Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 8 17:14:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi4_23839/10_2023/7mi4_23839_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi4_23839/10_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_23839/10_2023/7mi4_23839.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi4_23839/10_2023/7mi4_23839.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi4_23839/10_2023/7mi4_23839_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi4_23839/10_2023/7mi4_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-1.21rc1-5097/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: 8.90, per 1000 atoms: 0.52 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: 7.92 Conformation dependent library (CDL) restraints added in 2.4 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: 6.98 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: 5.75 Time building geometry restraints manager: 8.48 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: 1.190 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: 4.510 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 54.080 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.310 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.889 Fit side-chains revert: symmetry clash outliers start: 96 outliers final: 6 residues processed: 304 average time/residue: 0.3956 time to fit residues: 165.8878 Evaluate side-chains 180 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 174 time to evaluate : 2.003 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3517 time to fit residues: 5.5134 ------------------------------------------------------------------------------- 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: 0.8039 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17692 Z= 0.202 Angle : 0.615 7.198 24262 Z= 0.329 Chirality : 0.043 0.143 2628 Planarity : 0.005 0.052 2928 Dihedral : 16.625 140.071 2948 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.95 % Favored : 93.95 % Rotamer: Outliers : 1.33 % Allowed : 6.92 % Favored : 91.75 % 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: -0.79 (0.19), residues: 1966 helix: 0.97 (0.18), residues: 906 sheet: -1.18 (0.38), residues: 204 loop : -2.06 (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 242 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 220 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 233 average time/residue: 0.3676 time to fit residues: 121.4002 Evaluate side-chains 187 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 178 time to evaluate : 1.710 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1960 time to fit residues: 5.4934 ------------------------------------------------------------------------------- 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: 4.9990 chunk 152 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 183 optimal weight: 0.1980 chunk 198 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17692 Z= 0.308 Angle : 0.609 7.350 24262 Z= 0.323 Chirality : 0.044 0.152 2628 Planarity : 0.005 0.047 2928 Dihedral : 16.787 141.713 2948 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.66 % Favored : 93.23 % Rotamer: Outliers : 1.27 % Allowed : 9.95 % Favored : 88.77 % 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: -0.60 (0.19), residues: 1966 helix: 1.17 (0.18), residues: 900 sheet: -1.30 (0.35), residues: 236 loop : -1.93 (0.21), residues: 830 *********************** 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 210 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 5 residues processed: 202 average time/residue: 0.3796 time to fit residues: 110.3237 Evaluate side-chains 179 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 174 time to evaluate : 1.884 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2763 time to fit residues: 4.6939 ------------------------------------------------------------------------------- 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: 1.9990 chunk 138 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 87 optimal weight: 0.4980 chunk 123 optimal weight: 0.7980 chunk 184 optimal weight: 4.9990 chunk 195 optimal weight: 0.0370 chunk 96 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- 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** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2316 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= 0.191 Angle : 0.556 6.909 24262 Z= 0.294 Chirality : 0.042 0.142 2628 Planarity : 0.004 0.044 2928 Dihedral : 16.756 140.134 2948 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.60 % Favored : 94.30 % Rotamer: Outliers : 0.85 % Allowed : 11.65 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.20), residues: 1966 helix: 1.50 (0.18), residues: 898 sheet: -0.88 (0.38), residues: 200 loop : -1.97 (0.20), residues: 868 *********************** 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: 14 poor density : 189 time to evaluate : 2.013 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 197 average time/residue: 0.3605 time to fit residues: 104.3219 Evaluate side-chains 180 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 176 time to evaluate : 1.857 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1842 time to fit residues: 3.9147 ------------------------------------------------------------------------------- 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: 0.0980 chunk 110 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 D 342 ASN D 420 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17692 Z= 0.305 Angle : 0.590 7.227 24262 Z= 0.311 Chirality : 0.044 0.153 2628 Planarity : 0.004 0.044 2928 Dihedral : 16.909 140.244 2948 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.46 % Favored : 93.44 % Rotamer: Outliers : 0.97 % Allowed : 12.01 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.19), residues: 1966 helix: 1.37 (0.18), residues: 910 sheet: -1.16 (0.35), residues: 232 loop : -1.97 (0.20), residues: 824 *********************** 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 199 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 183 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 191 average time/residue: 0.3584 time to fit residues: 98.5766 Evaluate side-chains 179 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 173 time to evaluate : 1.833 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1583 time to fit residues: 4.3153 ------------------------------------------------------------------------------- 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: 0.9980 chunk 175 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 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: 0.8095 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17692 Z= 0.227 Angle : 0.566 9.352 24262 Z= 0.296 Chirality : 0.042 0.138 2628 Planarity : 0.004 0.042 2928 Dihedral : 16.921 139.674 2948 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.75 % Favored : 94.15 % Rotamer: Outliers : 0.67 % Allowed : 13.65 % Favored : 85.68 % 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: -0.31 (0.20), residues: 1966 helix: 1.47 (0.18), residues: 908 sheet: -1.01 (0.35), residues: 230 loop : -1.95 (0.20), residues: 828 *********************** 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 202 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 191 time to evaluate : 1.830 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 195 average time/residue: 0.3522 time to fit residues: 100.8968 Evaluate side-chains 180 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 176 time to evaluate : 1.822 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1790 time to fit residues: 3.7744 ------------------------------------------------------------------------------- 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: 0.9990 chunk 22 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 110 optimal weight: 0.0000 chunk 164 optimal weight: 0.1980 chunk 109 optimal weight: 0.8980 chunk 194 optimal weight: 0.4980 chunk 121 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17692 Z= 0.167 Angle : 0.541 8.189 24262 Z= 0.282 Chirality : 0.041 0.140 2628 Planarity : 0.004 0.041 2928 Dihedral : 16.877 138.454 2948 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.90 % Favored : 94.00 % Rotamer: Outliers : 0.42 % Allowed : 14.20 % Favored : 85.38 % 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: 1.70 (0.18), residues: 898 sheet: -0.93 (0.36), residues: 218 loop : -1.85 (0.20), residues: 850 *********************** 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 204 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 197 time to evaluate : 1.953 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 201 average time/residue: 0.3485 time to fit residues: 100.5720 Evaluate side-chains 179 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 177 time to evaluate : 1.764 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1712 time to fit residues: 3.0540 ------------------------------------------------------------------------------- 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: 0.2980 chunk 77 optimal weight: 0.5980 chunk 116 optimal weight: 0.4980 chunk 58 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 123 optimal weight: 0.3980 chunk 132 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 153 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 265 ASN D 342 ASN ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17692 Z= 0.161 Angle : 0.535 8.097 24262 Z= 0.278 Chirality : 0.040 0.137 2628 Planarity : 0.004 0.039 2928 Dihedral : 16.828 137.839 2948 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.75 % Favored : 94.15 % Rotamer: Outliers : 0.73 % Allowed : 14.14 % Favored : 85.13 % 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: -0.07 (0.20), residues: 1966 helix: 1.73 (0.18), residues: 908 sheet: -0.99 (0.36), residues: 214 loop : -1.86 (0.20), residues: 844 *********************** 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 208 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 196 time to evaluate : 1.878 Fit side-chains outliers start: 12 outliers final: 3 residues processed: 201 average time/residue: 0.3429 time to fit residues: 100.2927 Evaluate side-chains 184 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 181 time to evaluate : 2.007 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1645 time to fit residues: 3.5086 ------------------------------------------------------------------------------- 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: 0.7980 chunk 170 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 171 optimal weight: 9.9990 chunk 180 optimal weight: 0.7980 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 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 ASN ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17692 Z= 0.250 Angle : 0.567 6.904 24262 Z= 0.296 Chirality : 0.042 0.148 2628 Planarity : 0.004 0.039 2928 Dihedral : 16.889 138.126 2948 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.51 % Favored : 93.39 % Rotamer: Outliers : 0.30 % Allowed : 14.20 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1966 helix: 1.62 (0.18), residues: 910 sheet: -1.09 (0.35), residues: 226 loop : -1.84 (0.21), residues: 830 *********************** 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 194 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 189 time to evaluate : 1.787 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 191 average time/residue: 0.3504 time to fit residues: 97.1656 Evaluate side-chains 181 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.871 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5515 ------------------------------------------------------------------------------- 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: 0.5980 chunk 117 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 185 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17692 Z= 0.218 Angle : 0.566 9.949 24262 Z= 0.293 Chirality : 0.042 0.148 2628 Planarity : 0.004 0.039 2928 Dihedral : 16.887 138.136 2948 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.60 % Favored : 94.30 % Rotamer: Outliers : 0.24 % Allowed : 14.68 % Favored : 85.07 % 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 (0.19), residues: 1966 helix: 1.68 (0.18), residues: 908 sheet: -0.34 (0.43), residues: 164 loop : -1.97 (0.19), residues: 894 ********************** 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 187 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 183 time to evaluate : 1.986 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 186 average time/residue: 0.3656 time to fit residues: 98.7869 Evaluate side-chains 179 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 2.009 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1881 time to fit residues: 2.9634 ------------------------------------------------------------------------------- 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: 2.9990 chunk 170 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 147 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 160 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 164 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 29 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.126733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.098460 restraints weight = 27682.363| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.32 r_work: 0.3155 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3234 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= 0.184 Angle : 0.548 6.882 24262 Z= 0.284 Chirality : 0.041 0.144 2628 Planarity : 0.004 0.038 2928 Dihedral : 16.834 137.693 2948 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.64 % Rotamer: Outliers : 0.24 % Allowed : 14.26 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.20), residues: 1966 helix: 1.79 (0.18), residues: 900 sheet: -0.33 (0.43), residues: 164 loop : -1.91 (0.19), residues: 902 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3351.04 seconds wall clock time: 61 minutes 29.73 seconds (3689.73 seconds total)