Starting phenix.real_space_refine on Thu May 16 15:57:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uqv_42478/05_2024/8uqv_42478_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uqv_42478/05_2024/8uqv_42478.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uqv_42478/05_2024/8uqv_42478_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uqv_42478/05_2024/8uqv_42478_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uqv_42478/05_2024/8uqv_42478_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uqv_42478/05_2024/8uqv_42478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uqv_42478/05_2024/8uqv_42478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uqv_42478/05_2024/8uqv_42478_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uqv_42478/05_2024/8uqv_42478_trim_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16140 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 64 5.16 5 C 11488 2.51 5 N 3072 2.21 5 O 3396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 461": "OD1" <-> "OD2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 271": "OE1" <-> "OE2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 18024 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4460 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 40, 'TRANS': 506} Chain: "B" Number of atoms: 4460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4460 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 40, 'TRANS': 506} Chain: "C" Number of atoms: 4460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4460 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 40, 'TRANS': 506} Chain: "D" Number of atoms: 4460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4460 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 40, 'TRANS': 506} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 26 Unusual residues: {' CA': 1, 'GLC': 1, 'XVC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 26 Unusual residues: {' CA': 1, 'GLC': 1, 'XVC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 26 Unusual residues: {' CA': 1, 'GLC': 1, 'XVC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 26 Unusual residues: {' CA': 1, 'GLC': 1, 'XVC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Time building chain proxies: 9.64, per 1000 atoms: 0.53 Number of scatterers: 18024 At special positions: 0 Unit cell: (88.14, 141.25, 135.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 64 16.00 O 3396 8.00 N 3072 7.00 C 11488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.25 Conformation dependent library (CDL) restraints added in 3.5 seconds 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 14 sheets defined 23.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.04 Creating SS restraints... Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 116 through 127 removed outlier: 3.785A pdb=" N VAL A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.934A pdb=" N SER A 152 " --> pdb=" O TRP A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 224 through 230 removed outlier: 4.179A pdb=" N LEU A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLY A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 230 " --> pdb=" O PHE A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 224 through 230' Processing helix chain 'A' and resid 257 through 271 Processing helix chain 'A' and resid 308 through 320 Proline residue: A 312 - end of helix removed outlier: 4.572A pdb=" N PHE A 315 " --> pdb=" O MET A 311 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N MET A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 removed outlier: 4.607A pdb=" N ILE A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 369 removed outlier: 4.065A pdb=" N ASP A 363 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR A 366 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR A 369 " --> pdb=" O TYR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 393 through 405 Processing helix chain 'A' and resid 442 through 445 Processing helix chain 'A' and resid 481 through 492 Processing helix chain 'A' and resid 545 through 548 Processing helix chain 'B' and resid 75 through 81 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.787A pdb=" N ARG B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 216 through 230 removed outlier: 4.198A pdb=" N ILE B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 224 " --> pdb=" O MET B 220 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY B 229 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 230 " --> pdb=" O PHE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 257 through 270 Processing helix chain 'B' and resid 308 through 320 Proline residue: B 312 - end of helix removed outlier: 4.080A pdb=" N PHE B 315 " --> pdb=" O MET B 311 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 318 " --> pdb=" O ILE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 removed outlier: 4.237A pdb=" N ILE B 329 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE B 330 " --> pdb=" O ILE B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 393 through 405 removed outlier: 3.848A pdb=" N GLU B 397 " --> pdb=" O ARG B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 428 through 432 removed outlier: 4.133A pdb=" N GLY B 431 " --> pdb=" O ASP B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 445 No H-bonds generated for 'chain 'B' and resid 443 through 445' Processing helix chain 'B' and resid 481 through 492 removed outlier: 3.809A pdb=" N ARG B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 548 Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 75 through 81 removed outlier: 3.724A pdb=" N GLN C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 126 removed outlier: 3.823A pdb=" N VAL C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 152 Processing helix chain 'C' and resid 217 through 220 No H-bonds generated for 'chain 'C' and resid 217 through 220' Processing helix chain 'C' and resid 224 through 230 removed outlier: 3.908A pdb=" N GLY C 229 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU C 230 " --> pdb=" O PHE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 285 through 291 removed outlier: 3.903A pdb=" N VAL C 289 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLU C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR C 291 " --> pdb=" O ASP C 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 285 through 291' Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 308 through 320 Proline residue: C 312 - end of helix removed outlier: 4.368A pdb=" N PHE C 315 " --> pdb=" O MET C 311 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N MET C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 360 through 363 removed outlier: 4.154A pdb=" N ASP C 363 " --> pdb=" O GLU C 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 360 through 363' Processing helix chain 'C' and resid 385 through 388 No H-bonds generated for 'chain 'C' and resid 385 through 388' Processing helix chain 'C' and resid 393 through 404 removed outlier: 3.593A pdb=" N LEU C 404 " --> pdb=" O THR C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 445 No H-bonds generated for 'chain 'C' and resid 443 through 445' Processing helix chain 'C' and resid 481 through 494 removed outlier: 3.635A pdb=" N ARG C 494 " --> pdb=" O ALA C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 548 Processing helix chain 'D' and resid 69 through 72 No H-bonds generated for 'chain 'D' and resid 69 through 72' Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'D' and resid 116 through 126 Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 216 through 230 removed outlier: 3.972A pdb=" N ILE D 221 " --> pdb=" O GLN D 217 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE D 224 " --> pdb=" O MET D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 255 through 270 removed outlier: 3.589A pdb=" N ALA D 259 " --> pdb=" O PRO D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'D' and resid 308 through 319 Proline residue: D 312 - end of helix removed outlier: 4.333A pdb=" N PHE D 315 " --> pdb=" O MET D 311 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N MET D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 removed outlier: 3.981A pdb=" N ILE D 329 " --> pdb=" O PRO D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 368 removed outlier: 3.984A pdb=" N TYR D 366 " --> pdb=" O ASP D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 389 Processing helix chain 'D' and resid 393 through 405 Processing helix chain 'D' and resid 442 through 445 Processing helix chain 'D' and resid 481 through 492 Processing helix chain 'D' and resid 546 through 548 No H-bonds generated for 'chain 'D' and resid 546 through 548' Processing sheet with id= A, first strand: chain 'A' and resid 410 through 413 removed outlier: 7.307A pdb=" N CYS A 85 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG A 132 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU A 88 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 134 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 513 through 516 removed outlier: 3.793A pdb=" N LEU A 529 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 531 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 580 " --> pdb=" O VAL A 531 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 539 through 543 Processing sheet with id= D, first strand: chain 'B' and resid 49 through 51 Processing sheet with id= E, first strand: chain 'B' and resid 85 through 88 removed outlier: 6.275A pdb=" N ARG B 132 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU B 88 " --> pdb=" O ARG B 132 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE B 134 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 513 through 517 removed outlier: 3.858A pdb=" N CYS B 530 " --> pdb=" O TYR B 516 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 539 through 542 Processing sheet with id= H, first strand: chain 'C' and resid 411 through 413 removed outlier: 6.395A pdb=" N PHE C 49 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N CYS C 85 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL C 52 " --> pdb=" O CYS C 85 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TRP C 87 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG C 132 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU C 88 " --> pdb=" O ARG C 132 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE C 134 " --> pdb=" O LEU C 88 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 514 through 516 Processing sheet with id= J, first strand: chain 'C' and resid 539 through 542 Processing sheet with id= K, first strand: chain 'D' and resid 49 through 51 Processing sheet with id= L, first strand: chain 'D' and resid 85 through 88 removed outlier: 6.475A pdb=" N ARG D 132 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LEU D 88 " --> pdb=" O ARG D 132 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE D 134 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 137 " --> pdb=" O ARG D 236 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 513 through 517 Processing sheet with id= N, first strand: chain 'D' and resid 539 through 543 256 hydrogen bonds defined for protein. 696 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: 4.62 Time building geometry restraints manager: 7.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4691 1.33 - 1.45: 3896 1.45 - 1.57: 9797 1.57 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 18496 Sorted by residual: bond pdb=" N1 XVC B 602 " pdb=" N2 XVC B 602 " ideal model delta sigma weight residual 1.842 1.210 0.632 2.00e-02 2.50e+03 9.97e+02 bond pdb=" N1 XVC D 602 " pdb=" N2 XVC D 602 " ideal model delta sigma weight residual 1.842 1.211 0.631 2.00e-02 2.50e+03 9.96e+02 bond pdb=" N1 XVC A 602 " pdb=" N2 XVC A 602 " ideal model delta sigma weight residual 1.842 1.214 0.628 2.00e-02 2.50e+03 9.85e+02 bond pdb=" N1 XVC C 602 " pdb=" N2 XVC C 602 " ideal model delta sigma weight residual 1.842 1.214 0.628 2.00e-02 2.50e+03 9.85e+02 bond pdb=" N2 XVC B 602 " pdb=" N3 XVC B 602 " ideal model delta sigma weight residual 1.605 1.212 0.393 2.00e-02 2.50e+03 3.85e+02 ... (remaining 18491 not shown) Histogram of bond angle deviations from ideal: 99.58 - 115.65: 11570 115.65 - 131.72: 13602 131.72 - 147.79: 56 147.79 - 163.87: 0 163.87 - 179.94: 8 Bond angle restraints: 25236 Sorted by residual: angle pdb=" C6 XVC C 602 " pdb=" N1 XVC C 602 " pdb=" N2 XVC C 602 " ideal model delta sigma weight residual 121.95 179.94 -57.99 3.00e+00 1.11e-01 3.74e+02 angle pdb=" C6 XVC D 602 " pdb=" N1 XVC D 602 " pdb=" N2 XVC D 602 " ideal model delta sigma weight residual 121.95 178.65 -56.70 3.00e+00 1.11e-01 3.57e+02 angle pdb=" C6 XVC B 602 " pdb=" N1 XVC B 602 " pdb=" N2 XVC B 602 " ideal model delta sigma weight residual 121.95 178.62 -56.67 3.00e+00 1.11e-01 3.57e+02 angle pdb=" C6 XVC A 602 " pdb=" N1 XVC A 602 " pdb=" N2 XVC A 602 " ideal model delta sigma weight residual 121.95 176.23 -54.28 3.00e+00 1.11e-01 3.27e+02 angle pdb=" N ILE C 381 " pdb=" CA ILE C 381 " pdb=" C ILE C 381 " ideal model delta sigma weight residual 113.20 108.93 4.27 9.60e-01 1.09e+00 1.98e+01 ... (remaining 25231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.74: 10177 25.74 - 51.48: 605 51.48 - 77.23: 56 77.23 - 102.97: 20 102.97 - 128.71: 10 Dihedral angle restraints: 10868 sinusoidal: 4520 harmonic: 6348 Sorted by residual: dihedral pdb=" CA GLU B 361 " pdb=" C GLU B 361 " pdb=" N ARG B 362 " pdb=" CA ARG B 362 " ideal model delta harmonic sigma weight residual 180.00 155.82 24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA TYR B 516 " pdb=" C TYR B 516 " pdb=" N VAL B 517 " pdb=" CA VAL B 517 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA GLN A 217 " pdb=" C GLN A 217 " pdb=" N GLU A 218 " pdb=" CA GLU A 218 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 10865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2193 0.059 - 0.119: 410 0.119 - 0.178: 20 0.178 - 0.238: 2 0.238 - 0.297: 7 Chirality restraints: 2632 Sorted by residual: chirality pdb=" C5 XVC D 602 " pdb=" C4 XVC D 602 " pdb=" C6 XVC D 602 " pdb=" O5 XVC D 602 " both_signs ideal model delta sigma weight residual False -2.21 -2.51 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C5 XVC B 602 " pdb=" C4 XVC B 602 " pdb=" C6 XVC B 602 " pdb=" O5 XVC B 602 " both_signs ideal model delta sigma weight residual False -2.21 -2.49 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C1 GLC A 601 " pdb=" C2 GLC A 601 " pdb=" O1 GLC A 601 " pdb=" O5 GLC A 601 " both_signs ideal model delta sigma weight residual False -2.04 -2.31 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 2629 not shown) Planarity restraints: 3344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 191 " -0.055 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO C 192 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO C 192 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 192 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 254 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO B 255 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 255 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 255 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 166 " -0.010 2.00e-02 2.50e+03 1.22e-02 3.70e+00 pdb=" CG TRP A 166 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 166 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 166 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 166 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 166 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 166 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 166 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 166 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 166 " -0.001 2.00e-02 2.50e+03 ... (remaining 3341 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 86 2.35 - 2.98: 11291 2.98 - 3.62: 24608 3.62 - 4.26: 39400 4.26 - 4.90: 67724 Nonbonded interactions: 143109 Sorted by model distance: nonbonded pdb=" O PRO D 192 " pdb=" NH1 ARG D 195 " model vdw 1.708 2.520 nonbonded pdb=" OE2 GLU A 280 " pdb=" O3 XVC A 602 " model vdw 1.874 2.440 nonbonded pdb=" OD1 ASN B 253 " pdb=" OH TYR B 291 " model vdw 1.887 2.440 nonbonded pdb=" O ASN A 140 " pdb=" OD1 ASN A 140 " model vdw 1.932 3.040 nonbonded pdb=" CD GLU A 280 " pdb=" O3 XVC A 602 " model vdw 1.941 3.270 ... (remaining 143104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.020 Extract box with map and model: 12.620 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 49.100 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.140 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 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 : 0.013 0.632 18496 Z= 0.905 Angle : 0.939 57.986 25236 Z= 0.398 Chirality : 0.046 0.297 2632 Planarity : 0.005 0.085 3344 Dihedral : 16.240 128.710 6804 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 46.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 17.52 % Favored : 82.43 % Rotamer: Outliers : 0.05 % Allowed : 0.21 % Favored : 99.74 % 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: -3.66 (0.17), residues: 2180 helix: -1.41 (0.23), residues: 492 sheet: -2.74 (0.31), residues: 288 loop : -2.91 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 166 HIS 0.012 0.001 HIS D 307 PHE 0.016 0.001 PHE C 503 TYR 0.030 0.002 TYR A 101 ARG 0.004 0.000 ARG D 236 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 496 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.7269 (t) cc_final: 0.7005 (t) REVERT: A 556 LEU cc_start: 0.6091 (mt) cc_final: 0.5080 (mt) outliers start: 1 outliers final: 0 residues processed: 496 average time/residue: 0.3398 time to fit residues: 245.5433 Evaluate side-chains 299 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.0020 chunk 163 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 169 optimal weight: 0.0030 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 510 ASN C 146 HIS C 395 GLN C 443 ASN ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS D 187 ASN D 282 ASN D 283 GLN ** D 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 GLN D 470 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 18496 Z= 0.282 Angle : 0.778 10.272 25236 Z= 0.385 Chirality : 0.049 0.210 2632 Planarity : 0.006 0.090 3344 Dihedral : 7.859 97.159 2572 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.11 % Favored : 87.80 % Rotamer: Outliers : 2.80 % Allowed : 12.71 % Favored : 84.49 % 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: -3.46 (0.17), residues: 2180 helix: -1.41 (0.22), residues: 492 sheet: -2.73 (0.27), residues: 372 loop : -2.62 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 199 HIS 0.012 0.002 HIS B 200 PHE 0.020 0.002 PHE B 399 TYR 0.038 0.002 TYR D 173 ARG 0.011 0.001 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 347 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.6192 (tpp) cc_final: 0.5699 (tpp) REVERT: A 356 MET cc_start: 0.4383 (ppp) cc_final: 0.3433 (ppp) REVERT: D 187 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7509 (t0) outliers start: 53 outliers final: 30 residues processed: 380 average time/residue: 0.3061 time to fit residues: 176.4351 Evaluate side-chains 300 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 269 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 560 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 196 optimal weight: 0.8980 chunk 212 optimal weight: 0.2980 chunk 175 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 HIS A 140 ASN A 253 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 HIS ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN ** B 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS C 146 HIS ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS D 395 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.7367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 18496 Z= 0.374 Angle : 0.825 13.073 25236 Z= 0.419 Chirality : 0.051 0.358 2632 Planarity : 0.007 0.085 3344 Dihedral : 7.447 86.794 2572 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.95 % Favored : 84.82 % Rotamer: Outliers : 4.91 % Allowed : 15.98 % Favored : 79.11 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.78 (0.17), residues: 2180 helix: -1.79 (0.21), residues: 476 sheet: -2.67 (0.27), residues: 384 loop : -2.85 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP D 199 HIS 0.027 0.002 HIS B 307 PHE 0.030 0.003 PHE C 203 TYR 0.040 0.003 TYR A 198 ARG 0.028 0.001 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 334 time to evaluate : 1.900 Fit side-chains REVERT: A 127 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7990 (m170) REVERT: A 195 ARG cc_start: 0.7146 (mtm-85) cc_final: 0.6485 (mmt180) REVERT: A 356 MET cc_start: 0.4461 (ppp) cc_final: 0.3752 (ppp) REVERT: A 464 TYR cc_start: 0.8585 (m-10) cc_final: 0.8156 (m-80) REVERT: B 83 ILE cc_start: 0.7842 (mm) cc_final: 0.7509 (mm) REVERT: B 362 ARG cc_start: 0.4738 (ppt170) cc_final: 0.4354 (mmt-90) REVERT: C 396 ILE cc_start: 0.8957 (mm) cc_final: 0.8737 (mt) REVERT: D 374 ARG cc_start: 0.7341 (tpp-160) cc_final: 0.7084 (tpp-160) REVERT: D 381 ILE cc_start: 0.6786 (OUTLIER) cc_final: 0.6421 (mt) outliers start: 93 outliers final: 42 residues processed: 400 average time/residue: 0.2908 time to fit residues: 178.2194 Evaluate side-chains 290 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 246 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 544 ASP Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 560 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 208 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 577 HIS C 140 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS D 349 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.8255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18496 Z= 0.328 Angle : 0.741 12.723 25236 Z= 0.373 Chirality : 0.048 0.186 2632 Planarity : 0.006 0.058 3344 Dihedral : 7.234 89.852 2572 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.17 % Favored : 86.70 % Rotamer: Outliers : 4.06 % Allowed : 18.51 % Favored : 77.43 % 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: -3.69 (0.17), residues: 2180 helix: -1.53 (0.22), residues: 480 sheet: -2.80 (0.26), residues: 424 loop : -2.78 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 199 HIS 0.046 0.002 HIS A 127 PHE 0.025 0.002 PHE A 484 TYR 0.024 0.002 TYR D 173 ARG 0.005 0.001 ARG D 393 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 264 time to evaluate : 2.095 Fit side-chains REVERT: A 127 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7788 (m170) REVERT: A 144 GLU cc_start: 0.6598 (pp20) cc_final: 0.6235 (pp20) REVERT: A 195 ARG cc_start: 0.7687 (mtm-85) cc_final: 0.6943 (mmp-170) REVERT: A 262 LYS cc_start: 0.8102 (ttmt) cc_final: 0.7872 (mttp) REVERT: A 356 MET cc_start: 0.5268 (ppp) cc_final: 0.4578 (ppp) REVERT: A 464 TYR cc_start: 0.8721 (m-10) cc_final: 0.8477 (m-80) REVERT: A 472 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: A 561 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7431 (mm-30) REVERT: B 362 ARG cc_start: 0.4804 (ppt170) cc_final: 0.4355 (mmt-90) REVERT: B 422 ASP cc_start: 0.8629 (p0) cc_final: 0.8342 (p0) REVERT: B 472 GLU cc_start: 0.7418 (tp30) cc_final: 0.6949 (tt0) REVERT: B 551 TYR cc_start: 0.6549 (OUTLIER) cc_final: 0.5377 (m-80) REVERT: C 105 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: D 203 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7638 (t80) REVERT: D 347 ARG cc_start: 0.8520 (mmm160) cc_final: 0.8230 (mmm160) outliers start: 77 outliers final: 43 residues processed: 322 average time/residue: 0.2879 time to fit residues: 145.2944 Evaluate side-chains 278 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 230 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 551 TYR Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 560 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.1980 chunk 118 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 178 optimal weight: 2.9990 chunk 144 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 187 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 HIS A 140 ASN A 547 GLN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN C 146 HIS ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.8494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18496 Z= 0.193 Angle : 0.654 14.079 25236 Z= 0.324 Chirality : 0.045 0.174 2632 Planarity : 0.005 0.053 3344 Dihedral : 6.702 88.128 2572 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.42 % Favored : 88.53 % Rotamer: Outliers : 3.32 % Allowed : 20.31 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.17), residues: 2180 helix: -1.14 (0.23), residues: 492 sheet: -2.47 (0.28), residues: 368 loop : -2.54 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 199 HIS 0.013 0.001 HIS A 127 PHE 0.023 0.001 PHE A 484 TYR 0.018 0.001 TYR D 173 ARG 0.007 0.000 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 258 time to evaluate : 2.136 Fit side-chains REVERT: A 144 GLU cc_start: 0.6485 (pp20) cc_final: 0.6103 (pp20) REVERT: A 195 ARG cc_start: 0.7681 (mtm-85) cc_final: 0.6943 (mmp-170) REVERT: A 262 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7793 (mttp) REVERT: A 356 MET cc_start: 0.5270 (ppp) cc_final: 0.4674 (ppp) REVERT: A 464 TYR cc_start: 0.8584 (m-10) cc_final: 0.8353 (m-80) REVERT: A 472 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: B 154 ARG cc_start: 0.5861 (OUTLIER) cc_final: 0.5415 (ptt180) REVERT: B 233 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7272 (p0) REVERT: B 362 ARG cc_start: 0.5016 (ppt170) cc_final: 0.4280 (mmp80) REVERT: B 368 GLU cc_start: 0.6814 (mm-30) cc_final: 0.5788 (mm-30) REVERT: B 422 ASP cc_start: 0.8626 (p0) cc_final: 0.8317 (p0) REVERT: B 472 GLU cc_start: 0.7444 (tp30) cc_final: 0.6976 (tt0) REVERT: B 551 TYR cc_start: 0.6467 (OUTLIER) cc_final: 0.5259 (m-80) REVERT: C 220 MET cc_start: 0.8552 (mmm) cc_final: 0.8109 (mmp) REVERT: C 311 MET cc_start: 0.8728 (tmm) cc_final: 0.8432 (ttt) REVERT: C 346 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8002 (mt) REVERT: C 375 MET cc_start: 0.5979 (mtm) cc_final: 0.5633 (mtt) REVERT: D 187 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7288 (t0) REVERT: D 347 ARG cc_start: 0.8505 (mmm160) cc_final: 0.8267 (mmm160) REVERT: D 453 ARG cc_start: 0.8103 (mmt90) cc_final: 0.7521 (mmm-85) outliers start: 63 outliers final: 35 residues processed: 306 average time/residue: 0.2838 time to fit residues: 134.7537 Evaluate side-chains 275 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 234 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 551 TYR Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 544 ASP Chi-restraints excluded: chain D residue 560 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 208 optimal weight: 0.1980 chunk 173 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS A 547 GLN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 510 ASN B 532 ASN C 146 HIS ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.8768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18496 Z= 0.223 Angle : 0.652 14.896 25236 Z= 0.324 Chirality : 0.045 0.156 2632 Planarity : 0.005 0.061 3344 Dihedral : 6.618 87.336 2572 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.16 % Favored : 87.80 % Rotamer: Outliers : 4.17 % Allowed : 20.20 % Favored : 75.63 % 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: -3.12 (0.18), residues: 2180 helix: -1.06 (0.23), residues: 492 sheet: -2.35 (0.28), residues: 368 loop : -2.48 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 199 HIS 0.008 0.001 HIS A 200 PHE 0.026 0.001 PHE A 484 TYR 0.017 0.001 TYR D 173 ARG 0.007 0.000 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 251 time to evaluate : 1.995 Fit side-chains revert: symmetry clash REVERT: A 195 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7075 (mmp-170) REVERT: A 262 LYS cc_start: 0.8039 (ttmt) cc_final: 0.7837 (mttp) REVERT: A 356 MET cc_start: 0.5435 (ppp) cc_final: 0.4696 (ppp) REVERT: B 154 ARG cc_start: 0.5557 (OUTLIER) cc_final: 0.5196 (ptt180) REVERT: B 233 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7251 (p0) REVERT: B 341 GLN cc_start: 0.7437 (tp40) cc_final: 0.7024 (tp40) REVERT: B 362 ARG cc_start: 0.4858 (ppt170) cc_final: 0.4343 (mmp80) REVERT: B 368 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6058 (mm-30) REVERT: B 422 ASP cc_start: 0.8615 (p0) cc_final: 0.8302 (p0) REVERT: B 472 GLU cc_start: 0.7447 (tp30) cc_final: 0.6952 (tt0) REVERT: B 551 TYR cc_start: 0.6441 (OUTLIER) cc_final: 0.5147 (m-80) REVERT: C 311 MET cc_start: 0.8709 (tmm) cc_final: 0.8437 (ttt) REVERT: C 346 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7967 (mt) REVERT: C 375 MET cc_start: 0.6034 (mtm) cc_final: 0.5781 (mtt) REVERT: D 203 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7668 (t80) REVERT: D 453 ARG cc_start: 0.8228 (mmt90) cc_final: 0.7437 (mmt180) outliers start: 79 outliers final: 52 residues processed: 310 average time/residue: 0.2796 time to fit residues: 136.3668 Evaluate side-chains 293 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 236 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 551 TYR Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 560 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 119 optimal weight: 0.4980 chunk 152 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 208 optimal weight: 0.2980 chunk 130 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN C 146 HIS ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.9078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18496 Z= 0.208 Angle : 0.642 15.315 25236 Z= 0.320 Chirality : 0.045 0.156 2632 Planarity : 0.005 0.054 3344 Dihedral : 6.563 88.849 2572 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.38 % Favored : 88.58 % Rotamer: Outliers : 4.06 % Allowed : 20.52 % Favored : 75.42 % 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: -2.98 (0.18), residues: 2180 helix: -0.94 (0.23), residues: 484 sheet: -2.27 (0.28), residues: 368 loop : -2.39 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 199 HIS 0.006 0.001 HIS D 146 PHE 0.029 0.001 PHE B 345 TYR 0.016 0.001 TYR A 466 ARG 0.007 0.000 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 244 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.6356 (pp20) cc_final: 0.5984 (pp20) REVERT: A 195 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7069 (mmt180) REVERT: A 262 LYS cc_start: 0.8058 (ttmt) cc_final: 0.7725 (mttp) REVERT: A 356 MET cc_start: 0.5497 (ppp) cc_final: 0.4796 (ppp) REVERT: B 59 ASP cc_start: 0.8090 (t0) cc_final: 0.7785 (t70) REVERT: B 102 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6366 (t70) REVERT: B 154 ARG cc_start: 0.5636 (OUTLIER) cc_final: 0.5292 (ptt180) REVERT: B 233 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7320 (p0) REVERT: B 341 GLN cc_start: 0.7435 (tp40) cc_final: 0.7022 (tp40) REVERT: B 362 ARG cc_start: 0.5183 (ppt170) cc_final: 0.4281 (mmp80) REVERT: B 420 MET cc_start: 0.8257 (ttm) cc_final: 0.7663 (mtp) REVERT: B 422 ASP cc_start: 0.8625 (p0) cc_final: 0.8286 (p0) REVERT: B 551 TYR cc_start: 0.6364 (OUTLIER) cc_final: 0.5015 (m-80) REVERT: C 346 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7754 (mt) REVERT: C 375 MET cc_start: 0.6282 (mtm) cc_final: 0.5986 (mtt) REVERT: D 203 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7637 (t80) REVERT: D 453 ARG cc_start: 0.8214 (mmt90) cc_final: 0.7549 (mmm-85) outliers start: 77 outliers final: 52 residues processed: 302 average time/residue: 0.2767 time to fit residues: 130.7065 Evaluate side-chains 290 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 232 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 551 TYR Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 560 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 189 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 HIS C 146 HIS ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.9362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18496 Z= 0.220 Angle : 0.656 15.463 25236 Z= 0.325 Chirality : 0.045 0.182 2632 Planarity : 0.005 0.050 3344 Dihedral : 6.645 90.141 2572 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.34 % Favored : 87.61 % Rotamer: Outliers : 4.27 % Allowed : 20.62 % Favored : 75.11 % 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: -2.93 (0.18), residues: 2180 helix: -0.87 (0.23), residues: 488 sheet: -2.23 (0.28), residues: 368 loop : -2.37 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 199 HIS 0.014 0.001 HIS B 495 PHE 0.028 0.001 PHE B 345 TYR 0.015 0.001 TYR D 173 ARG 0.006 0.000 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 239 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.6680 (pp20) cc_final: 0.6237 (pp20) REVERT: A 195 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7137 (mmt180) REVERT: A 262 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7769 (mttp) REVERT: A 356 MET cc_start: 0.5449 (ppp) cc_final: 0.4681 (ppp) REVERT: A 414 TYR cc_start: 0.8741 (p90) cc_final: 0.8540 (p90) REVERT: B 59 ASP cc_start: 0.8115 (t0) cc_final: 0.7799 (t70) REVERT: B 102 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.6425 (t70) REVERT: B 154 ARG cc_start: 0.5695 (OUTLIER) cc_final: 0.5346 (ptt180) REVERT: B 341 GLN cc_start: 0.7496 (tp40) cc_final: 0.7102 (tp40) REVERT: B 362 ARG cc_start: 0.5116 (ppt170) cc_final: 0.4120 (mmp80) REVERT: B 420 MET cc_start: 0.8255 (ttm) cc_final: 0.7660 (mtp) REVERT: B 422 ASP cc_start: 0.8635 (p0) cc_final: 0.8268 (p0) REVERT: B 551 TYR cc_start: 0.6279 (OUTLIER) cc_final: 0.4973 (m-80) REVERT: C 346 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7468 (mt) REVERT: C 366 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6284 (t80) REVERT: C 375 MET cc_start: 0.6183 (mtm) cc_final: 0.5703 (mtt) REVERT: D 203 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7660 (t80) REVERT: D 453 ARG cc_start: 0.8216 (mmt90) cc_final: 0.7501 (mmm-85) REVERT: D 516 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.6473 (m-80) outliers start: 81 outliers final: 60 residues processed: 303 average time/residue: 0.2717 time to fit residues: 130.7970 Evaluate side-chains 295 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 228 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 551 TYR Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 560 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 183 optimal weight: 0.2980 chunk 193 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS A 547 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS D 510 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.9515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18496 Z= 0.211 Angle : 0.651 15.982 25236 Z= 0.323 Chirality : 0.045 0.186 2632 Planarity : 0.005 0.069 3344 Dihedral : 6.576 90.050 2572 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.74 % Favored : 88.21 % Rotamer: Outliers : 3.90 % Allowed : 20.83 % Favored : 75.26 % 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: -2.85 (0.18), residues: 2180 helix: -0.79 (0.23), residues: 488 sheet: -2.18 (0.28), residues: 368 loop : -2.33 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 199 HIS 0.005 0.001 HIS D 146 PHE 0.033 0.001 PHE B 345 TYR 0.016 0.001 TYR A 466 ARG 0.005 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 234 time to evaluate : 2.058 Fit side-chains revert: symmetry clash REVERT: A 144 GLU cc_start: 0.6468 (pp20) cc_final: 0.6054 (pp20) REVERT: A 195 ARG cc_start: 0.7884 (mtm-85) cc_final: 0.7217 (mmm160) REVERT: A 262 LYS cc_start: 0.8107 (ttmt) cc_final: 0.7761 (mttp) REVERT: A 356 MET cc_start: 0.5209 (ppp) cc_final: 0.4436 (ppp) REVERT: B 59 ASP cc_start: 0.8063 (t0) cc_final: 0.7731 (t70) REVERT: B 102 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.6574 (t70) REVERT: B 154 ARG cc_start: 0.5737 (OUTLIER) cc_final: 0.5377 (ptt180) REVERT: B 420 MET cc_start: 0.8269 (ttm) cc_final: 0.7673 (mtp) REVERT: B 422 ASP cc_start: 0.8581 (p0) cc_final: 0.8268 (p0) REVERT: B 551 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.4988 (m-80) REVERT: C 346 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7636 (mt) REVERT: C 366 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.6331 (t80) REVERT: C 375 MET cc_start: 0.6182 (mtm) cc_final: 0.5774 (mtt) REVERT: D 203 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7652 (t80) REVERT: D 360 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6364 (tm-30) REVERT: D 453 ARG cc_start: 0.8257 (mmt90) cc_final: 0.7551 (mmm-85) REVERT: D 516 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.6567 (m-80) outliers start: 74 outliers final: 58 residues processed: 291 average time/residue: 0.2563 time to fit residues: 119.0704 Evaluate side-chains 285 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 220 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 551 TYR Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 565 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 198 optimal weight: 0.0980 chunk 171 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 105 optimal weight: 0.1980 chunk 136 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.9724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18496 Z= 0.276 Angle : 0.687 15.741 25236 Z= 0.341 Chirality : 0.047 0.189 2632 Planarity : 0.005 0.067 3344 Dihedral : 6.799 92.770 2572 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.21 % Favored : 86.74 % Rotamer: Outliers : 3.69 % Allowed : 21.31 % Favored : 75.00 % 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: -2.93 (0.18), residues: 2180 helix: -0.82 (0.23), residues: 484 sheet: -2.25 (0.28), residues: 368 loop : -2.39 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 199 HIS 0.004 0.001 HIS D 146 PHE 0.016 0.002 PHE A 106 TYR 0.017 0.002 TYR A 198 ARG 0.005 0.000 ARG A 536 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 228 time to evaluate : 2.161 Fit side-chains revert: symmetry clash REVERT: A 195 ARG cc_start: 0.7956 (mtm-85) cc_final: 0.7234 (mmm160) REVERT: A 262 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7801 (mttm) REVERT: B 59 ASP cc_start: 0.8153 (t0) cc_final: 0.7828 (t70) REVERT: B 102 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.6739 (t70) REVERT: B 154 ARG cc_start: 0.5814 (OUTLIER) cc_final: 0.5507 (ptt180) REVERT: B 266 LYS cc_start: 0.8398 (tptm) cc_final: 0.8015 (ttpt) REVERT: B 422 ASP cc_start: 0.8659 (p0) cc_final: 0.8387 (p0) REVERT: B 551 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.4938 (m-80) REVERT: B 574 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6865 (mp) REVERT: C 366 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6340 (t80) REVERT: C 375 MET cc_start: 0.6174 (mtm) cc_final: 0.5854 (mtt) REVERT: D 203 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7696 (t80) REVERT: D 453 ARG cc_start: 0.8314 (mmt90) cc_final: 0.7579 (mmm-85) REVERT: D 516 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6677 (m-80) outliers start: 70 outliers final: 57 residues processed: 284 average time/residue: 0.2768 time to fit residues: 124.5229 Evaluate side-chains 289 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 225 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 551 TYR Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 560 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.0000 chunk 52 optimal weight: 0.0270 chunk 158 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 171 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 176 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 510 ASN C 146 HIS ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.155735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.142761 restraints weight = 24067.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.145883 restraints weight = 13896.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.148046 restraints weight = 9106.339| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.9828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18496 Z= 0.183 Angle : 0.644 16.003 25236 Z= 0.318 Chirality : 0.045 0.191 2632 Planarity : 0.005 0.066 3344 Dihedral : 6.534 91.822 2572 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.69 % Favored : 89.27 % Rotamer: Outliers : 3.59 % Allowed : 21.68 % Favored : 74.74 % 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: -2.76 (0.18), residues: 2180 helix: -0.67 (0.24), residues: 488 sheet: -2.14 (0.28), residues: 368 loop : -2.28 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 199 HIS 0.005 0.001 HIS A 146 PHE 0.017 0.001 PHE A 44 TYR 0.015 0.001 TYR A 466 ARG 0.005 0.000 ARG A 536 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3799.06 seconds wall clock time: 69 minutes 41.50 seconds (4181.50 seconds total)