Starting phenix.real_space_refine on Sat Feb 17 02:15:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi4_23839/02_2024/7mi4_23839_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi4_23839/02_2024/7mi4_23839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi4_23839/02_2024/7mi4_23839.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi4_23839/02_2024/7mi4_23839.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi4_23839/02_2024/7mi4_23839_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi4_23839/02_2024/7mi4_23839_updated.pdb" } resolution = 3.2 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 8 7.51 5 Fe 8 7.16 5 P 70 5.49 5 S 100 5.16 5 C 10594 2.51 5 N 3146 2.21 5 O 3236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "A ARG 47": "NH1" <-> "NH2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "A ARG 532": "NH1" <-> "NH2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 393": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 413": "NH1" <-> "NH2" Residue "B ARG 432": "NH1" <-> "NH2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B ARG 505": "NH1" <-> "NH2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B GLU 513": "OE1" <-> "OE2" Residue "B ARG 514": "NH1" <-> "NH2" Residue "B GLU 517": "OE1" <-> "OE2" Residue "B ARG 532": "NH1" <-> "NH2" Residue "B ARG 533": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C ARG 47": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C ASP 236": "OD1" <-> "OD2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C ARG 278": "NH1" <-> "NH2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C ARG 340": "NH1" <-> "NH2" Residue "C ARG 344": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 386": "NH1" <-> "NH2" Residue "C ARG 393": "NH1" <-> "NH2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "C ARG 413": "NH1" <-> "NH2" Residue "C ARG 432": "NH1" <-> "NH2" Residue "C ARG 447": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C GLU 485": "OE1" <-> "OE2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 513": "OE1" <-> "OE2" Residue "C ARG 514": "NH1" <-> "NH2" Residue "C ARG 532": "NH1" <-> "NH2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 245": "OE1" <-> "OE2" Residue "D GLU 275": "OE1" <-> "OE2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ARG 279": "NH1" <-> "NH2" Residue "D ARG 307": "NH1" <-> "NH2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 344": "NH1" <-> "NH2" Residue "D ARG 365": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 393": "NH1" <-> "NH2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "D ARG 413": "NH1" <-> "NH2" Residue "D ARG 432": "NH1" <-> "NH2" Residue "D ARG 447": "NH1" <-> "NH2" Residue "D ARG 454": "NH1" <-> "NH2" Residue "D ARG 457": "NH1" <-> "NH2" Residue "D PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 469": "NH1" <-> "NH2" Residue "D ARG 487": "NH1" <-> "NH2" Residue "D ARG 493": "NH1" <-> "NH2" Residue "D ARG 505": "NH1" <-> "NH2" Residue "D ARG 507": "NH1" <-> "NH2" Residue "D GLU 513": "OE1" <-> "OE2" Residue "D ARG 514": "NH1" <-> "NH2" Residue "D GLU 517": "OE1" <-> "OE2" Residue "D ARG 532": "NH1" <-> "NH2" Residue "D ARG 533": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 15": "NH1" <-> "NH2" Residue "E ARG 16": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 15": "NH1" <-> "NH2" Residue "F ARG 16": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 44": "NH1" <-> "NH2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F ASP 67": "OD1" <-> "OD2" Residue "F ARG 90": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17162 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4355 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 35, 'TRANS': 518} Chain: "B" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2711 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "C" Number of atoms: 4355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4355 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 35, 'TRANS': 518} Chain: "D" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2711 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "E" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 786 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 786 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "G" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 717 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "H" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 717 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 10 Unusual residues: {' MN': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 142 SG CYS A 22 72.626 59.201 118.374 1.00 50.21 S ATOM 1468 SG CYS A 196 67.121 60.303 119.003 1.00 54.73 S ATOM 1429 SG CYS A 190 67.978 56.403 114.756 1.00 55.03 S ATOM 1405 SG CYS A 187 70.056 61.435 114.328 1.00 56.92 S ATOM 7208 SG CYS C 22 50.242 66.716 54.499 1.00 52.30 S ATOM 8534 SG CYS C 196 55.355 64.535 53.489 1.00 53.19 S ATOM 8495 SG CYS C 190 52.700 61.667 57.813 1.00 55.11 S ATOM 8471 SG CYS C 187 53.864 66.976 58.343 1.00 57.72 S Time building chain proxies: 9.30, per 1000 atoms: 0.54 Number of scatterers: 17162 At special positions: 0 Unit cell: (115.62, 95.94, 174.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 8 26.01 Mn 8 24.99 S 100 16.00 P 70 15.00 O 3236 8.00 N 3146 7.00 C 10594 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: 7.73 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A 601 " pdb="FE4 SF4 A 601 " - pdb=" SG CYS A 187 " pdb="FE3 SF4 A 601 " - pdb=" SG CYS A 190 " pdb="FE2 SF4 A 601 " - pdb=" SG CYS A 196 " pdb="FE1 SF4 A 601 " - pdb=" SG CYS A 22 " pdb=" SF4 C 601 " pdb="FE4 SF4 C 601 " - pdb=" SG CYS C 187 " pdb="FE3 SF4 C 601 " - pdb=" SG CYS C 190 " pdb="FE2 SF4 C 601 " - pdb=" SG CYS C 196 " pdb="FE1 SF4 C 601 " - pdb=" SG CYS C 22 " Number of angles added : 24 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3628 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 24 sheets defined 43.9% alpha, 11.2% beta 20 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 7.69 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 39 through 52 removed outlier: 3.895A pdb=" N ARG A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 Processing helix chain 'A' and resid 155 through 174 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 193 through 196 No H-bonds generated for 'chain 'A' and resid 193 through 196' Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.681A pdb=" N ARG A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 317 through 341 Processing helix chain 'A' and resid 354 through 368 Processing helix chain 'A' and resid 373 through 389 Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 418 through 441 removed outlier: 4.066A pdb=" N ARG A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 433 " --> pdb=" O MET A 429 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 464 No H-bonds generated for 'chain 'A' and resid 461 through 464' Processing helix chain 'A' and resid 466 through 483 Proline residue: A 470 - end of helix removed outlier: 4.801A pdb=" N ALA A 473 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ASP A 474 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 475 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A 482 " --> pdb=" O MET A 479 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN A 483 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 502 through 516 removed outlier: 3.512A pdb=" N ARG A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 546 removed outlier: 3.551A pdb=" N GLU A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 Processing helix chain 'B' and resid 301 through 314 removed outlier: 3.725A pdb=" N GLU B 305 " --> pdb=" O HIS B 301 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR B 306 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 342 Processing helix chain 'B' and resid 354 through 368 Processing helix chain 'B' and resid 373 through 394 removed outlier: 3.921A pdb=" N HIS B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ARG B 393 " --> pdb=" O GLN B 389 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET B 394 " --> pdb=" O HIS B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 440 Processing helix chain 'B' and resid 461 through 464 No H-bonds generated for 'chain 'B' and resid 461 through 464' Processing helix chain 'B' and resid 469 through 472 No H-bonds generated for 'chain 'B' and resid 469 through 472' Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 531 through 545 removed outlier: 4.196A pdb=" N GLU B 536 " --> pdb=" O ARG B 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 19 Processing helix chain 'C' and resid 23 through 31 Processing helix chain 'C' and resid 39 through 52 removed outlier: 3.895A pdb=" N ARG C 50 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 130 Processing helix chain 'C' and resid 155 through 174 Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'C' and resid 193 through 196 No H-bonds generated for 'chain 'C' and resid 193 through 196' Processing helix chain 'C' and resid 198 through 204 Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.681A pdb=" N ARG C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 314 Processing helix chain 'C' and resid 317 through 341 Processing helix chain 'C' and resid 354 through 368 Processing helix chain 'C' and resid 373 through 389 Processing helix chain 'C' and resid 391 through 394 Processing helix chain 'C' and resid 407 through 409 No H-bonds generated for 'chain 'C' and resid 407 through 409' Processing helix chain 'C' and resid 418 through 441 removed outlier: 4.066A pdb=" N ARG C 432 " --> pdb=" O ALA C 428 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU C 433 " --> pdb=" O MET C 429 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 441 " --> pdb=" O ALA C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 464 No H-bonds generated for 'chain 'C' and resid 461 through 464' Processing helix chain 'C' and resid 466 through 483 Proline residue: C 470 - end of helix removed outlier: 4.801A pdb=" N ALA C 473 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ASP C 474 " --> pdb=" O LEU C 471 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C 475 " --> pdb=" O ILE C 472 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C 482 " --> pdb=" O MET C 479 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN C 483 " --> pdb=" O ALA C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 490 No H-bonds generated for 'chain 'C' and resid 488 through 490' Processing helix chain 'C' and resid 502 through 516 removed outlier: 3.512A pdb=" N ARG C 507 " --> pdb=" O SER C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 546 removed outlier: 3.551A pdb=" N GLU C 536 " --> pdb=" O ARG C 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 279 Processing helix chain 'D' and resid 301 through 314 removed outlier: 3.724A pdb=" N GLU D 305 " --> pdb=" O HIS D 301 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR D 306 " --> pdb=" O ARG D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 342 Processing helix chain 'D' and resid 354 through 368 Processing helix chain 'D' and resid 373 through 394 removed outlier: 3.921A pdb=" N HIS D 390 " --> pdb=" O ARG D 386 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER D 392 " --> pdb=" O PHE D 388 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ARG D 393 " --> pdb=" O GLN D 389 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET D 394 " --> pdb=" O HIS D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 440 Processing helix chain 'D' and resid 461 through 464 No H-bonds generated for 'chain 'D' and resid 461 through 464' Processing helix chain 'D' and resid 469 through 472 No H-bonds generated for 'chain 'D' and resid 469 through 472' Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 488 through 490 No H-bonds generated for 'chain 'D' and resid 488 through 490' Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 531 through 545 removed outlier: 4.197A pdb=" N GLU D 536 " --> pdb=" O ARG D 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 25 Processing helix chain 'E' and resid 42 through 53 removed outlier: 3.738A pdb=" N ASN E 53 " --> pdb=" O GLU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'F' and resid 14 through 25 Processing helix chain 'F' and resid 42 through 53 removed outlier: 3.738A pdb=" N ASN F 53 " --> pdb=" O GLU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 77 No H-bonds generated for 'chain 'F' and resid 75 through 77' Processing sheet with id= A, first strand: chain 'A' and resid 67 through 71 Processing sheet with id= B, first strand: chain 'A' and resid 73 through 77 Processing sheet with id= C, first strand: chain 'A' and resid 98 through 102 removed outlier: 4.324A pdb=" N PHE A 142 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU A 147 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 224 through 226 removed outlier: 7.863A pdb=" N LEU A 262 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 284 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 231 through 236 removed outlier: 3.575A pdb=" N ASP A 236 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N CYS A 239 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU A 244 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 491 through 493 Processing sheet with id= G, first strand: chain 'A' and resid 519 through 521 Processing sheet with id= H, first strand: chain 'B' and resid 224 through 226 Processing sheet with id= I, first strand: chain 'B' and resid 232 through 236 removed outlier: 3.815A pdb=" N ALA B 250 " --> pdb=" O ILE B 242 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 491 through 493 Processing sheet with id= K, first strand: chain 'B' and resid 283 through 286 removed outlier: 3.507A pdb=" N GLY B 294 " --> pdb=" O TRP B 285 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 67 through 71 Processing sheet with id= M, first strand: chain 'C' and resid 73 through 77 Processing sheet with id= N, first strand: chain 'C' and resid 98 through 102 removed outlier: 4.324A pdb=" N PHE C 142 " --> pdb=" O GLU C 147 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU C 147 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 224 through 226 removed outlier: 7.863A pdb=" N LEU C 262 " --> pdb=" O PRO C 282 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR C 284 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 231 through 236 removed outlier: 3.575A pdb=" N ASP C 236 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS C 239 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU C 244 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 491 through 493 Processing sheet with id= R, first strand: chain 'C' and resid 519 through 521 Processing sheet with id= S, first strand: chain 'D' and resid 224 through 226 Processing sheet with id= T, first strand: chain 'D' and resid 232 through 236 removed outlier: 3.816A pdb=" N ALA D 250 " --> pdb=" O ILE D 242 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 491 through 493 Processing sheet with id= V, first strand: chain 'D' and resid 283 through 286 removed outlier: 3.507A pdb=" N GLY D 294 " --> pdb=" O TRP D 285 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 62 through 69 removed outlier: 6.763A pdb=" N LEU E 4 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN E 37 " --> pdb=" O TRP E 30 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N TRP E 30 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 62 through 69 removed outlier: 6.764A pdb=" N LEU F 4 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN F 37 " --> pdb=" O TRP F 30 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TRP F 30 " --> pdb=" O GLN F 37 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 5.74 Time building geometry restraints manager: 8.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 7677 1.42 - 1.64: 9841 1.64 - 1.85: 150 1.85 - 2.06: 0 2.06 - 2.28: 24 Bond restraints: 17692 Sorted by residual: bond pdb=" C PRO B 414 " pdb=" N PRO B 415 " ideal model delta sigma weight residual 1.335 1.310 0.025 8.70e-03 1.32e+04 8.57e+00 bond pdb=" C PRO D 414 " pdb=" N PRO D 415 " ideal model delta sigma weight residual 1.335 1.310 0.025 8.70e-03 1.32e+04 8.21e+00 bond pdb=" CA HIS D 301 " pdb=" C HIS D 301 " ideal model delta sigma weight residual 1.524 1.467 0.057 2.25e-02 1.98e+03 6.38e+00 bond pdb=" CA HIS B 301 " pdb=" C HIS B 301 " ideal model delta sigma weight residual 1.524 1.467 0.056 2.25e-02 1.98e+03 6.26e+00 bond pdb=" CB LYS F 22 " pdb=" CG LYS F 22 " ideal model delta sigma weight residual 1.520 1.585 -0.065 3.00e-02 1.11e+03 4.71e+00 ... (remaining 17687 not shown) Histogram of bond angle deviations from ideal: 73.58 - 86.52: 24 86.52 - 99.46: 10 99.46 - 112.41: 9618 112.41 - 125.35: 14102 125.35 - 138.29: 508 Bond angle restraints: 24262 Sorted by residual: angle pdb=" CD ARG C 146 " pdb=" NE ARG C 146 " pdb=" CZ ARG C 146 " ideal model delta sigma weight residual 124.40 138.29 -13.89 1.40e+00 5.10e-01 9.85e+01 angle pdb=" CD ARG A 146 " pdb=" NE ARG A 146 " pdb=" CZ ARG A 146 " ideal model delta sigma weight residual 124.40 138.29 -13.89 1.40e+00 5.10e-01 9.84e+01 angle pdb=" CG ARG B 386 " pdb=" CD ARG B 386 " pdb=" NE ARG B 386 " ideal model delta sigma weight residual 112.00 130.84 -18.84 2.20e+00 2.07e-01 7.34e+01 angle pdb=" CG ARG D 386 " pdb=" CD ARG D 386 " pdb=" NE ARG D 386 " ideal model delta sigma weight residual 112.00 130.83 -18.83 2.20e+00 2.07e-01 7.33e+01 angle pdb=" CA LYS E 22 " pdb=" CB LYS E 22 " pdb=" CG LYS E 22 " ideal model delta sigma weight residual 114.10 129.59 -15.49 2.00e+00 2.50e-01 6.00e+01 ... (remaining 24257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.45: 9600 28.45 - 56.91: 722 56.91 - 85.36: 100 85.36 - 113.81: 6 113.81 - 142.27: 2 Dihedral angle restraints: 10430 sinusoidal: 4762 harmonic: 5668 Sorted by residual: dihedral pdb=" CD ARG C 146 " pdb=" NE ARG C 146 " pdb=" CZ ARG C 146 " pdb=" NH1 ARG C 146 " ideal model delta sinusoidal sigma weight residual 0.00 -58.10 58.10 1 1.00e+01 1.00e-02 4.53e+01 dihedral pdb=" CD ARG A 146 " pdb=" NE ARG A 146 " pdb=" CZ ARG A 146 " pdb=" NH1 ARG A 146 " ideal model delta sinusoidal sigma weight residual 0.00 -57.97 57.97 1 1.00e+01 1.00e-02 4.51e+01 dihedral pdb=" CA ARG C 412 " pdb=" C ARG C 412 " pdb=" N ARG C 413 " pdb=" CA ARG C 413 " ideal model delta harmonic sigma weight residual 180.00 -147.75 -32.25 0 5.00e+00 4.00e-02 4.16e+01 ... (remaining 10427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1917 0.056 - 0.113: 590 0.113 - 0.169: 109 0.169 - 0.225: 10 0.225 - 0.282: 2 Chirality restraints: 2628 Sorted by residual: chirality pdb=" CA ARG C 146 " pdb=" N ARG C 146 " pdb=" C ARG C 146 " pdb=" CB ARG C 146 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ARG A 146 " pdb=" N ARG A 146 " pdb=" C ARG A 146 " pdb=" CB ARG A 146 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb="FE3 SF4 A 601 " pdb=" S1 SF4 A 601 " pdb=" S2 SF4 A 601 " pdb=" S4 SF4 A 601 " both_signs ideal model delta sigma weight residual False -10.55 -10.34 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2625 not shown) Planarity restraints: 2928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 146 " 0.412 9.50e-02 1.11e+02 1.97e-01 8.04e+01 pdb=" NE ARG C 146 " -0.073 2.00e-02 2.50e+03 pdb=" CZ ARG C 146 " 0.128 2.00e-02 2.50e+03 pdb=" NH1 ARG C 146 " -0.044 2.00e-02 2.50e+03 pdb=" NH2 ARG C 146 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 146 " -0.412 9.50e-02 1.11e+02 1.97e-01 8.01e+01 pdb=" NE ARG A 146 " 0.073 2.00e-02 2.50e+03 pdb=" CZ ARG A 146 " -0.128 2.00e-02 2.50e+03 pdb=" NH1 ARG A 146 " 0.044 2.00e-02 2.50e+03 pdb=" NH2 ARG A 146 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 316 " -0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO B 317 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 317 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 317 " -0.036 5.00e-02 4.00e+02 ... (remaining 2925 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 32 2.25 - 2.91: 7387 2.91 - 3.58: 24901 3.58 - 4.24: 40937 4.24 - 4.90: 69425 Nonbonded interactions: 142682 Sorted by model distance: nonbonded pdb=" OP1 DG H 32 " pdb="MN MN H 801 " model vdw 1.590 2.320 nonbonded pdb=" NE2 HIS C 48 " pdb="MN MN C 603 " model vdw 1.827 2.400 nonbonded pdb=" NE2 HIS A 48 " pdb="MN MN H 801 " model vdw 1.828 2.400 nonbonded pdb=" OD2 ASP A 87 " pdb="MN MN H 801 " model vdw 1.848 2.320 nonbonded pdb=" OD2 ASP C 87 " pdb="MN MN C 603 " model vdw 1.848 2.320 ... (remaining 142677 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 5 through 558 or resid 601 through 602)) } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 1 through 35) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.480 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 56.000 Find NCS groups from input model: 0.970 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 17692 Z= 0.603 Angle : 0.984 18.843 24262 Z= 0.550 Chirality : 0.054 0.282 2628 Planarity : 0.008 0.197 2928 Dihedral : 18.974 142.266 6802 Min Nonbonded Distance : 1.590 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.44 % Favored : 91.45 % Rotamer: Outliers : 5.83 % Allowed : 2.06 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.33 (0.19), residues: 1966 helix: 0.32 (0.17), residues: 922 sheet: -1.42 (0.34), residues: 236 loop : -2.12 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 30 HIS 0.011 0.002 HIS D 522 PHE 0.023 0.002 PHE B 425 TYR 0.019 0.002 TYR D 545 ARG 0.133 0.002 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 266 time to evaluate : 1.976 Fit side-chains revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7877 (m-30) cc_final: 0.7655 (m-30) REVERT: A 166 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7865 (t0) REVERT: A 358 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7887 (tpt) REVERT: A 479 MET cc_start: 0.7369 (mtp) cc_final: 0.7106 (mtt) REVERT: A 483 ASN cc_start: 0.8453 (m-40) cc_final: 0.8124 (m-40) REVERT: A 485 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7184 (mt-10) REVERT: A 516 MET cc_start: 0.8801 (mmm) cc_final: 0.8541 (mmm) REVERT: B 230 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7785 (mmtp) REVERT: B 258 SER cc_start: 0.7115 (OUTLIER) cc_final: 0.6615 (m) REVERT: B 302 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6488 (tpp80) REVERT: B 319 THR cc_start: 0.8086 (m) cc_final: 0.7617 (m) REVERT: B 323 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8034 (mp) REVERT: B 343 TRP cc_start: 0.7177 (t-100) cc_final: 0.6729 (t-100) REVERT: B 479 MET cc_start: 0.7334 (mmp) cc_final: 0.7022 (mmm) REVERT: B 483 ASN cc_start: 0.8164 (m-40) cc_final: 0.7953 (m-40) REVERT: C 85 LYS cc_start: 0.8914 (tttt) cc_final: 0.8590 (ttmm) REVERT: C 162 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8206 (mt) REVERT: C 417 ASP cc_start: 0.6889 (m-30) cc_final: 0.6455 (m-30) REVERT: D 259 GLN cc_start: 0.7982 (pt0) cc_final: 0.7562 (pt0) REVERT: D 293 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7563 (mmm) REVERT: D 342 ASN cc_start: 0.8119 (t0) cc_final: 0.7870 (m-40) REVERT: D 386 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7719 (ptm160) REVERT: D 429 MET cc_start: 0.8694 (mtm) cc_final: 0.8452 (mtm) REVERT: D 516 MET cc_start: 0.8454 (mmm) cc_final: 0.8026 (tpp) outliers start: 96 outliers final: 6 residues processed: 304 average time/residue: 0.3870 time to fit residues: 163.6492 Evaluate side-chains 195 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 180 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 386 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 0.0870 chunk 117 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN B 361 GLN B 522 HIS ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17692 Z= 0.205 Angle : 0.612 7.519 24262 Z= 0.328 Chirality : 0.043 0.142 2628 Planarity : 0.005 0.049 2928 Dihedral : 17.196 139.836 3047 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.21 % Favored : 93.69 % Rotamer: Outliers : 1.94 % Allowed : 6.74 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.19), residues: 1966 helix: 0.95 (0.18), residues: 914 sheet: -1.18 (0.38), residues: 204 loop : -2.14 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 17 HIS 0.008 0.001 HIS D 366 PHE 0.030 0.002 PHE D 407 TYR 0.020 0.001 TYR C 527 ARG 0.013 0.001 ARG D 386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 217 time to evaluate : 1.890 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7748 (t0) REVERT: B 258 SER cc_start: 0.7139 (OUTLIER) cc_final: 0.6551 (m) REVERT: B 319 THR cc_start: 0.8366 (m) cc_final: 0.7860 (m) REVERT: B 323 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8014 (mp) REVERT: B 343 TRP cc_start: 0.6925 (t-100) cc_final: 0.6574 (t-100) REVERT: C 162 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8114 (mt) REVERT: C 326 ARG cc_start: 0.7332 (mmt-90) cc_final: 0.7115 (mmt-90) REVERT: C 417 ASP cc_start: 0.6639 (m-30) cc_final: 0.6193 (m-30) REVERT: D 259 GLN cc_start: 0.8031 (pt0) cc_final: 0.7653 (pt0) REVERT: D 322 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7541 (t0) REVERT: D 342 ASN cc_start: 0.8121 (m-40) cc_final: 0.7886 (m-40) REVERT: D 360 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.6482 (mp) REVERT: D 368 MET cc_start: 0.7569 (tmm) cc_final: 0.6312 (mtp) REVERT: D 483 ASN cc_start: 0.8704 (m-40) cc_final: 0.8456 (m-40) REVERT: E 24 MET cc_start: 0.9260 (mmm) cc_final: 0.8691 (mmp) REVERT: E 33 LEU cc_start: 0.8636 (tp) cc_final: 0.8269 (tp) REVERT: E 48 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8621 (ttp) REVERT: F 8 SER cc_start: 0.8493 (p) cc_final: 0.8207 (p) outliers start: 32 outliers final: 9 residues processed: 233 average time/residue: 0.3631 time to fit residues: 121.1422 Evaluate side-chains 204 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain E residue 48 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 ASN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN D 420 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 17692 Z= 0.426 Angle : 0.661 6.911 24262 Z= 0.350 Chirality : 0.047 0.163 2628 Planarity : 0.005 0.049 2928 Dihedral : 17.175 142.039 3015 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.17 % Favored : 92.73 % Rotamer: Outliers : 1.82 % Allowed : 10.13 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.19), residues: 1966 helix: 0.91 (0.17), residues: 916 sheet: -1.33 (0.35), residues: 236 loop : -2.15 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 17 HIS 0.007 0.001 HIS E 62 PHE 0.023 0.002 PHE D 525 TYR 0.016 0.002 TYR C 232 ARG 0.006 0.001 ARG A 412 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 195 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 363 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7325 (t0) REVERT: A 485 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7268 (mt-10) REVERT: B 323 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8011 (mp) REVERT: B 343 TRP cc_start: 0.7319 (t-100) cc_final: 0.6414 (t60) REVERT: C 417 ASP cc_start: 0.7018 (m-30) cc_final: 0.6651 (m-30) REVERT: D 259 GLN cc_start: 0.8238 (pt0) cc_final: 0.7666 (pt0) REVERT: D 322 ASN cc_start: 0.7979 (OUTLIER) cc_final: 0.7660 (t0) REVERT: E 77 LYS cc_start: 0.8629 (mttp) cc_final: 0.8414 (mttm) REVERT: F 22 LYS cc_start: 0.8714 (ttpp) cc_final: 0.8363 (tptt) outliers start: 30 outliers final: 13 residues processed: 215 average time/residue: 0.3542 time to fit residues: 109.9336 Evaluate side-chains 193 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 177 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 536 GLU Chi-restraints excluded: chain E residue 25 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 123 optimal weight: 8.9990 chunk 184 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN D 342 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17692 Z= 0.227 Angle : 0.574 7.283 24262 Z= 0.304 Chirality : 0.042 0.139 2628 Planarity : 0.004 0.046 2928 Dihedral : 17.072 140.926 3009 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.35 % Rotamer: Outliers : 1.64 % Allowed : 11.77 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.19), residues: 1966 helix: 1.32 (0.18), residues: 908 sheet: -1.10 (0.36), residues: 220 loop : -2.08 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 17 HIS 0.004 0.001 HIS B 295 PHE 0.022 0.001 PHE D 525 TYR 0.016 0.001 TYR D 527 ARG 0.006 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 193 time to evaluate : 1.977 Fit side-chains revert: symmetry clash REVERT: A 51 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7867 (m) REVERT: A 358 MET cc_start: 0.7813 (tpp) cc_final: 0.7542 (tpt) REVERT: A 363 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7318 (t0) REVERT: A 485 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7233 (mt-10) REVERT: B 432 ARG cc_start: 0.8439 (ttt90) cc_final: 0.8157 (tpt-90) REVERT: C 293 MET cc_start: 0.8657 (mmt) cc_final: 0.8437 (mmt) REVERT: C 417 ASP cc_start: 0.6741 (m-30) cc_final: 0.6432 (m-30) REVERT: D 259 GLN cc_start: 0.8181 (pt0) cc_final: 0.7567 (pt0) REVERT: D 309 TYR cc_start: 0.8174 (m-80) cc_final: 0.7951 (m-80) REVERT: D 322 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7543 (t0) REVERT: D 368 MET cc_start: 0.7748 (tmm) cc_final: 0.6691 (mtm) REVERT: D 376 LEU cc_start: 0.8416 (tp) cc_final: 0.8147 (tp) REVERT: E 77 LYS cc_start: 0.8651 (mttp) cc_final: 0.8392 (mttt) REVERT: F 8 SER cc_start: 0.8459 (p) cc_final: 0.8152 (p) REVERT: F 25 HIS cc_start: 0.8732 (OUTLIER) cc_final: 0.8032 (m-70) outliers start: 27 outliers final: 17 residues processed: 210 average time/residue: 0.3618 time to fit residues: 109.9310 Evaluate side-chains 205 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 184 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 72 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN D 322 ASN D 342 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17692 Z= 0.205 Angle : 0.555 6.902 24262 Z= 0.292 Chirality : 0.042 0.142 2628 Planarity : 0.004 0.044 2928 Dihedral : 17.052 139.692 3007 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.80 % Favored : 94.10 % Rotamer: Outliers : 2.00 % Allowed : 12.26 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.20), residues: 1966 helix: 1.49 (0.18), residues: 908 sheet: -1.03 (0.36), residues: 220 loop : -2.02 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 17 HIS 0.004 0.001 HIS B 390 PHE 0.021 0.001 PHE D 525 TYR 0.015 0.001 TYR D 527 ARG 0.007 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 195 time to evaluate : 1.736 Fit side-chains revert: symmetry clash REVERT: A 363 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7286 (t0) REVERT: A 485 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7228 (mt-10) REVERT: A 516 MET cc_start: 0.7892 (mmm) cc_final: 0.7663 (mmm) REVERT: C 293 MET cc_start: 0.8676 (mmt) cc_final: 0.8466 (mmt) REVERT: C 417 ASP cc_start: 0.6730 (m-30) cc_final: 0.6472 (m-30) REVERT: D 259 GLN cc_start: 0.8119 (pt0) cc_final: 0.7479 (pt0) REVERT: D 309 TYR cc_start: 0.8103 (m-80) cc_final: 0.7898 (m-80) REVERT: D 322 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7596 (t0) REVERT: D 376 LEU cc_start: 0.8366 (tp) cc_final: 0.8101 (tp) REVERT: D 433 GLU cc_start: 0.8028 (tp30) cc_final: 0.7802 (tp30) REVERT: E 77 LYS cc_start: 0.8668 (mttp) cc_final: 0.8422 (mttt) REVERT: F 25 HIS cc_start: 0.8775 (OUTLIER) cc_final: 0.8142 (m-70) outliers start: 33 outliers final: 15 residues processed: 216 average time/residue: 0.3346 time to fit residues: 104.3083 Evaluate side-chains 208 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 72 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 114 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 102 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN D 342 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17692 Z= 0.269 Angle : 0.579 8.889 24262 Z= 0.301 Chirality : 0.043 0.154 2628 Planarity : 0.004 0.042 2928 Dihedral : 17.129 139.533 3007 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.95 % Favored : 93.95 % Rotamer: Outliers : 1.64 % Allowed : 13.65 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.20), residues: 1966 helix: 1.44 (0.18), residues: 910 sheet: -1.23 (0.34), residues: 242 loop : -1.94 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 17 HIS 0.004 0.001 HIS B 522 PHE 0.021 0.001 PHE D 525 TYR 0.014 0.001 TYR A 527 ARG 0.006 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 194 time to evaluate : 2.075 Fit side-chains REVERT: A 236 ASP cc_start: 0.7994 (t0) cc_final: 0.7298 (t0) REVERT: A 363 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7373 (t0) REVERT: A 374 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7892 (mp0) REVERT: A 485 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7233 (mt-10) REVERT: C 417 ASP cc_start: 0.6787 (m-30) cc_final: 0.6529 (m-30) REVERT: D 259 GLN cc_start: 0.8136 (pt0) cc_final: 0.7490 (pt0) REVERT: D 309 TYR cc_start: 0.8174 (m-80) cc_final: 0.7955 (m-80) REVERT: D 322 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7672 (t0) REVERT: D 368 MET cc_start: 0.7731 (tmm) cc_final: 0.6695 (mtm) REVERT: D 376 LEU cc_start: 0.8447 (tp) cc_final: 0.8176 (tp) REVERT: D 403 MET cc_start: 0.5174 (mmm) cc_final: 0.4796 (mmp) REVERT: D 433 GLU cc_start: 0.8110 (tp30) cc_final: 0.7600 (tp30) REVERT: E 77 LYS cc_start: 0.8691 (mttp) cc_final: 0.8447 (mttt) REVERT: F 25 HIS cc_start: 0.8776 (OUTLIER) cc_final: 0.8115 (m-70) outliers start: 27 outliers final: 15 residues processed: 210 average time/residue: 0.3573 time to fit residues: 107.6970 Evaluate side-chains 201 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 183 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain F residue 25 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 110 optimal weight: 0.0370 chunk 164 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN D 342 ASN D 538 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17692 Z= 0.177 Angle : 0.549 7.639 24262 Z= 0.284 Chirality : 0.041 0.149 2628 Planarity : 0.004 0.041 2928 Dihedral : 17.078 138.585 3007 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.44 % Favored : 94.46 % Rotamer: Outliers : 1.58 % Allowed : 14.08 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1966 helix: 1.63 (0.18), residues: 904 sheet: -0.95 (0.37), residues: 208 loop : -1.94 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 17 HIS 0.004 0.001 HIS D 522 PHE 0.021 0.001 PHE D 525 TYR 0.017 0.001 TYR C 527 ARG 0.007 0.000 ARG F 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 203 time to evaluate : 1.876 Fit side-chains REVERT: A 363 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7328 (t0) REVERT: A 485 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7202 (mt-10) REVERT: B 479 MET cc_start: 0.7464 (mmm) cc_final: 0.7257 (mmm) REVERT: B 536 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: C 365 ARG cc_start: 0.8366 (tmm-80) cc_final: 0.7859 (ttp-110) REVERT: C 417 ASP cc_start: 0.6726 (m-30) cc_final: 0.6478 (m-30) REVERT: D 259 GLN cc_start: 0.8119 (pt0) cc_final: 0.7699 (pt0) REVERT: D 309 TYR cc_start: 0.8082 (m-80) cc_final: 0.7881 (m-80) REVERT: D 368 MET cc_start: 0.7751 (tmm) cc_final: 0.6698 (mtm) REVERT: D 376 LEU cc_start: 0.8369 (tp) cc_final: 0.8108 (tp) REVERT: D 403 MET cc_start: 0.5091 (mmm) cc_final: 0.4784 (mmp) REVERT: D 433 GLU cc_start: 0.7972 (tp30) cc_final: 0.7515 (tp30) REVERT: E 77 LYS cc_start: 0.8678 (mttp) cc_final: 0.8445 (mttm) REVERT: F 8 SER cc_start: 0.8416 (p) cc_final: 0.8099 (p) REVERT: F 25 HIS cc_start: 0.8697 (OUTLIER) cc_final: 0.8067 (m-70) outliers start: 26 outliers final: 15 residues processed: 217 average time/residue: 0.3511 time to fit residues: 109.0045 Evaluate side-chains 207 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 25 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 116 optimal weight: 0.0980 chunk 58 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 123 optimal weight: 0.0770 chunk 132 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 153 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN D 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17692 Z= 0.164 Angle : 0.541 8.884 24262 Z= 0.280 Chirality : 0.040 0.147 2628 Planarity : 0.004 0.040 2928 Dihedral : 17.036 137.822 3007 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.35 % Rotamer: Outliers : 1.82 % Allowed : 14.32 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1966 helix: 1.70 (0.18), residues: 906 sheet: -1.10 (0.37), residues: 214 loop : -1.91 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 17 HIS 0.005 0.001 HIS B 301 PHE 0.022 0.001 PHE D 525 TYR 0.016 0.001 TYR C 527 ARG 0.008 0.000 ARG F 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 198 time to evaluate : 1.962 Fit side-chains REVERT: A 236 ASP cc_start: 0.7908 (t0) cc_final: 0.7225 (t0) REVERT: A 363 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7302 (t0) REVERT: A 485 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7213 (mt-10) REVERT: A 516 MET cc_start: 0.8159 (mtp) cc_final: 0.7892 (mmm) REVERT: B 253 ARG cc_start: 0.6664 (mmt180) cc_final: 0.6121 (mpt180) REVERT: B 390 HIS cc_start: 0.7878 (m-70) cc_final: 0.7569 (m-70) REVERT: B 479 MET cc_start: 0.7463 (mmm) cc_final: 0.7236 (mmm) REVERT: B 536 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7390 (tt0) REVERT: C 365 ARG cc_start: 0.8383 (tmm-80) cc_final: 0.7834 (ttp-170) REVERT: C 417 ASP cc_start: 0.6658 (m-30) cc_final: 0.6448 (m-30) REVERT: D 259 GLN cc_start: 0.8115 (pt0) cc_final: 0.7698 (pt0) REVERT: D 322 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7586 (t0) REVERT: D 342 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.7639 (t0) REVERT: D 368 MET cc_start: 0.7672 (tmm) cc_final: 0.6610 (mtm) REVERT: D 376 LEU cc_start: 0.8367 (tp) cc_final: 0.8114 (tp) REVERT: D 394 MET cc_start: 0.5877 (OUTLIER) cc_final: 0.5610 (ttm) REVERT: D 403 MET cc_start: 0.5058 (mmm) cc_final: 0.4788 (mmp) REVERT: D 433 GLU cc_start: 0.7976 (tp30) cc_final: 0.7521 (tp30) REVERT: F 8 SER cc_start: 0.8352 (p) cc_final: 0.7983 (p) REVERT: F 57 ASN cc_start: 0.8906 (t0) cc_final: 0.8666 (t0) outliers start: 30 outliers final: 18 residues processed: 217 average time/residue: 0.3584 time to fit residues: 112.3747 Evaluate side-chains 216 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 193 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 342 ASN Chi-restraints excluded: chain D residue 394 MET Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 5.9990 chunk 186 optimal weight: 0.3980 chunk 170 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17692 Z= 0.185 Angle : 0.546 7.422 24262 Z= 0.285 Chirality : 0.041 0.138 2628 Planarity : 0.004 0.039 2928 Dihedral : 17.028 137.623 3007 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.35 % Rotamer: Outliers : 1.64 % Allowed : 14.26 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1966 helix: 1.73 (0.18), residues: 906 sheet: -1.14 (0.35), residues: 228 loop : -1.87 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 343 HIS 0.004 0.001 HIS D 522 PHE 0.023 0.001 PHE D 525 TYR 0.014 0.001 TYR A 527 ARG 0.009 0.000 ARG D 341 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 194 time to evaluate : 1.934 Fit side-chains REVERT: A 92 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6476 (pp20) REVERT: A 363 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7315 (t0) REVERT: A 416 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.6877 (mmmt) REVERT: A 485 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7230 (mt-10) REVERT: A 516 MET cc_start: 0.8092 (mtp) cc_final: 0.7850 (mmm) REVERT: B 253 ARG cc_start: 0.6525 (mmt180) cc_final: 0.6314 (mpt180) REVERT: B 465 MET cc_start: 0.8172 (ptm) cc_final: 0.7926 (ptm) REVERT: B 479 MET cc_start: 0.7460 (mmm) cc_final: 0.7237 (mmm) REVERT: B 536 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7410 (tt0) REVERT: C 358 MET cc_start: 0.6225 (mmp) cc_final: 0.6020 (mmm) REVERT: C 365 ARG cc_start: 0.8381 (tmm-80) cc_final: 0.7837 (ttp-170) REVERT: C 394 MET cc_start: 0.8570 (ptm) cc_final: 0.8071 (ptm) REVERT: C 417 ASP cc_start: 0.6670 (m-30) cc_final: 0.6463 (m-30) REVERT: D 259 GLN cc_start: 0.8121 (pt0) cc_final: 0.7701 (pt0) REVERT: D 342 ASN cc_start: 0.8178 (t0) cc_final: 0.7674 (t0) REVERT: D 368 MET cc_start: 0.7665 (tmm) cc_final: 0.6550 (mtm) REVERT: D 376 LEU cc_start: 0.8377 (tp) cc_final: 0.8130 (tp) REVERT: D 403 MET cc_start: 0.5059 (mmm) cc_final: 0.4815 (mmp) REVERT: D 433 GLU cc_start: 0.7905 (tp30) cc_final: 0.7471 (tp30) REVERT: F 8 SER cc_start: 0.8380 (p) cc_final: 0.8018 (p) REVERT: F 57 ASN cc_start: 0.8902 (t0) cc_final: 0.8659 (t0) outliers start: 27 outliers final: 16 residues processed: 209 average time/residue: 0.3532 time to fit residues: 107.0860 Evaluate side-chains 211 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 191 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 54 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 0.5980 chunk 191 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17692 Z= 0.222 Angle : 0.552 7.409 24262 Z= 0.288 Chirality : 0.042 0.158 2628 Planarity : 0.004 0.039 2928 Dihedral : 17.074 137.814 3007 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.95 % Favored : 93.95 % Rotamer: Outliers : 1.46 % Allowed : 14.38 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1966 helix: 1.69 (0.18), residues: 906 sheet: -1.02 (0.36), residues: 218 loop : -1.85 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 17 HIS 0.004 0.001 HIS D 522 PHE 0.022 0.001 PHE D 525 TYR 0.014 0.001 TYR A 527 ARG 0.007 0.000 ARG E 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 1.829 Fit side-chains REVERT: A 92 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6505 (pp20) REVERT: A 236 ASP cc_start: 0.7675 (t0) cc_final: 0.7074 (t0) REVERT: A 363 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7604 (t70) REVERT: A 416 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.6887 (mmmt) REVERT: A 485 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7276 (mt-10) REVERT: A 516 MET cc_start: 0.8148 (mtp) cc_final: 0.7776 (mmm) REVERT: B 253 ARG cc_start: 0.6419 (mmt180) cc_final: 0.6215 (mmp-170) REVERT: B 390 HIS cc_start: 0.7899 (m-70) cc_final: 0.7641 (m-70) REVERT: B 465 MET cc_start: 0.8221 (ptm) cc_final: 0.7956 (ptm) REVERT: B 479 MET cc_start: 0.7491 (mmm) cc_final: 0.7287 (mmm) REVERT: B 536 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: C 358 MET cc_start: 0.6248 (mmp) cc_final: 0.6036 (mmm) REVERT: C 417 ASP cc_start: 0.6723 (m-30) cc_final: 0.6514 (m-30) REVERT: D 259 GLN cc_start: 0.8139 (pt0) cc_final: 0.7687 (pt0) REVERT: D 342 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7465 (t0) REVERT: D 368 MET cc_start: 0.7704 (tmm) cc_final: 0.6499 (mtm) REVERT: D 376 LEU cc_start: 0.8379 (tp) cc_final: 0.8113 (tp) REVERT: D 403 MET cc_start: 0.5144 (mmm) cc_final: 0.4909 (mmp) REVERT: D 433 GLU cc_start: 0.7954 (tp30) cc_final: 0.7489 (tp30) REVERT: F 57 ASN cc_start: 0.8904 (t0) cc_final: 0.8702 (t0) outliers start: 24 outliers final: 15 residues processed: 210 average time/residue: 0.3435 time to fit residues: 103.9384 Evaluate side-chains 209 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 189 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 342 ASN Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain E residue 25 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.118987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.090248 restraints weight = 27330.050| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.47 r_work: 0.3017 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17692 Z= 0.275 Angle : 0.580 7.328 24262 Z= 0.300 Chirality : 0.043 0.156 2628 Planarity : 0.004 0.042 2928 Dihedral : 17.130 138.009 3007 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.64 % Rotamer: Outliers : 1.33 % Allowed : 14.50 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1966 helix: 1.64 (0.18), residues: 908 sheet: -1.05 (0.36), residues: 220 loop : -1.86 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 343 HIS 0.004 0.001 HIS D 522 PHE 0.022 0.001 PHE D 525 TYR 0.014 0.001 TYR A 527 ARG 0.007 0.000 ARG C 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3452.60 seconds wall clock time: 63 minutes 18.99 seconds (3798.99 seconds total)