Starting phenix.real_space_refine on Wed Mar 13 05:25:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ih5_35440/03_2024/8ih5_35440_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ih5_35440/03_2024/8ih5_35440.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ih5_35440/03_2024/8ih5_35440_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ih5_35440/03_2024/8ih5_35440_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ih5_35440/03_2024/8ih5_35440_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ih5_35440/03_2024/8ih5_35440.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ih5_35440/03_2024/8ih5_35440.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ih5_35440/03_2024/8ih5_35440_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ih5_35440/03_2024/8ih5_35440_updated.pdb" } resolution = 4.0 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= 0.006 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 32946 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 P 12 5.49 5 S 210 5.16 5 C 21034 2.51 5 N 5655 2.21 5 O 6215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ASP 105": "OD1" <-> "OD2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ASP 119": "OD1" <-> "OD2" Residue "F PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "F ASP 192": "OD1" <-> "OD2" Residue "F ASP 258": "OD1" <-> "OD2" Residue "F PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 344": "OD1" <-> "OD2" Residue "F ASP 384": "OD1" <-> "OD2" Residue "F PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 469": "OD1" <-> "OD2" Residue "F ASP 486": "OD1" <-> "OD2" Residue "F GLU 606": "OE1" <-> "OE2" Residue "F PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 614": "OD1" <-> "OD2" Residue "F ASP 615": "OD1" <-> "OD2" Residue "F ARG 622": "NH1" <-> "NH2" Residue "F GLU 640": "OE1" <-> "OE2" Residue "F TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 690": "NH1" <-> "NH2" Residue "F GLU 752": "OE1" <-> "OE2" Residue "F ASP 759": "OD1" <-> "OD2" Residue "A ASP 85": "OD1" <-> "OD2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A ASP 128": "OD1" <-> "OD2" Residue "A PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A ASP 207": "OD1" <-> "OD2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A ASP 271": "OD1" <-> "OD2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 459": "OD1" <-> "OD2" Residue "A ASP 469": "OD1" <-> "OD2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "A PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 570": "NH1" <-> "NH2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A GLU 655": "OE1" <-> "OE2" Residue "A TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 719": "NH1" <-> "NH2" Residue "A PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 765": "OD1" <-> "OD2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 219": "OD1" <-> "OD2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B ASP 459": "OD1" <-> "OD2" Residue "B TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 509": "OD1" <-> "OD2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 549": "OD1" <-> "OD2" Residue "B GLU 606": "OE1" <-> "OE2" Residue "B ARG 622": "NH1" <-> "NH2" Residue "B GLU 643": "OE1" <-> "OE2" Residue "B GLU 672": "OE1" <-> "OE2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "B ARG 730": "NH1" <-> "NH2" Residue "B GLU 752": "OE1" <-> "OE2" Residue "C ARG 114": "NH1" <-> "NH2" Residue "C ASP 142": "OD1" <-> "OD2" Residue "C PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ASP 213": "OD1" <-> "OD2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 219": "OD1" <-> "OD2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 240": "OD1" <-> "OD2" Residue "C ASP 324": "OD1" <-> "OD2" Residue "C TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 365": "OD1" <-> "OD2" Residue "C GLU 403": "OE1" <-> "OE2" Residue "C GLU 525": "OE1" <-> "OE2" Residue "C PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 585": "OD1" <-> "OD2" Residue "C ARG 622": "NH1" <-> "NH2" Residue "C GLU 655": "OE1" <-> "OE2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C ARG 719": "NH1" <-> "NH2" Residue "C ASP 755": "OD1" <-> "OD2" Residue "D ASP 85": "OD1" <-> "OD2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ASP 170": "OD1" <-> "OD2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D ASP 211": "OD1" <-> "OD2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "D ASP 219": "OD1" <-> "OD2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D ASP 298": "OD1" <-> "OD2" Residue "D ASP 341": "OD1" <-> "OD2" Residue "D TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 394": "OD1" <-> "OD2" Residue "D PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 549": "OD1" <-> "OD2" Residue "D ARG 622": "NH1" <-> "NH2" Residue "D GLU 636": "OE1" <-> "OE2" Residue "D TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D GLU 695": "OE1" <-> "OE2" Residue "D ASP 711": "OD1" <-> "OD2" Residue "D ARG 719": "NH1" <-> "NH2" Residue "D ASP 759": "OD1" <-> "OD2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "E ASP 119": "OD1" <-> "OD2" Residue "E PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 258": "OD1" <-> "OD2" Residue "E GLU 262": "OE1" <-> "OE2" Residue "E GLU 318": "OE1" <-> "OE2" Residue "E GLU 340": "OE1" <-> "OE2" Residue "E ASP 341": "OD1" <-> "OD2" Residue "E ASP 344": "OD1" <-> "OD2" Residue "E TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 417": "NH1" <-> "NH2" Residue "E ASP 427": "OD1" <-> "OD2" Residue "E ARG 445": "NH1" <-> "NH2" Residue "E GLU 463": "OE1" <-> "OE2" Residue "E TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 605": "OE1" <-> "OE2" Residue "E GLU 606": "OE1" <-> "OE2" Residue "E GLU 643": "OE1" <-> "OE2" Residue "E GLU 655": "OE1" <-> "OE2" Residue "E GLU 672": "OE1" <-> "OE2" Residue "E ARG 690": "NH1" <-> "NH2" Residue "E GLU 701": "OE1" <-> "OE2" Residue "E ASP 711": "OD1" <-> "OD2" Residue "E PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 759": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33126 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 5460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5460 Classifications: {'peptide': 682} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 657} Chain breaks: 1 Chain: "A" Number of atoms: 5508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5508 Classifications: {'peptide': 689} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 663} Chain: "B" Number of atoms: 5501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5501 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "C" Number of atoms: 5481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5481 Classifications: {'peptide': 684} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 658} Chain breaks: 1 Chain: "D" Number of atoms: 5501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5501 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "E" Number of atoms: 5501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5501 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'GRG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'GRG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'GRG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'GRG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'GRG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'GRG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.04, per 1000 atoms: 0.39 Number of scatterers: 33126 At special positions: 0 Unit cell: (160.5, 172.27, 162.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 210 16.00 P 12 15.00 O 6215 8.00 N 5655 7.00 C 21034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.23 Conformation dependent library (CDL) restraints added in 4.3 seconds 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7708 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 1 sheets defined 58.8% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.29 Creating SS restraints... Processing helix chain 'F' and resid 81 through 92 Processing helix chain 'F' and resid 103 through 110 Processing helix chain 'F' and resid 124 through 132 Processing helix chain 'F' and resid 149 through 162 removed outlier: 4.089A pdb=" N ALA F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 187 removed outlier: 4.033A pdb=" N GLU F 173 " --> pdb=" O THR F 169 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG F 174 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY F 175 " --> pdb=" O LYS F 171 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU F 176 " --> pdb=" O CYS F 172 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TRP F 184 " --> pdb=" O GLN F 180 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU F 186 " --> pdb=" O ASN F 182 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ALA F 187 " --> pdb=" O MET F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 211 Proline residue: F 203 - end of helix removed outlier: 4.313A pdb=" N ASP F 211 " --> pdb=" O ASP F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 236 removed outlier: 4.153A pdb=" N ILE F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 243 Processing helix chain 'F' and resid 248 through 251 removed outlier: 3.771A pdb=" N HIS F 251 " --> pdb=" O THR F 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 248 through 251' Processing helix chain 'F' and resid 261 through 267 removed outlier: 5.100A pdb=" N LYS F 266 " --> pdb=" O GLU F 262 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU F 267 " --> pdb=" O LYS F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 287 removed outlier: 3.624A pdb=" N GLN F 287 " --> pdb=" O THR F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 304 removed outlier: 3.908A pdb=" N PHE F 304 " --> pdb=" O ILE F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 327 Processing helix chain 'F' and resid 332 through 335 Processing helix chain 'F' and resid 338 through 349 removed outlier: 4.601A pdb=" N TYR F 345 " --> pdb=" O ASP F 341 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE F 346 " --> pdb=" O CYS F 342 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN F 349 " --> pdb=" O TYR F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 378 removed outlier: 4.079A pdb=" N ARG F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 391 Processing helix chain 'F' and resid 410 through 418 Processing helix chain 'F' and resid 429 through 443 removed outlier: 4.021A pdb=" N VAL F 435 " --> pdb=" O GLY F 431 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG F 438 " --> pdb=" O GLU F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 469 Processing helix chain 'F' and resid 472 through 474 No H-bonds generated for 'chain 'F' and resid 472 through 474' Processing helix chain 'F' and resid 477 through 484 Processing helix chain 'F' and resid 510 through 540 removed outlier: 3.997A pdb=" N ASN F 531 " --> pdb=" O ARG F 527 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP F 536 " --> pdb=" O GLY F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 562 Processing helix chain 'F' and resid 571 through 594 removed outlier: 3.614A pdb=" N GLY F 576 " --> pdb=" O ALA F 572 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA F 581 " --> pdb=" O TRP F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 610 removed outlier: 3.568A pdb=" N ILE F 608 " --> pdb=" O GLU F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 634 Processing helix chain 'F' and resid 643 through 656 Processing helix chain 'F' and resid 667 through 695 removed outlier: 3.768A pdb=" N GLU F 695 " --> pdb=" O VAL F 691 " (cutoff:3.500A) Processing helix chain 'F' and resid 700 through 721 removed outlier: 3.680A pdb=" N GLU F 704 " --> pdb=" O THR F 700 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU F 716 " --> pdb=" O LEU F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 730 through 747 removed outlier: 4.367A pdb=" N PHE F 736 " --> pdb=" O THR F 732 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU F 737 " --> pdb=" O ARG F 733 " (cutoff:3.500A) Processing helix chain 'F' and resid 751 through 761 Processing helix chain 'A' and resid 81 through 93 removed outlier: 3.673A pdb=" N SER A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 149 through 164 removed outlier: 3.741A pdb=" N SER A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 182 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 198 through 210 Proline residue: A 203 - end of helix Processing helix chain 'A' and resid 222 through 236 Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 278 through 287 Processing helix chain 'A' and resid 292 through 303 Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 339 through 349 removed outlier: 3.885A pdb=" N ASN A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 378 Processing helix chain 'A' and resid 385 through 391 removed outlier: 3.604A pdb=" N LEU A 388 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 418 Processing helix chain 'A' and resid 429 through 446 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 477 through 484 Processing helix chain 'A' and resid 510 through 540 removed outlier: 3.643A pdb=" N GLU A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 550 through 564 removed outlier: 3.899A pdb=" N ALA A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 594 Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'A' and resid 618 through 634 Processing helix chain 'A' and resid 643 through 658 Processing helix chain 'A' and resid 667 through 694 Processing helix chain 'A' and resid 701 through 722 removed outlier: 4.203A pdb=" N ILE A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 747 Processing helix chain 'A' and resid 751 through 762 Processing helix chain 'B' and resid 81 through 91 Processing helix chain 'B' and resid 103 through 109 Processing helix chain 'B' and resid 124 through 130 Processing helix chain 'B' and resid 148 through 165 removed outlier: 3.942A pdb=" N ALA B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER B 164 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TRP B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 188 removed outlier: 5.987A pdb=" N TRP B 184 " --> pdb=" O GLN B 180 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ALA B 187 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N HIS B 188 " --> pdb=" O TRP B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 Proline residue: B 203 - end of helix Processing helix chain 'B' and resid 221 through 236 removed outlier: 4.044A pdb=" N ALA B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 242 No H-bonds generated for 'chain 'B' and resid 239 through 242' Processing helix chain 'B' and resid 248 through 251 Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 278 through 287 Processing helix chain 'B' and resid 291 through 304 Processing helix chain 'B' and resid 315 through 327 Processing helix chain 'B' and resid 331 through 334 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 367 through 378 Processing helix chain 'B' and resid 385 through 391 removed outlier: 3.732A pdb=" N LYS B 390 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 391 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 429 through 446 Processing helix chain 'B' and resid 461 through 468 Processing helix chain 'B' and resid 472 through 474 No H-bonds generated for 'chain 'B' and resid 472 through 474' Processing helix chain 'B' and resid 477 through 484 Processing helix chain 'B' and resid 510 through 539 removed outlier: 3.702A pdb=" N ARG B 535 " --> pdb=" O ASN B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 564 removed outlier: 4.170A pdb=" N ALA B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 594 Processing helix chain 'B' and resid 605 through 610 removed outlier: 3.750A pdb=" N LEU B 610 " --> pdb=" O LEU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 634 Processing helix chain 'B' and resid 643 through 656 Processing helix chain 'B' and resid 667 through 695 Processing helix chain 'B' and resid 701 through 722 Processing helix chain 'B' and resid 730 through 748 Processing helix chain 'B' and resid 751 through 761 Processing helix chain 'C' and resid 81 through 91 Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 124 through 132 Processing helix chain 'C' and resid 148 through 165 removed outlier: 4.846A pdb=" N MET C 153 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TRP C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 185 removed outlier: 5.575A pdb=" N TRP C 184 " --> pdb=" O GLN C 180 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ARG C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 211 removed outlier: 3.569A pdb=" N ASP C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 236 Processing helix chain 'C' and resid 241 through 243 No H-bonds generated for 'chain 'C' and resid 241 through 243' Processing helix chain 'C' and resid 248 through 250 No H-bonds generated for 'chain 'C' and resid 248 through 250' Processing helix chain 'C' and resid 278 through 287 removed outlier: 4.312A pdb=" N THR C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 304 Processing helix chain 'C' and resid 317 through 329 Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 339 through 348 removed outlier: 4.638A pdb=" N ASP C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR C 345 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 379 removed outlier: 3.780A pdb=" N TYR C 379 " --> pdb=" O LEU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 391 removed outlier: 3.565A pdb=" N LYS C 390 " --> pdb=" O VAL C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 removed outlier: 4.849A pdb=" N TYR C 416 " --> pdb=" O MET C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 446 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 472 through 474 No H-bonds generated for 'chain 'C' and resid 472 through 474' Processing helix chain 'C' and resid 477 through 486 removed outlier: 4.458A pdb=" N ASP C 486 " --> pdb=" O ARG C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 539 Processing helix chain 'C' and resid 550 through 562 removed outlier: 4.391A pdb=" N ALA C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 594 Processing helix chain 'C' and resid 605 through 610 removed outlier: 4.065A pdb=" N ILE C 608 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 610 " --> pdb=" O LEU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 634 Processing helix chain 'C' and resid 643 through 658 Processing helix chain 'C' and resid 667 through 695 Processing helix chain 'C' and resid 700 through 722 removed outlier: 3.975A pdb=" N GLU C 713 " --> pdb=" O GLN C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 747 removed outlier: 4.007A pdb=" N ALA C 747 " --> pdb=" O PHE C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 761 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 103 through 110 Processing helix chain 'D' and resid 124 through 132 removed outlier: 4.005A pdb=" N GLN D 132 " --> pdb=" O ASP D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 165 removed outlier: 3.900A pdb=" N TRP D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 185 removed outlier: 3.665A pdb=" N PHE D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TRP D 184 " --> pdb=" O GLN D 180 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 211 Proline residue: D 203 - end of helix Processing helix chain 'D' and resid 221 through 236 removed outlier: 4.238A pdb=" N ALA D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 226 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 251 removed outlier: 3.866A pdb=" N HIS D 251 " --> pdb=" O THR D 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 248 through 251' Processing helix chain 'D' and resid 261 through 263 No H-bonds generated for 'chain 'D' and resid 261 through 263' Processing helix chain 'D' and resid 278 through 287 removed outlier: 3.559A pdb=" N GLN D 287 " --> pdb=" O THR D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 304 removed outlier: 3.763A pdb=" N PHE D 304 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 327 Processing helix chain 'D' and resid 332 through 335 Processing helix chain 'D' and resid 339 through 349 removed outlier: 3.858A pdb=" N ASP D 344 " --> pdb=" O GLU D 340 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR D 345 " --> pdb=" O ASP D 341 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN D 349 " --> pdb=" O TYR D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 378 removed outlier: 4.629A pdb=" N MET D 371 " --> pdb=" O ALA D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 391 Processing helix chain 'D' and resid 409 through 419 Processing helix chain 'D' and resid 428 through 446 Processing helix chain 'D' and resid 460 through 469 Processing helix chain 'D' and resid 472 through 474 No H-bonds generated for 'chain 'D' and resid 472 through 474' Processing helix chain 'D' and resid 477 through 484 Processing helix chain 'D' and resid 510 through 539 removed outlier: 3.773A pdb=" N GLU D 525 " --> pdb=" O ASN D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 562 removed outlier: 4.147A pdb=" N ALA D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 592 removed outlier: 4.207A pdb=" N GLY D 576 " --> pdb=" O ALA D 572 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER D 589 " --> pdb=" O ASP D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 610 removed outlier: 3.824A pdb=" N ILE D 608 " --> pdb=" O GLU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 634 Processing helix chain 'D' and resid 643 through 656 Processing helix chain 'D' and resid 667 through 695 Processing helix chain 'D' and resid 700 through 722 removed outlier: 3.808A pdb=" N GLU D 713 " --> pdb=" O GLN D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 745 Processing helix chain 'D' and resid 751 through 761 Processing helix chain 'E' and resid 82 through 91 Processing helix chain 'E' and resid 103 through 110 Processing helix chain 'E' and resid 124 through 132 Processing helix chain 'E' and resid 148 through 165 removed outlier: 4.339A pdb=" N ALA E 157 " --> pdb=" O MET E 153 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 188 removed outlier: 5.990A pdb=" N TRP E 184 " --> pdb=" O GLN E 180 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU E 186 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA E 187 " --> pdb=" O MET E 183 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N HIS E 188 " --> pdb=" O TRP E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 211 Proline residue: E 203 - end of helix removed outlier: 3.573A pdb=" N ASP E 211 " --> pdb=" O ASP E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 236 removed outlier: 3.758A pdb=" N ARG E 230 " --> pdb=" O ILE E 226 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLU E 231 " --> pdb=" O TYR E 227 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS E 233 " --> pdb=" O GLU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 242 No H-bonds generated for 'chain 'E' and resid 239 through 242' Processing helix chain 'E' and resid 248 through 251 Processing helix chain 'E' and resid 261 through 266 removed outlier: 3.912A pdb=" N LYS E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 287 removed outlier: 3.780A pdb=" N GLN E 287 " --> pdb=" O THR E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 303 Processing helix chain 'E' and resid 315 through 329 removed outlier: 4.228A pdb=" N ARG E 319 " --> pdb=" O ASP E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 348 removed outlier: 3.677A pdb=" N PHE E 335 " --> pdb=" O SER E 332 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR E 336 " --> pdb=" O ARG E 333 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N SER E 337 " --> pdb=" O HIS E 334 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU E 340 " --> pdb=" O SER E 337 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP E 344 " --> pdb=" O ASP E 341 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR E 345 " --> pdb=" O CYS E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 377 Processing helix chain 'E' and resid 385 through 391 removed outlier: 3.802A pdb=" N LYS E 390 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE E 391 " --> pdb=" O LEU E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 420 Processing helix chain 'E' and resid 429 through 446 removed outlier: 3.513A pdb=" N PHE E 436 " --> pdb=" O ARG E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 469 Processing helix chain 'E' and resid 472 through 474 No H-bonds generated for 'chain 'E' and resid 472 through 474' Processing helix chain 'E' and resid 477 through 484 Processing helix chain 'E' and resid 511 through 539 Processing helix chain 'E' and resid 550 through 562 removed outlier: 4.275A pdb=" N ALA E 561 " --> pdb=" O SER E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 594 removed outlier: 4.123A pdb=" N GLY E 576 " --> pdb=" O ALA E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 597 through 599 No H-bonds generated for 'chain 'E' and resid 597 through 599' Processing helix chain 'E' and resid 605 through 610 removed outlier: 3.685A pdb=" N ILE E 608 " --> pdb=" O GLU E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 634 removed outlier: 4.195A pdb=" N GLU E 623 " --> pdb=" O GLY E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 643 through 658 Processing helix chain 'E' and resid 667 through 695 removed outlier: 3.996A pdb=" N GLU E 695 " --> pdb=" O VAL E 691 " (cutoff:3.500A) Processing helix chain 'E' and resid 702 through 722 Processing helix chain 'E' and resid 730 through 746 Processing helix chain 'E' and resid 751 through 761 Processing sheet with id= A, first strand: chain 'F' and resid 494 through 496 removed outlier: 3.976A pdb=" N HIS F 501 " --> pdb=" O TRP F 495 " (cutoff:3.500A) 1556 hydrogen bonds defined for protein. 4491 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: 7.66 Time building geometry restraints manager: 11.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9556 1.33 - 1.45: 5520 1.45 - 1.57: 18448 1.57 - 1.69: 18 1.69 - 1.81: 312 Bond restraints: 33854 Sorted by residual: bond pdb=" O1 GRG E 801 " pdb=" PA GRG E 801 " ideal model delta sigma weight residual 1.665 1.597 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" O1 GRG C 801 " pdb=" PA GRG C 801 " ideal model delta sigma weight residual 1.665 1.598 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C1 GRG E 801 " pdb=" C2 GRG E 801 " ideal model delta sigma weight residual 1.551 1.484 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" O3A GRG C 801 " pdb=" PA GRG C 801 " ideal model delta sigma weight residual 1.656 1.591 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O3A GRG E 801 " pdb=" PA GRG E 801 " ideal model delta sigma weight residual 1.656 1.592 0.064 2.00e-02 2.50e+03 1.04e+01 ... (remaining 33849 not shown) Histogram of bond angle deviations from ideal: 97.97 - 105.22: 599 105.22 - 112.47: 16822 112.47 - 119.72: 11685 119.72 - 126.97: 16231 126.97 - 134.22: 469 Bond angle restraints: 45806 Sorted by residual: angle pdb=" C10 GRG B 801 " pdb=" C8 GRG B 801 " pdb=" C9 GRG B 801 " ideal model delta sigma weight residual 74.50 120.11 -45.61 3.00e+00 1.11e-01 2.31e+02 angle pdb=" C14 GRG D 801 " pdb=" C13 GRG D 801 " pdb=" C15 GRG D 801 " ideal model delta sigma weight residual 74.51 120.06 -45.55 3.00e+00 1.11e-01 2.31e+02 angle pdb=" C19 GRG D 801 " pdb=" C18 GRG D 801 " pdb=" C20 GRG D 801 " ideal model delta sigma weight residual 74.50 120.03 -45.53 3.00e+00 1.11e-01 2.30e+02 angle pdb=" C19 GRG F 801 " pdb=" C18 GRG F 801 " pdb=" C20 GRG F 801 " ideal model delta sigma weight residual 74.50 119.99 -45.49 3.00e+00 1.11e-01 2.30e+02 angle pdb=" C14 GRG F 801 " pdb=" C13 GRG F 801 " pdb=" C15 GRG F 801 " ideal model delta sigma weight residual 74.51 120.00 -45.49 3.00e+00 1.11e-01 2.30e+02 ... (remaining 45801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 18069 17.94 - 35.88: 1831 35.88 - 53.82: 314 53.82 - 71.76: 68 71.76 - 89.70: 30 Dihedral angle restraints: 20312 sinusoidal: 8361 harmonic: 11951 Sorted by residual: dihedral pdb=" C ASP F 365 " pdb=" N ASP F 365 " pdb=" CA ASP F 365 " pdb=" CB ASP F 365 " ideal model delta harmonic sigma weight residual -122.60 -103.51 -19.09 0 2.50e+00 1.60e-01 5.83e+01 dihedral pdb=" CA PHE A 398 " pdb=" C PHE A 398 " pdb=" N CYS A 399 " pdb=" CA CYS A 399 " ideal model delta harmonic sigma weight residual 180.00 157.39 22.61 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA PHE A 146 " pdb=" C PHE A 146 " pdb=" N MET A 147 " pdb=" CA MET A 147 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 20309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 4927 0.117 - 0.234: 42 0.234 - 0.351: 0 0.351 - 0.468: 0 0.468 - 0.585: 1 Chirality restraints: 4970 Sorted by residual: chirality pdb=" CA ASP F 365 " pdb=" N ASP F 365 " pdb=" C ASP F 365 " pdb=" CB ASP F 365 " both_signs ideal model delta sigma weight residual False 2.51 3.10 -0.59 2.00e-01 2.50e+01 8.56e+00 chirality pdb=" CA VAL F 363 " pdb=" N VAL F 363 " pdb=" C VAL F 363 " pdb=" CB VAL F 363 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.95e-01 chirality pdb=" CA VAL F 499 " pdb=" N VAL F 499 " pdb=" C VAL F 499 " pdb=" CB VAL F 499 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 4967 not shown) Planarity restraints: 5882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 193 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.59e+00 pdb=" C TRP A 193 " -0.037 2.00e-02 2.50e+03 pdb=" O TRP A 193 " 0.014 2.00e-02 2.50e+03 pdb=" N MET A 194 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 577 " 0.008 2.00e-02 2.50e+03 1.15e-02 3.29e+00 pdb=" CG TRP F 577 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP F 577 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP F 577 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 577 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP F 577 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 577 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 577 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 577 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 577 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 216 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO E 217 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 217 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 217 " 0.020 5.00e-02 4.00e+02 ... (remaining 5879 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 2 2.18 - 2.86: 11434 2.86 - 3.54: 46053 3.54 - 4.22: 67811 4.22 - 4.90: 121380 Nonbonded interactions: 246680 Sorted by model distance: nonbonded pdb=" O ALA F 356 " pdb=" OD2 ASP F 368 " model vdw 1.496 3.040 nonbonded pdb=" OH TYR A 488 " pdb=" O PHE A 506 " model vdw 2.163 2.440 nonbonded pdb=" OE1 GLU C 254 " pdb=" OG1 THR C 283 " model vdw 2.198 2.440 nonbonded pdb=" OG1 THR A 351 " pdb=" O GLY A 354 " model vdw 2.228 2.440 nonbonded pdb=" O TRP A 129 " pdb=" ND2 ASN A 133 " model vdw 2.246 2.520 ... (remaining 246675 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 80 through 116 or resid 121 through 544 or resid 551 throu \ gh 767 or resid 801)) selection = (chain 'B' and (resid 80 through 116 or resid 121 through 544 or resid 551 throu \ gh 767 or resid 801)) selection = (chain 'C' and (resid 80 through 544 or resid 551 through 767 or resid 801)) selection = (chain 'D' and (resid 80 through 116 or resid 121 through 544 or resid 551 throu \ gh 767 or resid 801)) selection = (chain 'E' and (resid 80 through 116 or resid 121 through 544 or resid 551 throu \ gh 767 or resid 801)) selection = (chain 'F' and (resid 80 through 116 or resid 121 through 767 or resid 801)) } 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.300 Construct map_model_manager: 0.020 Extract box with map and model: 5.770 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 64.390 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 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 : 0.004 0.068 33854 Z= 0.258 Angle : 1.129 45.612 45806 Z= 0.479 Chirality : 0.040 0.585 4970 Planarity : 0.003 0.037 5882 Dihedral : 14.757 89.704 12604 Min Nonbonded Distance : 1.496 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.34 % Allowed : 4.14 % Favored : 95.52 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.05 % 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: -2.34 (0.12), residues: 4103 helix: -0.54 (0.10), residues: 2533 sheet: None (None), residues: 0 loop : -3.29 (0.13), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 577 HIS 0.003 0.001 HIS B 738 PHE 0.013 0.001 PHE B 178 TYR 0.014 0.001 TYR F 617 ARG 0.004 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 443 time to evaluate : 2.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 294 PHE cc_start: 0.7264 (t80) cc_final: 0.6803 (t80) REVERT: B 365 ASP cc_start: 0.8029 (p0) cc_final: 0.7742 (p0) REVERT: B 392 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7222 (tt0) REVERT: B 393 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7893 (tptm) REVERT: C 147 MET cc_start: 0.7473 (ttt) cc_final: 0.7174 (ttt) REVERT: C 190 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7362 (mt-10) REVERT: C 417 ARG cc_start: 0.8882 (ttp80) cc_final: 0.8658 (ttp80) REVERT: C 525 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7561 (tp30) REVERT: C 605 GLU cc_start: 0.8267 (tm-30) cc_final: 0.8046 (tm-30) REVERT: D 176 LEU cc_start: 0.8156 (tt) cc_final: 0.7944 (tt) REVERT: E 353 ASP cc_start: 0.6422 (t0) cc_final: 0.5874 (t0) REVERT: E 448 ASN cc_start: 0.7598 (t0) cc_final: 0.7392 (t0) REVERT: E 503 MET cc_start: 0.8576 (mtp) cc_final: 0.8239 (mtp) REVERT: E 530 LEU cc_start: 0.9097 (tp) cc_final: 0.8852 (tp) REVERT: E 632 TRP cc_start: 0.8690 (OUTLIER) cc_final: 0.7733 (t60) outliers start: 12 outliers final: 2 residues processed: 454 average time/residue: 0.3380 time to fit residues: 254.0525 Evaluate side-chains 318 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 313 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain E residue 632 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 8.9990 chunk 309 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 319 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 238 optimal weight: 0.0670 chunk 370 optimal weight: 6.9990 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 133 ASN F 305 ASN F 349 ASN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 678 GLN F 708 GLN F 757 HIS A 122 GLN A 243 HIS ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 GLN A 715 GLN A 764 GLN B 166 ASN B 188 HIS B 243 HIS B 286 GLN ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 531 ASN B 675 GLN B 696 ASN B 708 GLN C 182 ASN C 251 HIS C 405 ASN C 551 GLN C 564 ASN C 603 ASN C 675 GLN C 715 GLN C 764 GLN D 122 GLN D 243 HIS D 564 ASN D 675 GLN D 708 GLN E 180 GLN ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 420 GLN E 541 ASN E 599 ASN E 709 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33854 Z= 0.263 Angle : 0.907 22.914 45806 Z= 0.366 Chirality : 0.041 0.215 4970 Planarity : 0.004 0.049 5882 Dihedral : 6.462 59.024 4666 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.65 % Allowed : 11.62 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.13), residues: 4103 helix: 0.45 (0.11), residues: 2541 sheet: -2.94 (1.79), residues: 5 loop : -2.93 (0.13), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 165 HIS 0.004 0.001 HIS D 334 PHE 0.015 0.001 PHE B 198 TYR 0.023 0.001 TYR A 227 ARG 0.007 0.000 ARG D 593 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 328 time to evaluate : 2.854 Fit side-chains revert: symmetry clash REVERT: F 503 MET cc_start: 0.8868 (mmm) cc_final: 0.8545 (mmm) REVERT: F 555 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6856 (tmm) REVERT: B 365 ASP cc_start: 0.7842 (p0) cc_final: 0.7382 (p0) REVERT: B 371 MET cc_start: 0.8399 (tpp) cc_final: 0.8122 (tpp) REVERT: C 190 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7318 (mt-10) REVERT: C 412 MET cc_start: 0.7853 (mmm) cc_final: 0.7264 (mmm) REVERT: C 525 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7584 (tp30) REVERT: C 605 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7749 (tm-30) REVERT: E 353 ASP cc_start: 0.6482 (t0) cc_final: 0.5942 (t0) REVERT: E 448 ASN cc_start: 0.7825 (t0) cc_final: 0.7604 (t0) REVERT: E 503 MET cc_start: 0.8591 (mtp) cc_final: 0.8236 (mtp) REVERT: E 530 LEU cc_start: 0.9165 (tp) cc_final: 0.8880 (tp) REVERT: E 632 TRP cc_start: 0.8929 (OUTLIER) cc_final: 0.7557 (t60) outliers start: 59 outliers final: 30 residues processed: 367 average time/residue: 0.3255 time to fit residues: 204.6820 Evaluate side-chains 336 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 304 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 555 MET Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 551 GLN Chi-restraints excluded: chain E residue 632 TRP Chi-restraints excluded: chain E residue 691 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 0.0020 chunk 114 optimal weight: 7.9990 chunk 308 optimal weight: 3.9990 chunk 252 optimal weight: 6.9990 chunk 102 optimal weight: 0.2980 chunk 371 optimal weight: 8.9990 chunk 400 optimal weight: 0.9990 chunk 330 optimal weight: 7.9990 chunk 368 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 297 optimal weight: 1.9990 overall best weight: 1.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS A 564 ASN ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 GLN ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33854 Z= 0.167 Angle : 0.873 21.945 45806 Z= 0.344 Chirality : 0.039 0.227 4970 Planarity : 0.003 0.050 5882 Dihedral : 6.082 59.626 4657 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.74 % Allowed : 14.03 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 4103 helix: 0.93 (0.11), residues: 2550 sheet: -2.62 (2.05), residues: 5 loop : -2.66 (0.14), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP F 165 HIS 0.003 0.000 HIS F 501 PHE 0.014 0.001 PHE B 198 TYR 0.015 0.001 TYR A 227 ARG 0.006 0.000 ARG D 593 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 319 time to evaluate : 2.817 Fit side-chains revert: symmetry clash REVERT: F 503 MET cc_start: 0.8847 (mmm) cc_final: 0.8510 (mmm) REVERT: F 555 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6790 (tmm) REVERT: B 233 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7521 (ttmm) REVERT: B 294 PHE cc_start: 0.7253 (t80) cc_final: 0.7006 (t80) REVERT: B 318 GLU cc_start: 0.8462 (tp30) cc_final: 0.8201 (tp30) REVERT: B 365 ASP cc_start: 0.7746 (p0) cc_final: 0.7336 (p0) REVERT: B 538 LEU cc_start: 0.8878 (tp) cc_final: 0.8668 (tp) REVERT: B 632 TRP cc_start: 0.9067 (OUTLIER) cc_final: 0.7084 (t60) REVERT: C 190 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7359 (mt-10) REVERT: C 412 MET cc_start: 0.7848 (mmm) cc_final: 0.7313 (mmm) REVERT: C 525 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7504 (tp30) REVERT: C 605 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7673 (tm-30) REVERT: E 448 ASN cc_start: 0.7838 (t0) cc_final: 0.7600 (t0) REVERT: E 503 MET cc_start: 0.8561 (mtp) cc_final: 0.8180 (mtp) outliers start: 62 outliers final: 45 residues processed: 360 average time/residue: 0.3131 time to fit residues: 194.6754 Evaluate side-chains 347 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 299 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 555 MET Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 632 TRP Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 551 GLN Chi-restraints excluded: chain E residue 632 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 0.2980 chunk 279 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 chunk 372 optimal weight: 5.9990 chunk 394 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 353 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 ASN B 305 ASN ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33854 Z= 0.189 Angle : 0.874 21.882 45806 Z= 0.344 Chirality : 0.039 0.223 4970 Planarity : 0.003 0.051 5882 Dihedral : 5.893 59.659 4657 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.13 % Allowed : 15.40 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 4103 helix: 1.16 (0.11), residues: 2537 sheet: -2.06 (2.70), residues: 5 loop : -2.44 (0.14), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 577 HIS 0.003 0.000 HIS D 334 PHE 0.013 0.001 PHE B 198 TYR 0.016 0.001 TYR F 484 ARG 0.005 0.000 ARG E 592 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 313 time to evaluate : 2.836 Fit side-chains revert: symmetry clash REVERT: F 147 MET cc_start: 0.6831 (tmm) cc_final: 0.6616 (tmm) REVERT: F 503 MET cc_start: 0.8846 (mmm) cc_final: 0.8568 (mmm) REVERT: F 555 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6795 (tmm) REVERT: A 748 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: B 365 ASP cc_start: 0.7710 (p0) cc_final: 0.7373 (p0) REVERT: B 632 TRP cc_start: 0.9070 (OUTLIER) cc_final: 0.7086 (t60) REVERT: C 190 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7325 (mt-10) REVERT: C 412 MET cc_start: 0.7798 (mmm) cc_final: 0.7345 (mmm) REVERT: C 525 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7599 (tp30) REVERT: C 605 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7779 (tm-30) REVERT: E 448 ASN cc_start: 0.7838 (t0) cc_final: 0.7588 (t0) REVERT: E 503 MET cc_start: 0.8615 (mtp) cc_final: 0.8218 (mtp) outliers start: 76 outliers final: 48 residues processed: 366 average time/residue: 0.3093 time to fit residues: 196.0196 Evaluate side-chains 343 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 292 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 555 MET Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 748 TYR Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 632 TRP Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 551 GLN Chi-restraints excluded: chain E residue 632 TRP Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 691 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 2.9990 chunk 223 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 336 optimal weight: 3.9990 chunk 272 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 353 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 ASN B 709 GLN ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 33854 Z= 0.318 Angle : 0.919 22.032 45806 Z= 0.373 Chirality : 0.042 0.231 4970 Planarity : 0.004 0.052 5882 Dihedral : 5.994 59.705 4653 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.66 % Allowed : 16.38 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 4103 helix: 1.05 (0.11), residues: 2552 sheet: -1.92 (2.72), residues: 5 loop : -2.45 (0.14), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 577 HIS 0.004 0.001 HIS D 334 PHE 0.018 0.001 PHE B 506 TYR 0.024 0.002 TYR F 484 ARG 0.004 0.000 ARG D 593 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 298 time to evaluate : 2.854 Fit side-chains revert: symmetry clash REVERT: F 111 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7800 (pp) REVERT: F 147 MET cc_start: 0.6908 (tmm) cc_final: 0.6634 (tmm) REVERT: F 555 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6873 (tmm) REVERT: A 748 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: B 365 ASP cc_start: 0.7851 (p0) cc_final: 0.7458 (p0) REVERT: B 629 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8987 (mp) REVERT: C 148 MET cc_start: 0.6954 (mpp) cc_final: 0.6741 (mmt) REVERT: C 176 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8028 (tt) REVERT: C 190 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7309 (mt-10) REVERT: C 412 MET cc_start: 0.7947 (mmm) cc_final: 0.7328 (mmm) REVERT: C 525 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7708 (tp30) REVERT: C 605 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8091 (tm-30) REVERT: E 353 ASP cc_start: 0.6513 (t0) cc_final: 0.6092 (t0) REVERT: E 448 ASN cc_start: 0.7889 (t0) cc_final: 0.7684 (t0) REVERT: E 503 MET cc_start: 0.8604 (mtp) cc_final: 0.8171 (mtp) outliers start: 95 outliers final: 68 residues processed: 366 average time/residue: 0.2958 time to fit residues: 189.8246 Evaluate side-chains 363 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 290 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 357 HIS Chi-restraints excluded: chain F residue 449 ARG Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 555 MET Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain F residue 712 LEU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 748 TYR Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 551 GLN Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 632 TRP Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 664 THR Chi-restraints excluded: chain E residue 691 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 4.9990 chunk 355 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 231 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 394 optimal weight: 0.9980 chunk 327 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS D 188 HIS ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 33854 Z= 0.140 Angle : 0.869 21.594 45806 Z= 0.339 Chirality : 0.038 0.232 4970 Planarity : 0.003 0.053 5882 Dihedral : 5.677 58.315 4653 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.30 % Allowed : 17.53 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 4103 helix: 1.37 (0.11), residues: 2535 sheet: -1.27 (2.53), residues: 5 loop : -2.25 (0.14), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 454 HIS 0.003 0.000 HIS F 501 PHE 0.014 0.001 PHE B 198 TYR 0.017 0.001 TYR F 484 ARG 0.004 0.000 ARG D 593 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 325 time to evaluate : 2.836 Fit side-chains revert: symmetry clash REVERT: F 111 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7767 (pp) REVERT: F 555 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6745 (tmm) REVERT: B 365 ASP cc_start: 0.7659 (p0) cc_final: 0.7313 (p0) REVERT: B 629 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8813 (mp) REVERT: B 632 TRP cc_start: 0.9019 (OUTLIER) cc_final: 0.6945 (t60) REVERT: C 525 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7635 (tp30) REVERT: C 605 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7760 (tm-30) REVERT: D 147 MET cc_start: 0.8236 (ttt) cc_final: 0.8035 (ttt) REVERT: E 503 MET cc_start: 0.8551 (mtp) cc_final: 0.8092 (mtp) REVERT: E 643 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8111 (mm-30) outliers start: 82 outliers final: 47 residues processed: 386 average time/residue: 0.3173 time to fit residues: 212.6351 Evaluate side-chains 349 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 298 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 555 MET Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 632 TRP Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 312 TYR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 551 GLN Chi-restraints excluded: chain E residue 632 TRP Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 691 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 224 optimal weight: 0.0170 chunk 288 optimal weight: 0.3980 chunk 223 optimal weight: 4.9990 chunk 332 optimal weight: 3.9990 chunk 220 optimal weight: 8.9990 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 0.6980 chunk 239 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 GLN ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33854 Z= 0.142 Angle : 0.869 21.556 45806 Z= 0.338 Chirality : 0.038 0.217 4970 Planarity : 0.003 0.052 5882 Dihedral : 5.540 59.608 4653 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.82 % Allowed : 18.73 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 4103 helix: 1.47 (0.11), residues: 2538 sheet: -0.70 (2.43), residues: 5 loop : -2.16 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 184 HIS 0.004 0.000 HIS A 401 PHE 0.014 0.001 PHE B 198 TYR 0.027 0.001 TYR F 484 ARG 0.005 0.000 ARG E 592 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 320 time to evaluate : 2.875 Fit side-chains revert: symmetry clash REVERT: F 111 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7703 (pp) REVERT: F 450 MET cc_start: 0.7253 (mmm) cc_final: 0.7024 (tpt) REVERT: F 555 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6763 (tmm) REVERT: F 655 GLU cc_start: 0.7802 (tp30) cc_final: 0.7513 (tp30) REVERT: B 365 ASP cc_start: 0.7652 (p0) cc_final: 0.7334 (p0) REVERT: B 629 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8797 (mp) REVERT: B 632 TRP cc_start: 0.9022 (OUTLIER) cc_final: 0.7015 (t60) REVERT: C 214 LEU cc_start: 0.7489 (mp) cc_final: 0.7125 (mp) REVERT: C 417 ARG cc_start: 0.8896 (ttp80) cc_final: 0.8589 (ttp80) REVERT: C 525 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7576 (tp30) REVERT: C 605 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7738 (tm-30) REVERT: C 632 TRP cc_start: 0.8660 (OUTLIER) cc_final: 0.7776 (t60) outliers start: 65 outliers final: 49 residues processed: 370 average time/residue: 0.3058 time to fit residues: 196.2533 Evaluate side-chains 348 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 294 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 357 HIS Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 555 MET Chi-restraints excluded: chain F residue 670 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 632 TRP Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain E residue 312 TYR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 413 TYR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 551 GLN Chi-restraints excluded: chain E residue 632 TRP Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 691 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 250 optimal weight: 8.9990 chunk 267 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 309 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 33854 Z= 0.310 Angle : 0.929 21.877 45806 Z= 0.374 Chirality : 0.042 0.215 4970 Planarity : 0.004 0.053 5882 Dihedral : 5.771 59.949 4653 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.24 % Allowed : 18.84 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 4103 helix: 1.31 (0.11), residues: 2543 sheet: -0.89 (2.38), residues: 5 loop : -2.19 (0.14), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 184 HIS 0.004 0.001 HIS D 334 PHE 0.025 0.001 PHE C 146 TYR 0.027 0.002 TYR F 484 ARG 0.004 0.000 ARG E 592 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 291 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 111 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7771 (pp) REVERT: F 147 MET cc_start: 0.6804 (tmm) cc_final: 0.6511 (tmm) REVERT: F 555 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6841 (tmm) REVERT: B 365 ASP cc_start: 0.7789 (p0) cc_final: 0.7424 (p0) REVERT: B 629 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8944 (mp) REVERT: C 605 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8072 (tm-30) REVERT: E 353 ASP cc_start: 0.6508 (t0) cc_final: 0.6114 (t0) outliers start: 80 outliers final: 66 residues processed: 352 average time/residue: 0.3029 time to fit residues: 186.1803 Evaluate side-chains 352 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 283 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 357 HIS Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 472 TRP Chi-restraints excluded: chain F residue 555 MET Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain F residue 670 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 632 TRP Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 478 ARG Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain E residue 312 TYR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 413 TYR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 551 GLN Chi-restraints excluded: chain E residue 632 TRP Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 664 THR Chi-restraints excluded: chain E residue 691 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 3.9990 chunk 376 optimal weight: 5.9990 chunk 343 optimal weight: 0.8980 chunk 366 optimal weight: 4.9990 chunk 220 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 331 optimal weight: 0.8980 chunk 346 optimal weight: 8.9990 chunk 365 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33854 Z= 0.228 Angle : 0.906 21.817 45806 Z= 0.359 Chirality : 0.040 0.214 4970 Planarity : 0.003 0.052 5882 Dihedral : 5.760 59.553 4653 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.99 % Allowed : 19.48 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 4103 helix: 1.38 (0.11), residues: 2532 sheet: -0.84 (2.43), residues: 5 loop : -2.12 (0.14), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 184 HIS 0.003 0.001 HIS D 334 PHE 0.028 0.001 PHE C 146 TYR 0.023 0.001 TYR F 484 ARG 0.004 0.000 ARG E 592 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 294 time to evaluate : 2.900 Fit side-chains revert: symmetry clash REVERT: F 111 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7760 (pp) REVERT: F 147 MET cc_start: 0.6582 (tmm) cc_final: 0.6226 (tmm) REVERT: F 218 TYR cc_start: 0.5865 (m-10) cc_final: 0.5520 (m-10) REVERT: F 450 MET cc_start: 0.7309 (mmm) cc_final: 0.7043 (tpt) REVERT: F 555 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6860 (tmm) REVERT: A 503 MET cc_start: 0.8376 (mtp) cc_final: 0.7981 (mtp) REVERT: B 258 ASP cc_start: 0.5877 (t70) cc_final: 0.5623 (t0) REVERT: B 365 ASP cc_start: 0.7716 (p0) cc_final: 0.7363 (p0) REVERT: B 629 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8874 (mp) REVERT: B 632 TRP cc_start: 0.9136 (OUTLIER) cc_final: 0.6849 (t60) REVERT: C 605 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8050 (tm-30) REVERT: E 353 ASP cc_start: 0.6503 (t0) cc_final: 0.6120 (t0) REVERT: E 643 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8146 (mm-30) outliers start: 71 outliers final: 61 residues processed: 348 average time/residue: 0.3055 time to fit residues: 186.0503 Evaluate side-chains 353 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 288 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 357 HIS Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 555 MET Chi-restraints excluded: chain F residue 670 LEU Chi-restraints excluded: chain F residue 712 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 632 TRP Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 413 TYR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 551 GLN Chi-restraints excluded: chain E residue 632 TRP Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 691 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 10.0000 chunk 387 optimal weight: 0.9980 chunk 236 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 269 optimal weight: 0.6980 chunk 406 optimal weight: 0.4980 chunk 374 optimal weight: 1.9990 chunk 323 optimal weight: 5.9990 chunk 33 optimal weight: 0.1980 chunk 250 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 33854 Z= 0.138 Angle : 0.882 21.500 45806 Z= 0.343 Chirality : 0.038 0.215 4970 Planarity : 0.003 0.053 5882 Dihedral : 5.517 59.258 4653 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.62 % Allowed : 20.07 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.14), residues: 4103 helix: 1.58 (0.11), residues: 2527 sheet: -1.04 (2.37), residues: 5 loop : -2.01 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 184 HIS 0.003 0.000 HIS A 501 PHE 0.017 0.001 PHE C 146 TYR 0.023 0.001 TYR F 484 ARG 0.004 0.000 ARG E 592 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8206 Ramachandran restraints generated. 4103 Oldfield, 0 Emsley, 4103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 317 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 111 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7795 (pp) REVERT: F 218 TYR cc_start: 0.6017 (m-10) cc_final: 0.5669 (m-10) REVERT: F 555 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6770 (tmm) REVERT: A 503 MET cc_start: 0.8262 (mtp) cc_final: 0.7840 (mtp) REVERT: B 258 ASP cc_start: 0.5963 (t70) cc_final: 0.5577 (t0) REVERT: B 365 ASP cc_start: 0.7590 (p0) cc_final: 0.7265 (p0) REVERT: B 629 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8789 (mp) REVERT: B 632 TRP cc_start: 0.8996 (OUTLIER) cc_final: 0.7012 (t60) REVERT: C 605 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7726 (tm-30) REVERT: C 632 TRP cc_start: 0.8634 (OUTLIER) cc_final: 0.7734 (t60) REVERT: D 555 MET cc_start: 0.8489 (mmm) cc_final: 0.8172 (tpp) REVERT: E 643 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7926 (mm-30) outliers start: 58 outliers final: 46 residues processed: 365 average time/residue: 0.3034 time to fit residues: 192.9768 Evaluate side-chains 348 residues out of total 3572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 297 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 357 HIS Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 555 MET Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain F residue 670 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 632 TRP Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain E residue 413 TYR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 632 TRP Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 691 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 0.0040 chunk 344 optimal weight: 0.5980 chunk 99 optimal weight: 0.0870 chunk 298 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 324 optimal weight: 0.3980 chunk 135 optimal weight: 6.9990 chunk 332 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.6172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 ASN ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.097656 restraints weight = 59504.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.095505 restraints weight = 71093.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.096839 restraints weight = 67158.136| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 33854 Z= 0.133 Angle : 0.880 21.420 45806 Z= 0.342 Chirality : 0.038 0.191 4970 Planarity : 0.003 0.053 5882 Dihedral : 5.358 59.722 4653 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.57 % Allowed : 20.27 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 4103 helix: 1.64 (0.11), residues: 2537 sheet: -1.07 (2.19), residues: 5 loop : -1.94 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 184 HIS 0.002 0.000 HIS F 357 PHE 0.029 0.001 PHE B 178 TYR 0.027 0.001 TYR F 484 ARG 0.004 0.000 ARG E 592 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4454.65 seconds wall clock time: 80 minutes 46.00 seconds (4846.00 seconds total)