm) REVERT: D 289 HIS cc_start: 0.8891 (m90) cc_final: 0.8211 (m90) REVERT: D 308 MET cc_start: 0.8666 (tpt) cc_final: 0.8356 (tpt) REVERT: D 636 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7808 (mm-30) REVERT: D 698 LYS cc_start: 0.8872 (mttp) cc_final: 0.8263 (mtmm) REVERT: D 707 ASP cc_start: 0.8185 (t0) cc_final: 0.7967 (t0) REVERT: D 716 MET cc_start: 0.5624 (mmm) cc_final: 0.4708 (mmm) outliers start: 53 outliers final: 46 residues processed: 437 average time/residue: 0.2754 time to fit residues: 181.2058 Evaluate side-chains 455 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 407 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 445 MET Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 735 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 169 optimal weight: 0.1980 chunk 20 optimal weight: 8.9990 chunk 30 optimal weight: 0.0980 chunk 145 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.196485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.134480 restraints weight = 60318.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.137393 restraints weight = 22017.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.138742 restraints weight = 13045.543| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 17748 Z= 0.175 Angle : 0.629 15.564 24020 Z= 0.314 Chirality : 0.039 0.236 2708 Planarity : 0.003 0.037 2964 Dihedral : 6.158 57.781 2432 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.47 % Allowed : 20.44 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.61 (0.19), residues: 2112 helix: 1.72 (0.15), residues: 1224 sheet: 0.65 (0.60), residues: 56 loop : -1.71 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 697 HIS 0.003 0.001 HIS A 206 PHE 0.031 0.001 PHE B 304 TYR 0.015 0.001 TYR D 351 ARG 0.009 0.001 ARG D 499 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4259.09 seconds wall clock time: 76 minutes 57.71 seconds (4617.71 seconds total)