Starting phenix.real_space_refine on Mon Apr 8 03:42:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nez_12295/04_2024/7nez_12295_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nez_12295/04_2024/7nez_12295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nez_12295/04_2024/7nez_12295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nez_12295/04_2024/7nez_12295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nez_12295/04_2024/7nez_12295_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nez_12295/04_2024/7nez_12295_neut_trim_updated.pdb" } resolution = 3.39 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= -0.002 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 7965 2.51 5 N 2033 2.21 5 O 2279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12345 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4379 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 18, 'TRANS': 544} Chain breaks: 3 Chain: "B" Number of atoms: 4379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4379 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 18, 'TRANS': 544} Chain breaks: 3 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'NAG': 1, 'TTC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.17, per 1000 atoms: 0.58 Number of scatterers: 12345 At special positions: 0 Unit cell: (101.64, 97.02, 144.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2279 8.00 N 2033 7.00 C 7965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.71 Conformation dependent library (CDL) restraints added in 2.2 seconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2884 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 12 sheets defined 37.4% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 88 through 93 Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 154 through 162 removed outlier: 4.035A pdb=" N ILE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 198 removed outlier: 3.895A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 232 removed outlier: 3.519A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 4.670A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.727A pdb=" N LEU A 274 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE A 277 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 removed outlier: 4.037A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 340 through 352 removed outlier: 3.565A pdb=" N THR A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLN A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 380 through 389 removed outlier: 3.582A pdb=" N SER A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 412 removed outlier: 3.850A pdb=" N VAL A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 450 removed outlier: 4.110A pdb=" N SER A 443 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLU A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 466 through 476 removed outlier: 3.761A pdb=" N LEU A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 483 No H-bonds generated for 'chain 'A' and resid 480 through 483' Processing helix chain 'A' and resid 485 through 497 removed outlier: 4.021A pdb=" N THR A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 527 removed outlier: 3.650A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 552 removed outlier: 3.620A pdb=" N ILE A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 573 through 585 removed outlier: 3.501A pdb=" N GLY A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 578 " --> pdb=" O PRO A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 616 Processing helix chain 'A' and resid 623 through 649 removed outlier: 4.293A pdb=" N LYS A 628 " --> pdb=" O GLY A 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 154 through 162 removed outlier: 4.036A pdb=" N ILE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 198 removed outlier: 3.894A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 232 removed outlier: 3.519A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 4.669A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.727A pdb=" N LEU B 274 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE B 277 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 296 removed outlier: 4.037A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 340 through 352 removed outlier: 3.566A pdb=" N THR B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLN B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 380 through 389 removed outlier: 3.582A pdb=" N SER B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 412 removed outlier: 3.591A pdb=" N VAL B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 442 removed outlier: 3.994A pdb=" N VAL B 442 " --> pdb=" O CYS B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 450 removed outlier: 3.670A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 Processing helix chain 'B' and resid 466 through 476 removed outlier: 3.761A pdb=" N LEU B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 483 No H-bonds generated for 'chain 'B' and resid 480 through 483' Processing helix chain 'B' and resid 485 through 497 removed outlier: 4.021A pdb=" N THR B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 526 removed outlier: 3.650A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 550 removed outlier: 3.647A pdb=" N ILE B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 560 No H-bonds generated for 'chain 'B' and resid 558 through 560' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 573 through 585 removed outlier: 3.502A pdb=" N GLY B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 578 " --> pdb=" O PRO B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 616 Processing helix chain 'B' and resid 623 through 649 removed outlier: 4.292A pdb=" N LYS B 628 " --> pdb=" O GLY B 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing sheet with id= A, first strand: chain 'A' and resid 37 through 39 removed outlier: 3.571A pdb=" N GLY A 69 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.123A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 238 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE A 78 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE A 240 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLY A 80 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 241 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 37 through 39 removed outlier: 3.570A pdb=" N GLY B 69 " --> pdb=" O PHE B 39 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.123A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE B 238 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE B 78 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N PHE B 240 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N GLY B 80 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 241 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 19 through 24 removed outlier: 3.654A pdb=" N TYR C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 88 through 90 removed outlier: 6.100A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 19 through 23 Processing sheet with id= H, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.371A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TYR D 51 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TRP D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 19 through 24 removed outlier: 3.653A pdb=" N TYR E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 88 through 90 removed outlier: 6.101A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 19 through 23 Processing sheet with id= L, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.372A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TRP F 35 " --> pdb=" O TYR F 51 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1077 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: 4.09 Time building geometry restraints manager: 5.15 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: 1948 1.31 - 1.43: 3535 1.43 - 1.56: 7021 1.56 - 1.69: 11 1.69 - 1.82: 106 Bond restraints: 12621 Sorted by residual: bond pdb=" C16 TTC A1201 " pdb=" C17 TTC A1201 " ideal model delta sigma weight residual 1.411 1.641 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C13 TTC A1201 " pdb=" C17 TTC A1201 " ideal model delta sigma weight residual 1.359 1.571 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C15 TTC A1201 " pdb=" C16 TTC A1201 " ideal model delta sigma weight residual 1.364 1.557 -0.193 2.00e-02 2.50e+03 9.27e+01 bond pdb=" C14 TTC A1201 " pdb=" C15 TTC A1201 " ideal model delta sigma weight residual 1.441 1.631 -0.190 2.00e-02 2.50e+03 8.99e+01 bond pdb=" C13 TTC A1201 " pdb=" C9 TTC A1201 " ideal model delta sigma weight residual 1.456 1.630 -0.174 2.00e-02 2.50e+03 7.58e+01 ... (remaining 12616 not shown) Histogram of bond angle deviations from ideal: 98.20 - 105.36: 229 105.36 - 112.52: 6477 112.52 - 119.67: 4283 119.67 - 126.83: 5968 126.83 - 133.99: 150 Bond angle restraints: 17107 Sorted by residual: angle pdb=" N VAL B 442 " pdb=" CA VAL B 442 " pdb=" C VAL B 442 " ideal model delta sigma weight residual 112.17 100.50 11.67 9.50e-01 1.11e+00 1.51e+02 angle pdb=" N THR A 402 " pdb=" CA THR A 402 " pdb=" C THR A 402 " ideal model delta sigma weight residual 111.36 99.81 11.55 1.09e+00 8.42e-01 1.12e+02 angle pdb=" N GLY A 406 " pdb=" CA GLY A 406 " pdb=" C GLY A 406 " ideal model delta sigma weight residual 113.86 101.20 12.66 1.50e+00 4.44e-01 7.12e+01 angle pdb=" C ILE B 543 " pdb=" CA ILE B 543 " pdb=" CB ILE B 543 " ideal model delta sigma weight residual 112.14 101.79 10.35 1.35e+00 5.49e-01 5.88e+01 angle pdb=" N LEU B 430 " pdb=" CA LEU B 430 " pdb=" C LEU B 430 " ideal model delta sigma weight residual 111.07 103.60 7.47 1.07e+00 8.73e-01 4.88e+01 ... (remaining 17102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.75: 7097 15.75 - 31.50: 309 31.50 - 47.26: 61 47.26 - 63.01: 7 63.01 - 78.76: 8 Dihedral angle restraints: 7482 sinusoidal: 2966 harmonic: 4516 Sorted by residual: dihedral pdb=" C PHE A 439 " pdb=" N PHE A 439 " pdb=" CA PHE A 439 " pdb=" CB PHE A 439 " ideal model delta harmonic sigma weight residual -122.60 -140.56 17.96 0 2.50e+00 1.60e-01 5.16e+01 dihedral pdb=" N PHE A 439 " pdb=" C PHE A 439 " pdb=" CA PHE A 439 " pdb=" CB PHE A 439 " ideal model delta harmonic sigma weight residual 122.80 137.58 -14.78 0 2.50e+00 1.60e-01 3.49e+01 dihedral pdb=" C THR A 402 " pdb=" N THR A 402 " pdb=" CA THR A 402 " pdb=" CB THR A 402 " ideal model delta harmonic sigma weight residual -122.00 -108.52 -13.48 0 2.50e+00 1.60e-01 2.91e+01 ... (remaining 7479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 1913 0.152 - 0.304: 28 0.304 - 0.456: 9 0.456 - 0.607: 0 0.607 - 0.759: 1 Chirality restraints: 1951 Sorted by residual: chirality pdb=" CA PHE A 439 " pdb=" N PHE A 439 " pdb=" C PHE A 439 " pdb=" CB PHE A 439 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CA GLN B 126 " pdb=" N GLN B 126 " pdb=" C GLN B 126 " pdb=" CB GLN B 126 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" C21 TTC A1201 " pdb=" C16 TTC A1201 " pdb=" C20 TTC A1201 " pdb=" O24 TTC A1201 " both_signs ideal model delta sigma weight residual False -2.50 -2.90 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 1948 not shown) Planarity restraints: 2130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 440 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C SER B 440 " -0.067 2.00e-02 2.50e+03 pdb=" O SER B 440 " 0.025 2.00e-02 2.50e+03 pdb=" N SER B 441 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 437 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.10e+00 pdb=" C GLN A 437 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN A 437 " 0.019 2.00e-02 2.50e+03 pdb=" N CYS A 438 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 125 " -0.016 2.00e-02 2.50e+03 3.01e-02 9.07e+00 pdb=" C VAL B 125 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL B 125 " -0.019 2.00e-02 2.50e+03 pdb=" N GLN B 126 " -0.017 2.00e-02 2.50e+03 ... (remaining 2127 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 103 2.55 - 3.13: 10171 3.13 - 3.72: 18800 3.72 - 4.31: 27218 4.31 - 4.90: 44609 Nonbonded interactions: 100901 Sorted by model distance: nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 1.958 2.440 nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 1.958 2.440 nonbonded pdb=" OH TYR C 36 " pdb=" OE1 GLN C 89 " model vdw 2.182 2.440 nonbonded pdb=" OH TYR E 36 " pdb=" OE1 GLN E 89 " model vdw 2.183 2.440 nonbonded pdb=" O ILE C 2 " pdb=" OG1 THR C 97 " model vdw 2.183 2.440 ... (remaining 100896 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 35 through 654 or resid 1202)) selection = (chain 'B' and (resid 35 through 654 or resid 702)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = (chain 'D' and resid 2 through 119) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.890 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: 12.820 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 35.300 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 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 : 0.009 0.230 12621 Z= 0.591 Angle : 0.796 12.658 17107 Z= 0.498 Chirality : 0.059 0.759 1951 Planarity : 0.004 0.038 2130 Dihedral : 9.749 78.761 4577 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.67 % Allowed : 3.79 % Favored : 95.54 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.20), residues: 1552 helix: -1.06 (0.19), residues: 602 sheet: -1.96 (0.30), residues: 252 loop : -1.92 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 627 HIS 0.004 0.001 HIS B 457 PHE 0.021 0.002 PHE B 545 TYR 0.013 0.001 TYR F 95 ARG 0.002 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 384 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LEU cc_start: 0.8216 (mt) cc_final: 0.8014 (tp) REVERT: A 186 VAL cc_start: 0.5535 (t) cc_final: 0.4964 (p) REVERT: A 198 MET cc_start: 0.6399 (mtp) cc_final: 0.6189 (mtp) REVERT: A 264 LEU cc_start: 0.5610 (tp) cc_final: 0.5375 (tp) REVERT: A 446 GLU cc_start: 0.8823 (tt0) cc_final: 0.8373 (tm-30) REVERT: A 450 VAL cc_start: 0.8924 (t) cc_final: 0.8504 (m) REVERT: A 475 LEU cc_start: 0.8404 (tp) cc_final: 0.8156 (mp) REVERT: A 491 CYS cc_start: 0.7666 (m) cc_final: 0.7280 (m) REVERT: A 509 MET cc_start: 0.7875 (ttt) cc_final: 0.7558 (ttp) REVERT: A 534 VAL cc_start: 0.8622 (t) cc_final: 0.8353 (m) REVERT: A 544 CYS cc_start: 0.9028 (m) cc_final: 0.8582 (m) REVERT: B 152 MET cc_start: -0.0101 (mtp) cc_final: -0.0373 (mmp) REVERT: B 198 MET cc_start: 0.6646 (mtp) cc_final: 0.6350 (mmt) REVERT: B 227 LEU cc_start: 0.6829 (tp) cc_final: 0.6304 (tp) REVERT: B 255 SER cc_start: 0.7377 (t) cc_final: 0.6610 (t) REVERT: B 288 ASN cc_start: 0.7414 (t0) cc_final: 0.6930 (p0) REVERT: B 523 MET cc_start: 0.8768 (ttt) cc_final: 0.8416 (ttm) REVERT: B 540 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8651 (mp) REVERT: B 544 CYS cc_start: 0.9257 (m) cc_final: 0.8943 (m) REVERT: B 584 ASN cc_start: 0.7631 (t0) cc_final: 0.7421 (t0) REVERT: C 17 ASP cc_start: 0.7552 (t70) cc_final: 0.7149 (t0) REVERT: D 6 GLU cc_start: 0.8112 (mp0) cc_final: 0.7890 (mp0) REVERT: D 44 LYS cc_start: 0.7895 (mptp) cc_final: 0.7610 (mmtm) REVERT: E 17 ASP cc_start: 0.6756 (t70) cc_final: 0.5919 (m-30) REVERT: E 33 LEU cc_start: 0.8864 (tm) cc_final: 0.8631 (tm) REVERT: E 79 GLN cc_start: 0.8234 (mm110) cc_final: 0.8017 (mm-40) REVERT: F 100 TYR cc_start: 0.7193 (t80) cc_final: 0.6868 (t80) outliers start: 9 outliers final: 3 residues processed: 391 average time/residue: 0.2529 time to fit residues: 139.6359 Evaluate side-chains 236 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 232 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 540 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 62 optimal weight: 0.0980 chunk 120 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 139 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 HIS A 375 HIS ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN A 582 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 243 HIS B 582 GLN D 5 GLN D 78 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12621 Z= 0.188 Angle : 0.625 7.866 17107 Z= 0.321 Chirality : 0.042 0.205 1951 Planarity : 0.005 0.041 2130 Dihedral : 6.978 64.341 1806 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.90 % Allowed : 11.09 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.21), residues: 1552 helix: -0.26 (0.20), residues: 610 sheet: -1.64 (0.30), residues: 252 loop : -1.63 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 379 HIS 0.005 0.001 HIS A 40 PHE 0.023 0.002 PHE A 250 TYR 0.024 0.001 TYR E 91 ARG 0.008 0.001 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 259 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.4465 (t-90) cc_final: 0.4242 (t-170) REVERT: A 193 ARG cc_start: 0.7304 (mtt180) cc_final: 0.6994 (mtp85) REVERT: A 198 MET cc_start: 0.6448 (mtp) cc_final: 0.6153 (mtp) REVERT: A 446 GLU cc_start: 0.8739 (tt0) cc_final: 0.8192 (tm-30) REVERT: A 451 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7310 (tp30) REVERT: A 475 LEU cc_start: 0.8459 (tp) cc_final: 0.8106 (mp) REVERT: A 483 MET cc_start: 0.6928 (ptt) cc_final: 0.6715 (ppp) REVERT: A 491 CYS cc_start: 0.7736 (m) cc_final: 0.7354 (m) REVERT: A 581 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8597 (mp) REVERT: B 162 ASN cc_start: 0.8885 (t0) cc_final: 0.8266 (m-40) REVERT: B 198 MET cc_start: 0.7133 (mtp) cc_final: 0.6812 (mmt) REVERT: B 231 MET cc_start: 0.8571 (mtt) cc_final: 0.8305 (mtm) REVERT: B 288 ASN cc_start: 0.7555 (t0) cc_final: 0.6937 (p0) REVERT: B 442 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8852 (p) REVERT: B 515 MET cc_start: 0.8777 (mmt) cc_final: 0.8355 (mmt) REVERT: B 518 TYR cc_start: 0.8842 (m-80) cc_final: 0.8484 (m-80) REVERT: B 536 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8426 (p) REVERT: B 540 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8242 (mt) REVERT: B 544 CYS cc_start: 0.9048 (m) cc_final: 0.8635 (m) REVERT: C 17 ASP cc_start: 0.7618 (t70) cc_final: 0.7362 (t0) REVERT: E 17 ASP cc_start: 0.7021 (t70) cc_final: 0.6206 (m-30) REVERT: E 79 GLN cc_start: 0.8083 (mm110) cc_final: 0.7377 (mp10) REVERT: F 5 GLN cc_start: 0.7787 (pm20) cc_final: 0.7461 (pm20) outliers start: 39 outliers final: 19 residues processed: 282 average time/residue: 0.2610 time to fit residues: 108.5566 Evaluate side-chains 232 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 209 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 116 optimal weight: 0.0980 chunk 95 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 138 optimal weight: 0.0060 chunk 47 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12621 Z= 0.186 Angle : 0.600 9.285 17107 Z= 0.305 Chirality : 0.042 0.179 1951 Planarity : 0.004 0.041 2130 Dihedral : 6.698 65.059 1801 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.57 % Allowed : 13.02 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1552 helix: -0.08 (0.20), residues: 606 sheet: -1.33 (0.30), residues: 270 loop : -1.52 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 379 HIS 0.005 0.001 HIS A 457 PHE 0.020 0.002 PHE F 79 TYR 0.015 0.001 TYR E 91 ARG 0.008 0.001 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 237 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.3941 (mtt) cc_final: 0.3658 (ttt) REVERT: A 198 MET cc_start: 0.6480 (mtp) cc_final: 0.6205 (mtm) REVERT: A 200 LEU cc_start: 0.5891 (OUTLIER) cc_final: 0.5684 (mt) REVERT: A 446 GLU cc_start: 0.8723 (tt0) cc_final: 0.8099 (tm-30) REVERT: A 451 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7319 (tp30) REVERT: A 483 MET cc_start: 0.6968 (ptt) cc_final: 0.6753 (ppp) REVERT: A 491 CYS cc_start: 0.8161 (m) cc_final: 0.7759 (m) REVERT: A 581 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8602 (mp) REVERT: B 71 MET cc_start: 0.4759 (mmm) cc_final: 0.4545 (mmm) REVERT: B 162 ASN cc_start: 0.8871 (t0) cc_final: 0.8358 (m-40) REVERT: B 265 MET cc_start: 0.6101 (mpp) cc_final: 0.5895 (mpp) REVERT: B 288 ASN cc_start: 0.7591 (t0) cc_final: 0.6861 (p0) REVERT: B 398 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7346 (mp10) REVERT: B 442 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8730 (p) REVERT: B 451 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8638 (mt-10) REVERT: B 540 LEU cc_start: 0.8754 (mm) cc_final: 0.7972 (tp) REVERT: B 544 CYS cc_start: 0.9027 (m) cc_final: 0.8572 (m) REVERT: C 17 ASP cc_start: 0.7746 (t70) cc_final: 0.7523 (t0) REVERT: C 82 ASP cc_start: 0.7953 (m-30) cc_final: 0.7600 (t0) REVERT: E 17 ASP cc_start: 0.7318 (t70) cc_final: 0.6453 (m-30) REVERT: F 5 GLN cc_start: 0.7810 (pm20) cc_final: 0.7542 (pm20) REVERT: F 20 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7462 (mt) outliers start: 48 outliers final: 25 residues processed: 264 average time/residue: 0.2337 time to fit residues: 90.4920 Evaluate side-chains 231 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 202 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 66 ASN A 116 ASN A 120 ASN A 424 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12621 Z= 0.243 Angle : 0.632 8.591 17107 Z= 0.322 Chirality : 0.043 0.280 1951 Planarity : 0.004 0.042 2130 Dihedral : 6.382 63.995 1797 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.24 % Allowed : 14.06 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.21), residues: 1552 helix: -0.05 (0.21), residues: 618 sheet: -1.08 (0.31), residues: 272 loop : -1.55 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 379 HIS 0.007 0.001 HIS A 457 PHE 0.025 0.002 PHE F 79 TYR 0.032 0.002 TYR B 518 ARG 0.010 0.001 ARG B 465 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 231 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6471 (mtp) cc_final: 0.6185 (mtm) REVERT: A 231 MET cc_start: 0.8727 (mmm) cc_final: 0.8139 (mtt) REVERT: A 442 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8668 (t) REVERT: A 451 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7775 (tp30) REVERT: A 458 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7963 (mt-10) REVERT: A 483 MET cc_start: 0.7050 (ptt) cc_final: 0.6757 (ptm) REVERT: A 491 CYS cc_start: 0.8402 (m) cc_final: 0.8024 (m) REVERT: B 162 ASN cc_start: 0.8958 (t0) cc_final: 0.8489 (m-40) REVERT: B 288 ASN cc_start: 0.7569 (t0) cc_final: 0.6720 (p0) REVERT: B 451 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8785 (mt-10) REVERT: B 540 LEU cc_start: 0.8786 (mm) cc_final: 0.7970 (tp) REVERT: B 544 CYS cc_start: 0.9080 (m) cc_final: 0.8618 (m) REVERT: B 558 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8896 (mt) REVERT: C 17 ASP cc_start: 0.7828 (t70) cc_final: 0.7613 (t0) REVERT: E 11 PHE cc_start: 0.8263 (m-80) cc_final: 0.8045 (m-80) REVERT: F 5 GLN cc_start: 0.7882 (pm20) cc_final: 0.7589 (pm20) REVERT: F 20 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7301 (mt) REVERT: F 47 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7605 (tt0) outliers start: 57 outliers final: 33 residues processed: 268 average time/residue: 0.2089 time to fit residues: 85.0462 Evaluate side-chains 237 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 200 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 47 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 425 ASN ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN B 109 ASN ** B 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN B 601 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12621 Z= 0.336 Angle : 0.701 12.158 17107 Z= 0.356 Chirality : 0.045 0.256 1951 Planarity : 0.005 0.043 2130 Dihedral : 6.673 64.100 1797 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.51 % Favored : 93.43 % Rotamer: Outliers : 4.84 % Allowed : 15.77 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.21), residues: 1552 helix: -0.19 (0.20), residues: 618 sheet: -1.00 (0.31), residues: 272 loop : -1.61 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 379 HIS 0.008 0.002 HIS A 457 PHE 0.035 0.002 PHE A 294 TYR 0.031 0.002 TYR A 44 ARG 0.005 0.001 ARG B 465 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 219 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7326 (mtp85) REVERT: A 254 ASP cc_start: 0.4905 (m-30) cc_final: 0.4274 (m-30) REVERT: A 259 LEU cc_start: 0.7158 (mt) cc_final: 0.6893 (mt) REVERT: A 407 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8774 (mp) REVERT: A 446 GLU cc_start: 0.8713 (tt0) cc_final: 0.8133 (tm-30) REVERT: A 451 GLU cc_start: 0.8599 (mm-30) cc_final: 0.7925 (tp30) REVERT: A 454 LEU cc_start: 0.8478 (tp) cc_final: 0.8111 (tp) REVERT: A 491 CYS cc_start: 0.8609 (m) cc_final: 0.8217 (m) REVERT: A 540 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8423 (tm) REVERT: B 76 ASN cc_start: 0.7947 (m110) cc_final: 0.7510 (m-40) REVERT: B 162 ASN cc_start: 0.9032 (t0) cc_final: 0.8720 (m-40) REVERT: B 198 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7430 (tpp) REVERT: B 247 TYR cc_start: 0.5310 (t80) cc_final: 0.5106 (t80) REVERT: B 288 ASN cc_start: 0.7562 (t0) cc_final: 0.6620 (p0) REVERT: B 398 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7380 (mp10) REVERT: B 451 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8854 (mt-10) REVERT: B 540 LEU cc_start: 0.8848 (mm) cc_final: 0.8054 (tp) REVERT: B 544 CYS cc_start: 0.9143 (m) cc_final: 0.8704 (m) REVERT: C 17 ASP cc_start: 0.8001 (t70) cc_final: 0.7795 (t0) REVERT: D 5 GLN cc_start: 0.7041 (mm110) cc_final: 0.6732 (mm110) REVERT: F 5 GLN cc_start: 0.7862 (pm20) cc_final: 0.7600 (pm20) REVERT: F 20 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7289 (mt) REVERT: F 47 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7589 (tt0) outliers start: 65 outliers final: 44 residues processed: 261 average time/residue: 0.2254 time to fit residues: 86.6685 Evaluate side-chains 246 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 197 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 47 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 425 ASN ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN ** B 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12621 Z= 0.270 Angle : 0.635 9.240 17107 Z= 0.324 Chirality : 0.043 0.207 1951 Planarity : 0.004 0.043 2130 Dihedral : 6.503 63.500 1797 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.32 % Allowed : 17.19 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1552 helix: -0.03 (0.21), residues: 620 sheet: -0.85 (0.31), residues: 270 loop : -1.56 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 379 HIS 0.006 0.001 HIS A 457 PHE 0.028 0.002 PHE B 506 TYR 0.034 0.002 TYR A 44 ARG 0.005 0.001 ARG B 465 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 213 time to evaluate : 1.371 Fit side-chains revert: symmetry clash REVERT: A 193 ARG cc_start: 0.8024 (mtt180) cc_final: 0.7583 (mtp85) REVERT: A 198 MET cc_start: 0.6582 (mtp) cc_final: 0.6293 (mtp) REVERT: A 231 MET cc_start: 0.8825 (mmm) cc_final: 0.8544 (mtp) REVERT: A 259 LEU cc_start: 0.7317 (mt) cc_final: 0.7112 (mt) REVERT: A 407 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8782 (mp) REVERT: A 442 VAL cc_start: 0.8870 (t) cc_final: 0.8621 (t) REVERT: A 446 GLU cc_start: 0.8660 (tt0) cc_final: 0.8067 (tm-30) REVERT: A 451 GLU cc_start: 0.8620 (mm-30) cc_final: 0.7885 (tp30) REVERT: A 454 LEU cc_start: 0.8468 (tp) cc_final: 0.8216 (tp) REVERT: A 491 CYS cc_start: 0.8593 (m) cc_final: 0.8207 (m) REVERT: B 162 ASN cc_start: 0.9061 (t0) cc_final: 0.8830 (m-40) REVERT: B 198 MET cc_start: 0.8103 (ttp) cc_final: 0.7477 (tpp) REVERT: B 247 TYR cc_start: 0.5441 (t80) cc_final: 0.5224 (t80) REVERT: B 283 HIS cc_start: 0.3789 (t-90) cc_final: 0.3383 (m-70) REVERT: B 288 ASN cc_start: 0.7528 (t0) cc_final: 0.6519 (p0) REVERT: B 398 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7403 (mp10) REVERT: B 451 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8829 (mt-10) REVERT: B 540 LEU cc_start: 0.8827 (mm) cc_final: 0.8028 (tp) REVERT: B 544 CYS cc_start: 0.9113 (m) cc_final: 0.8612 (m) REVERT: C 17 ASP cc_start: 0.7910 (t70) cc_final: 0.7642 (t0) REVERT: D 59 THR cc_start: 0.8736 (m) cc_final: 0.8488 (p) REVERT: F 5 GLN cc_start: 0.7849 (pm20) cc_final: 0.7605 (pm20) REVERT: F 20 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7261 (mt) REVERT: F 47 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7587 (tt0) outliers start: 58 outliers final: 46 residues processed: 251 average time/residue: 0.2175 time to fit residues: 82.3596 Evaluate side-chains 243 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 194 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 47 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 76 ASN A 425 ASN ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.6663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12621 Z= 0.277 Angle : 0.641 10.236 17107 Z= 0.326 Chirality : 0.043 0.199 1951 Planarity : 0.004 0.042 2130 Dihedral : 6.495 64.001 1797 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.76 % Allowed : 16.96 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.21), residues: 1552 helix: 0.00 (0.21), residues: 616 sheet: -0.87 (0.31), residues: 270 loop : -1.52 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 379 HIS 0.022 0.002 HIS A 40 PHE 0.030 0.002 PHE B 506 TYR 0.024 0.002 TYR A 44 ARG 0.005 0.001 ARG E 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 207 time to evaluate : 1.420 Fit side-chains revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7525 (mtp85) REVERT: A 198 MET cc_start: 0.6550 (mtp) cc_final: 0.6233 (mtp) REVERT: A 231 MET cc_start: 0.8821 (mmm) cc_final: 0.8615 (mtp) REVERT: A 259 LEU cc_start: 0.7544 (mt) cc_final: 0.7315 (mt) REVERT: A 407 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8766 (mp) REVERT: A 442 VAL cc_start: 0.8865 (t) cc_final: 0.8613 (t) REVERT: A 446 GLU cc_start: 0.8614 (tt0) cc_final: 0.8031 (tm-30) REVERT: A 491 CYS cc_start: 0.8585 (m) cc_final: 0.8179 (m) REVERT: A 510 MET cc_start: 0.8682 (ttp) cc_final: 0.8395 (ttm) REVERT: B 198 MET cc_start: 0.8076 (ttp) cc_final: 0.7474 (tpp) REVERT: B 210 ASP cc_start: 0.7224 (t0) cc_final: 0.6986 (t70) REVERT: B 247 TYR cc_start: 0.5553 (t80) cc_final: 0.5324 (t80) REVERT: B 283 HIS cc_start: 0.3836 (t-90) cc_final: 0.3419 (m-70) REVERT: B 288 ASN cc_start: 0.7492 (t0) cc_final: 0.6453 (p0) REVERT: B 451 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8814 (mt-10) REVERT: B 540 LEU cc_start: 0.8838 (mm) cc_final: 0.8046 (tp) REVERT: B 544 CYS cc_start: 0.9086 (m) cc_final: 0.8569 (m) REVERT: C 17 ASP cc_start: 0.7949 (t70) cc_final: 0.7679 (t0) REVERT: F 5 GLN cc_start: 0.7878 (pm20) cc_final: 0.7638 (pm20) REVERT: F 20 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7288 (mt) REVERT: F 47 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7593 (tt0) outliers start: 64 outliers final: 47 residues processed: 251 average time/residue: 0.2245 time to fit residues: 84.3187 Evaluate side-chains 247 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 197 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 47 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 116 optimal weight: 0.3980 chunk 135 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN B 582 GLN ** B 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN F 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.6845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12621 Z= 0.168 Angle : 0.602 9.215 17107 Z= 0.302 Chirality : 0.041 0.185 1951 Planarity : 0.004 0.042 2130 Dihedral : 6.184 62.775 1797 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.20 % Allowed : 18.60 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.22), residues: 1552 helix: 0.18 (0.21), residues: 618 sheet: -0.85 (0.30), residues: 290 loop : -1.34 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 379 HIS 0.004 0.001 HIS B 583 PHE 0.030 0.001 PHE B 506 TYR 0.021 0.001 TYR A 44 ARG 0.005 0.001 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 207 time to evaluate : 1.452 Fit side-chains revert: symmetry clash REVERT: A 193 ARG cc_start: 0.8029 (mtt180) cc_final: 0.7480 (mtt-85) REVERT: A 198 MET cc_start: 0.6535 (mtp) cc_final: 0.6252 (mtp) REVERT: A 259 LEU cc_start: 0.7520 (mt) cc_final: 0.7312 (mt) REVERT: A 407 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8781 (mp) REVERT: A 442 VAL cc_start: 0.8821 (t) cc_final: 0.8552 (t) REVERT: A 451 GLU cc_start: 0.8536 (mm-30) cc_final: 0.7712 (tp30) REVERT: A 491 CYS cc_start: 0.8602 (m) cc_final: 0.8224 (m) REVERT: B 198 MET cc_start: 0.8000 (ttp) cc_final: 0.7436 (tpp) REVERT: B 210 ASP cc_start: 0.7279 (t0) cc_final: 0.7071 (t70) REVERT: B 247 TYR cc_start: 0.5488 (t80) cc_final: 0.5280 (t80) REVERT: B 283 HIS cc_start: 0.3853 (t-90) cc_final: 0.3480 (m-70) REVERT: B 288 ASN cc_start: 0.7435 (t0) cc_final: 0.6418 (p0) REVERT: B 451 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8779 (mt-10) REVERT: B 540 LEU cc_start: 0.8771 (mm) cc_final: 0.7994 (tp) REVERT: B 544 CYS cc_start: 0.9019 (m) cc_final: 0.8536 (m) REVERT: C 17 ASP cc_start: 0.7809 (t70) cc_final: 0.7595 (t70) REVERT: C 82 ASP cc_start: 0.8094 (m-30) cc_final: 0.7609 (t0) REVERT: D 111 GLN cc_start: 0.8047 (mp10) cc_final: 0.7802 (mp10) REVERT: F 20 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7274 (mt) outliers start: 43 outliers final: 32 residues processed: 237 average time/residue: 0.2277 time to fit residues: 80.7022 Evaluate side-chains 222 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 188 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 138 optimal weight: 0.1980 chunk 83 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 130 optimal weight: 0.0570 chunk 137 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.7012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12621 Z= 0.159 Angle : 0.607 11.507 17107 Z= 0.301 Chirality : 0.041 0.244 1951 Planarity : 0.004 0.042 2130 Dihedral : 6.195 63.006 1797 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.98 % Allowed : 19.72 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.22), residues: 1552 helix: 0.22 (0.21), residues: 618 sheet: -0.70 (0.31), residues: 290 loop : -1.23 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 379 HIS 0.006 0.001 HIS A 40 PHE 0.029 0.001 PHE B 506 TYR 0.019 0.001 TYR D 51 ARG 0.006 0.000 ARG E 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 209 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7483 (mtt-85) REVERT: A 198 MET cc_start: 0.6548 (mtp) cc_final: 0.6290 (mtp) REVERT: A 442 VAL cc_start: 0.8786 (t) cc_final: 0.8500 (t) REVERT: A 451 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7662 (tp30) REVERT: A 491 CYS cc_start: 0.8519 (m) cc_final: 0.8152 (m) REVERT: B 107 LEU cc_start: 0.7420 (mm) cc_final: 0.6350 (pt) REVERT: B 152 MET cc_start: 0.0400 (mmm) cc_final: 0.0085 (mtp) REVERT: B 198 MET cc_start: 0.7983 (ttp) cc_final: 0.7470 (tpp) REVERT: B 210 ASP cc_start: 0.7297 (t0) cc_final: 0.7082 (t70) REVERT: B 229 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7697 (tmmt) REVERT: B 283 HIS cc_start: 0.3818 (t-90) cc_final: 0.3439 (m-70) REVERT: B 379 TRP cc_start: 0.7013 (m-10) cc_final: 0.6783 (m-10) REVERT: B 451 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8744 (mt-10) REVERT: B 540 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.7957 (tp) REVERT: B 544 CYS cc_start: 0.8957 (m) cc_final: 0.8471 (m) REVERT: C 17 ASP cc_start: 0.7739 (t70) cc_final: 0.7449 (t0) REVERT: C 33 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8183 (tm) REVERT: C 82 ASP cc_start: 0.8047 (m-30) cc_final: 0.7582 (t0) REVERT: D 91 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8190 (t) REVERT: D 111 GLN cc_start: 0.8039 (mp10) cc_final: 0.7793 (mp10) REVERT: F 20 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7294 (mt) REVERT: F 98 THR cc_start: 0.8579 (m) cc_final: 0.8141 (p) outliers start: 40 outliers final: 27 residues processed: 236 average time/residue: 0.2191 time to fit residues: 77.2837 Evaluate side-chains 228 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 69 optimal weight: 30.0000 chunk 101 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 122 optimal weight: 0.0670 chunk 12 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.7187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12621 Z= 0.192 Angle : 0.632 11.886 17107 Z= 0.310 Chirality : 0.041 0.220 1951 Planarity : 0.004 0.040 2130 Dihedral : 6.157 63.126 1797 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.83 % Allowed : 20.01 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.22), residues: 1552 helix: 0.24 (0.21), residues: 620 sheet: -0.67 (0.32), residues: 290 loop : -1.17 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 379 HIS 0.005 0.001 HIS B 583 PHE 0.029 0.001 PHE B 506 TYR 0.031 0.001 TYR B 247 ARG 0.006 0.000 ARG E 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 205 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.7803 (mmt180) cc_final: 0.7474 (mmt180) REVERT: A 193 ARG cc_start: 0.8039 (mtt180) cc_final: 0.7455 (mtt-85) REVERT: A 198 MET cc_start: 0.6575 (mtp) cc_final: 0.6328 (mtm) REVERT: A 442 VAL cc_start: 0.8800 (t) cc_final: 0.8518 (t) REVERT: A 451 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7678 (tp30) REVERT: A 491 CYS cc_start: 0.8555 (m) cc_final: 0.8173 (m) REVERT: B 107 LEU cc_start: 0.7468 (mm) cc_final: 0.6400 (pt) REVERT: B 152 MET cc_start: 0.0311 (mmm) cc_final: -0.0134 (mtp) REVERT: B 210 ASP cc_start: 0.7272 (t0) cc_final: 0.7046 (t70) REVERT: B 229 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7749 (tmmt) REVERT: B 283 HIS cc_start: 0.3893 (t-90) cc_final: 0.3436 (m-70) REVERT: B 451 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8768 (mt-10) REVERT: B 540 LEU cc_start: 0.8728 (mm) cc_final: 0.7925 (tp) REVERT: B 544 CYS cc_start: 0.8962 (m) cc_final: 0.8470 (m) REVERT: C 17 ASP cc_start: 0.7739 (t70) cc_final: 0.7513 (t70) REVERT: C 33 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8176 (tm) REVERT: C 82 ASP cc_start: 0.8078 (m-30) cc_final: 0.7632 (t0) REVERT: C 103 LYS cc_start: 0.8367 (tttt) cc_final: 0.8096 (tttp) REVERT: F 20 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7378 (mt) REVERT: F 98 THR cc_start: 0.8567 (m) cc_final: 0.8114 (p) outliers start: 38 outliers final: 32 residues processed: 232 average time/residue: 0.2207 time to fit residues: 76.3709 Evaluate side-chains 232 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 197 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.0010 chunk 37 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN B 387 ASN ** B 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.139620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110701 restraints weight = 23941.462| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.91 r_work: 0.3465 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.7317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12621 Z= 0.161 Angle : 0.606 10.981 17107 Z= 0.299 Chirality : 0.041 0.217 1951 Planarity : 0.004 0.039 2130 Dihedral : 6.215 64.634 1797 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.98 % Allowed : 19.94 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.22), residues: 1552 helix: 0.23 (0.21), residues: 632 sheet: -0.70 (0.31), residues: 290 loop : -1.20 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 379 HIS 0.003 0.001 HIS A 40 PHE 0.015 0.001 PHE A 240 TYR 0.019 0.001 TYR D 51 ARG 0.004 0.000 ARG B 465 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2985.36 seconds wall clock time: 55 minutes 11.07 seconds (3311.07 seconds total)