Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 8 17:04:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi4_23839/07_2023/7mi4_23839_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi4_23839/07_2023/7mi4_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_23839/07_2023/7mi4_23839.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi4_23839/07_2023/7mi4_23839.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi4_23839/07_2023/7mi4_23839_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi4_23839/07_2023/7mi4_23839_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-5013/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: 8.80, per 1000 atoms: 0.51 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: 7.19 Conformation dependent library (CDL) restraints added in 2.3 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: 5.61 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: 5.56 Time building geometry restraints manager: 7.66 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: 9568 28.45 - 56.91: 698 56.91 - 85.36: 100 85.36 - 113.81: 6 113.81 - 142.27: 2 Dihedral angle restraints: 10374 sinusoidal: 4706 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 10371 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: 0.670 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: 0.020 Extract box with map and model: 5.250 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 51.370 Find NCS groups from input model: 0.910 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: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.680 ------------------------------------------------------------------------------- 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 : 18.889 142.266 6746 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 % 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 *********************** 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 : 1.832 Fit side-chains revert: symmetry clash outliers start: 96 outliers final: 6 residues processed: 304 average time/residue: 0.3902 time to fit residues: 163.9001 Evaluate side-chains 180 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 174 time to evaluate : 1.751 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3444 time to fit residues: 5.1301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 0.0470 chunk 153 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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: 0.8044 moved from start: 0.1545 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= 0.212 Angle : 0.618 7.374 24262 Z= 0.331 Chirality : 0.043 0.142 2628 Planarity : 0.005 0.049 2928 Dihedral : 16.627 140.271 2948 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.15 % Favored : 93.74 % Rotamer Outliers : 1.33 % 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: -0.80 (0.19), residues: 1966 helix: 0.96 (0.18), residues: 906 sheet: -1.18 (0.38), residues: 204 loop : -2.07 (0.20), residues: 856 *********************** 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 236 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 214 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 225 average time/residue: 0.3579 time to fit residues: 114.5839 Evaluate side-chains 187 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 177 time to evaluate : 1.786 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2535 time to fit residues: 6.3452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 183 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 182 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 ASN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN D 342 ASN D 420 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.082 17692 Z= 0.480 Angle : 0.703 6.768 24262 Z= 0.372 Chirality : 0.049 0.169 2628 Planarity : 0.006 0.054 2928 Dihedral : 17.005 143.266 2948 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.48 % Favored : 92.42 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.19), residues: 1966 helix: 0.72 (0.17), residues: 914 sheet: -1.39 (0.35), residues: 236 loop : -2.14 (0.20), residues: 816 *********************** 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 200 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 5 residues processed: 191 average time/residue: 0.3429 time to fit residues: 94.6952 Evaluate side-chains 167 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 162 time to evaluate : 1.732 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1624 time to fit residues: 3.7663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 195 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 174 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 D 342 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 17692 Z= 0.205 Angle : 0.579 8.087 24262 Z= 0.306 Chirality : 0.042 0.138 2628 Planarity : 0.004 0.046 2928 Dihedral : 16.922 141.909 2948 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.35 % Rotamer Outliers : 1.09 % 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: -0.56 (0.19), residues: 1966 helix: 1.25 (0.18), residues: 906 sheet: -1.21 (0.35), residues: 232 loop : -2.03 (0.20), residues: 828 *********************** 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 203 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 185 time to evaluate : 1.872 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 197 average time/residue: 0.3539 time to fit residues: 100.9076 Evaluate side-chains 182 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 175 time to evaluate : 1.834 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2066 time to fit residues: 4.9130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 0.0060 chunk 110 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- 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 ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 17692 Z= 0.262 Angle : 0.571 7.024 24262 Z= 0.303 Chirality : 0.043 0.140 2628 Planarity : 0.004 0.045 2928 Dihedral : 16.978 140.555 2948 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.64 % Rotamer Outliers : 0.67 % 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: -0.49 (0.19), residues: 1966 helix: 1.33 (0.18), residues: 906 sheet: -1.26 (0.34), residues: 242 loop : -1.99 (0.20), residues: 818 *********************** 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 196 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 185 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 192 average time/residue: 0.3677 time to fit residues: 102.6296 Evaluate side-chains 174 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 172 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1624 time to fit residues: 3.1690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 17692 Z= 0.306 Angle : 0.597 8.390 24262 Z= 0.311 Chirality : 0.044 0.151 2628 Planarity : 0.004 0.044 2928 Dihedral : 17.054 140.482 2948 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.64 % Rotamer Outliers : 1.09 % 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: -0.50 (0.19), residues: 1966 helix: 1.30 (0.18), residues: 908 sheet: -1.24 (0.34), residues: 242 loop : -1.98 (0.21), residues: 816 *********************** 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 210 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 192 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 5 residues processed: 204 average time/residue: 0.3497 time to fit residues: 103.9368 Evaluate side-chains 182 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 177 time to evaluate : 1.725 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1589 time to fit residues: 3.8424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 111 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 110 optimal weight: 0.0270 chunk 164 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 194 optimal weight: 0.4980 chunk 121 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 D 538 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 17692 Z= 0.174 Angle : 0.550 8.469 24262 Z= 0.288 Chirality : 0.041 0.144 2628 Planarity : 0.004 0.042 2928 Dihedral : 16.980 139.057 2948 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.90 % Favored : 94.00 % Rotamer Outliers : 0.67 % 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: -0.27 (0.20), residues: 1966 helix: 1.54 (0.18), residues: 904 sheet: -1.02 (0.36), residues: 218 loop : -1.95 (0.20), residues: 844 *********************** 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 206 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 195 time to evaluate : 1.883 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 0 residues processed: 202 average time/residue: 0.3539 time to fit residues: 103.9295 Evaluate side-chains 177 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.864 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 4.9990 chunk 77 optimal weight: 0.0970 chunk 116 optimal weight: 0.0000 chunk 58 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 153 optimal weight: 0.3980 overall best weight: 0.4382 ------------------------------------------------------------------------------- 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** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 17692 Z= 0.161 Angle : 0.550 9.558 24262 Z= 0.284 Chirality : 0.040 0.139 2628 Planarity : 0.004 0.040 2928 Dihedral : 16.923 138.359 2948 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.44 % Favored : 94.46 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1966 helix: 1.66 (0.18), residues: 904 sheet: -0.87 (0.37), residues: 208 loop : -1.94 (0.20), residues: 854 *********************** 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 200 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 193 time to evaluate : 1.903 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 198 average time/residue: 0.3716 time to fit residues: 105.7071 Evaluate side-chains 182 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 1.815 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4556 time to fit residues: 3.6722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 chunk 109 optimal weight: 0.4980 chunk 79 optimal weight: 0.0870 chunk 142 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 171 optimal weight: 6.9990 chunk 180 optimal weight: 0.6980 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 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 17692 Z= 0.173 Angle : 0.545 7.598 24262 Z= 0.282 Chirality : 0.041 0.134 2628 Planarity : 0.004 0.039 2928 Dihedral : 16.880 138.141 2948 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.80 % Favored : 94.10 % Rotamer Outliers : 0.30 % 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: -0.12 (0.20), residues: 1966 helix: 1.69 (0.18), residues: 904 sheet: -0.76 (0.37), residues: 208 loop : -1.93 (0.20), residues: 854 *********************** 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 196 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 191 time to evaluate : 1.789 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 194 average time/residue: 0.3472 time to fit residues: 97.9601 Evaluate side-chains 185 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 1.847 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1711 time to fit residues: 3.0752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 2.9990 chunk 191 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 201 optimal weight: 5.9990 chunk 185 optimal weight: 0.6980 chunk 160 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 123 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 17692 Z= 0.189 Angle : 0.555 10.483 24262 Z= 0.285 Chirality : 0.041 0.136 2628 Planarity : 0.004 0.039 2928 Dihedral : 16.872 138.015 2948 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.49 % Favored : 94.40 % Rotamer Outliers : 0.18 % 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: -0.09 (0.19), residues: 1966 helix: 1.69 (0.18), residues: 906 sheet: -0.35 (0.43), residues: 164 loop : -1.96 (0.19), residues: 896 ********************** 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 197 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 194 time to evaluate : 1.907 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 194 average time/residue: 0.3563 time to fit residues: 101.0881 Evaluate side-chains 190 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 1.911 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1874 time to fit residues: 3.2903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 0.9980 chunk 170 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 160 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.125071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.096662 restraints weight = 27728.506| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.35 r_work: 0.3121 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 17692 Z= 0.244 Angle : 0.573 7.469 24262 Z= 0.298 Chirality : 0.042 0.148 2628 Planarity : 0.004 0.039 2928 Dihedral : 16.919 138.192 2948 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.64 % Rotamer Outliers : 0.18 % 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: -0.16 (0.19), residues: 1966 helix: 1.61 (0.18), residues: 908 sheet: -0.52 (0.43), residues: 168 loop : -1.94 (0.20), residues: 890 =============================================================================== Job complete usr+sys time: 3213.60 seconds wall clock time: 59 minutes 9.86 seconds (3549.86 seconds total)