Starting phenix.real_space_refine on Sat Dec 16 20:51:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypi_34001/12_2023/7ypi_34001_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypi_34001/12_2023/7ypi_34001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypi_34001/12_2023/7ypi_34001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypi_34001/12_2023/7ypi_34001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypi_34001/12_2023/7ypi_34001_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypi_34001/12_2023/7ypi_34001_updated.pdb" } resolution = 3.8 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= 0.009 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 128 5.16 5 C 23012 2.51 5 N 6412 2.21 5 O 6918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 222": "NH1" <-> "NH2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ASP 425": "OD1" <-> "OD2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B ARG 541": "NH1" <-> "NH2" Residue "C ARG 370": "NH1" <-> "NH2" Residue "C ARG 394": "NH1" <-> "NH2" Residue "C GLU 521": "OE1" <-> "OE2" Residue "C ASP 570": "OD1" <-> "OD2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "D TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 247": "OE1" <-> "OE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 589": "OE1" <-> "OE2" Residue "D GLU 631": "OE1" <-> "OE2" Residue "E GLU 186": "OE1" <-> "OE2" Residue "E ARG 212": "NH1" <-> "NH2" Residue "E GLU 215": "OE1" <-> "OE2" Residue "E ARG 227": "NH1" <-> "NH2" Residue "E ARG 395": "NH1" <-> "NH2" Residue "E GLU 486": "OE1" <-> "OE2" Residue "E TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 35": "OE1" <-> "OE2" Residue "F GLU 295": "OE1" <-> "OE2" Residue "F GLU 317": "OE1" <-> "OE2" Residue "F TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 36476 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "C" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "D" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "E" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "F" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.10, per 1000 atoms: 0.55 Number of scatterers: 36476 At special positions: 0 Unit cell: (189.24, 177.62, 186.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 128 16.00 P 6 15.00 O 6918 8.00 N 6412 7.00 C 23012 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: 14.03 Conformation dependent library (CDL) restraints added in 6.8 seconds 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8616 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 174 helices and 37 sheets defined 39.5% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.32 Creating SS restraints... Processing helix chain 'A' and resid 31 through 35 Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 118 through 138 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 158 through 169 Processing helix chain 'A' and resid 173 through 181 removed outlier: 4.035A pdb=" N LEU A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 234 removed outlier: 3.639A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 255 removed outlier: 3.765A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 272 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.601A pdb=" N VAL A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 372 Processing helix chain 'A' and resid 387 through 390 No H-bonds generated for 'chain 'A' and resid 387 through 390' Processing helix chain 'A' and resid 404 through 411 Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 445 through 450 removed outlier: 4.006A pdb=" N ASN A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N THR A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 450' Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 506 through 512 Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'A' and resid 541 through 560 Processing helix chain 'A' and resid 572 through 577 Proline residue: A 575 - end of helix No H-bonds generated for 'chain 'A' and resid 572 through 577' Processing helix chain 'A' and resid 631 through 646 Processing helix chain 'A' and resid 680 through 692 removed outlier: 3.899A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 727 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 762 through 768 Processing helix chain 'B' and resid 31 through 38 Processing helix chain 'B' and resid 119 through 136 Processing helix chain 'B' and resid 138 through 142 removed outlier: 4.201A pdb=" N SER B 141 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.682A pdb=" N VAL B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 168 Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 185 through 232 removed outlier: 3.668A pdb=" N THR B 219 " --> pdb=" O GLU B 215 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 223 " --> pdb=" O THR B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 240 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 309 through 317 Processing helix chain 'B' and resid 320 through 322 No H-bonds generated for 'chain 'B' and resid 320 through 322' Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 361 through 372 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 435 through 441 removed outlier: 3.567A pdb=" N MET B 439 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 507 through 513 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 541 through 559 Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 631 through 647 removed outlier: 3.567A pdb=" N HIS B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 692 Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 737 through 744 removed outlier: 4.511A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 769 Processing helix chain 'C' and resid 31 through 38 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 118 through 137 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 158 through 167 Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 185 through 236 removed outlier: 4.182A pdb=" N LYS C 235 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLU C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 252 removed outlier: 3.996A pdb=" N LYS C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LYS C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 272 removed outlier: 3.556A pdb=" N ASP C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 295 Processing helix chain 'C' and resid 309 through 317 Processing helix chain 'C' and resid 325 through 338 removed outlier: 3.858A pdb=" N LEU C 338 " --> pdb=" O ALA C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 371 Processing helix chain 'C' and resid 404 through 411 Processing helix chain 'C' and resid 435 through 441 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'C' and resid 495 through 505 Processing helix chain 'C' and resid 507 through 514 Processing helix chain 'C' and resid 524 through 532 Processing helix chain 'C' and resid 542 through 559 Processing helix chain 'C' and resid 572 through 576 removed outlier: 3.583A pdb=" N THR C 576 " --> pdb=" O SER C 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 572 through 576' Processing helix chain 'C' and resid 632 through 646 Processing helix chain 'C' and resid 680 through 692 Processing helix chain 'C' and resid 718 through 727 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 742 through 744 No H-bonds generated for 'chain 'C' and resid 742 through 744' Processing helix chain 'C' and resid 748 through 751 No H-bonds generated for 'chain 'C' and resid 748 through 751' Processing helix chain 'C' and resid 762 through 769 Processing helix chain 'D' and resid 28 through 37 removed outlier: 4.086A pdb=" N ARG D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 138 Processing helix chain 'D' and resid 158 through 168 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 185 through 232 Processing helix chain 'D' and resid 241 through 244 No H-bonds generated for 'chain 'D' and resid 241 through 244' Processing helix chain 'D' and resid 246 through 254 Processing helix chain 'D' and resid 260 through 271 Processing helix chain 'D' and resid 282 through 295 Processing helix chain 'D' and resid 308 through 318 removed outlier: 4.042A pdb=" N ASP D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 338 Processing helix chain 'D' and resid 361 through 371 Processing helix chain 'D' and resid 387 through 390 No H-bonds generated for 'chain 'D' and resid 387 through 390' Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 435 through 441 Processing helix chain 'D' and resid 447 through 449 No H-bonds generated for 'chain 'D' and resid 447 through 449' Processing helix chain 'D' and resid 495 through 505 removed outlier: 3.942A pdb=" N GLN D 504 " --> pdb=" O ALA D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 513 Processing helix chain 'D' and resid 525 through 534 Processing helix chain 'D' and resid 541 through 559 removed outlier: 4.254A pdb=" N ARG D 545 " --> pdb=" O ARG D 541 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU D 546 " --> pdb=" O GLY D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 589 No H-bonds generated for 'chain 'D' and resid 587 through 589' Processing helix chain 'D' and resid 631 through 645 Processing helix chain 'D' and resid 649 through 651 No H-bonds generated for 'chain 'D' and resid 649 through 651' Processing helix chain 'D' and resid 680 through 692 Processing helix chain 'D' and resid 718 through 727 Processing helix chain 'D' and resid 742 through 744 No H-bonds generated for 'chain 'D' and resid 742 through 744' Processing helix chain 'D' and resid 748 through 751 No H-bonds generated for 'chain 'D' and resid 748 through 751' Processing helix chain 'D' and resid 762 through 766 Processing helix chain 'E' and resid 28 through 39 removed outlier: 3.662A pdb=" N ARG E 32 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 142 removed outlier: 3.568A pdb=" N HIS E 139 " --> pdb=" O TYR E 135 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER E 141 " --> pdb=" O ALA E 137 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU E 142 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'E' and resid 187 through 222 Processing helix chain 'E' and resid 225 through 233 Processing helix chain 'E' and resid 240 through 255 removed outlier: 3.505A pdb=" N SER E 244 " --> pdb=" O GLU E 240 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP E 245 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 272 Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 309 through 318 removed outlier: 3.953A pdb=" N ASP E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 335 removed outlier: 4.480A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 371 Processing helix chain 'E' and resid 404 through 411 Processing helix chain 'E' and resid 435 through 443 Processing helix chain 'E' and resid 462 through 464 No H-bonds generated for 'chain 'E' and resid 462 through 464' Processing helix chain 'E' and resid 495 through 504 Processing helix chain 'E' and resid 506 through 513 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 541 through 559 Processing helix chain 'E' and resid 574 through 578 Processing helix chain 'E' and resid 632 through 645 Processing helix chain 'E' and resid 649 through 651 No H-bonds generated for 'chain 'E' and resid 649 through 651' Processing helix chain 'E' and resid 680 through 692 Processing helix chain 'E' and resid 718 through 728 Processing helix chain 'E' and resid 737 through 739 No H-bonds generated for 'chain 'E' and resid 737 through 739' Processing helix chain 'E' and resid 762 through 766 Processing helix chain 'F' and resid 28 through 39 removed outlier: 3.559A pdb=" N ALA F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 138 Processing helix chain 'F' and resid 147 through 152 removed outlier: 3.912A pdb=" N VAL F 152 " --> pdb=" O GLN F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 168 Processing helix chain 'F' and resid 173 through 181 Processing helix chain 'F' and resid 187 through 237 removed outlier: 3.695A pdb=" N LYS F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN F 220 " --> pdb=" O GLN F 216 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU F 236 " --> pdb=" O ALA F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 255 removed outlier: 4.337A pdb=" N GLU F 254 " --> pdb=" O ARG F 250 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 271 Processing helix chain 'F' and resid 281 through 295 Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 325 through 337 Processing helix chain 'F' and resid 362 through 371 Processing helix chain 'F' and resid 404 through 411 Processing helix chain 'F' and resid 436 through 442 Processing helix chain 'F' and resid 479 through 482 No H-bonds generated for 'chain 'F' and resid 479 through 482' Processing helix chain 'F' and resid 495 through 504 Processing helix chain 'F' and resid 506 through 514 Processing helix chain 'F' and resid 524 through 533 Processing helix chain 'F' and resid 541 through 559 Processing helix chain 'F' and resid 574 through 578 removed outlier: 3.716A pdb=" N LEU F 578 " --> pdb=" O ILE F 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 574 through 578' Processing helix chain 'F' and resid 631 through 646 Processing helix chain 'F' and resid 648 through 650 No H-bonds generated for 'chain 'F' and resid 648 through 650' Processing helix chain 'F' and resid 680 through 692 Processing helix chain 'F' and resid 718 through 727 Processing helix chain 'F' and resid 737 through 745 removed outlier: 4.327A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 751 No H-bonds generated for 'chain 'F' and resid 748 through 751' Processing helix chain 'F' and resid 762 through 765 No H-bonds generated for 'chain 'F' and resid 762 through 765' Processing sheet with id= A, first strand: chain 'A' and resid 7 through 10 removed outlier: 8.591A pdb=" N ILE A 8 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE A 45 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU A 10 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL A 47 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 46 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL A 67 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA A 48 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N TRP A 65 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 90 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL A 70 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA A 88 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 352 through 354 removed outlier: 7.673A pdb=" N THR A 469 " --> pdb=" O LEU A 353 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 376 through 380 removed outlier: 6.705A pdb=" N VAL A 418 " --> pdb=" O HIS A 377 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ILE A 379 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 420 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N PHE A 466 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU A 421 " --> pdb=" O PHE A 466 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE A 468 " --> pdb=" O LEU A 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.279A pdb=" N ARG A 567 " --> pdb=" O GLU A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 597 through 603 removed outlier: 3.702A pdb=" N ALA A 601 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 613 through 618 removed outlier: 3.916A pdb=" N GLU A 613 " --> pdb=" O HIS A 666 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS A 666 " --> pdb=" O GLU A 613 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 700 through 702 removed outlier: 6.287A pdb=" N LYS A 732 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU A 755 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU A 735 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LYS A 757 " --> pdb=" O LEU A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 21 through 23 removed outlier: 3.509A pdb=" N THR B 21 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL B 84 " --> pdb=" O VAL B 23 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 43 through 46 Processing sheet with id= J, first strand: chain 'B' and resid 487 through 489 removed outlier: 6.881A pdb=" N VAL B 352 " --> pdb=" O ILE B 488 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU B 353 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR B 469 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 379 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 613 through 618 removed outlier: 3.565A pdb=" N GLU B 613 " --> pdb=" O HIS B 666 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS B 664 " --> pdb=" O ALA B 615 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 7 through 9 removed outlier: 8.146A pdb=" N ILE C 8 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N PHE C 45 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL C 70 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ALA C 88 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 82 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL C 86 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 73 through 77 removed outlier: 3.991A pdb=" N GLN C 73 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 352 through 355 Processing sheet with id= O, first strand: chain 'C' and resid 378 through 380 removed outlier: 8.151A pdb=" N ILE C 379 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU C 420 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE C 466 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU C 421 " --> pdb=" O PHE C 466 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE C 468 " --> pdb=" O LEU C 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 520 through 522 removed outlier: 6.680A pdb=" N ARG C 567 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 613 through 615 removed outlier: 3.533A pdb=" N GLU C 613 " --> pdb=" O HIS C 666 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS C 666 " --> pdb=" O GLU C 613 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 700 through 702 removed outlier: 7.062A pdb=" N LYS C 732 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU C 755 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU C 735 " --> pdb=" O GLU C 755 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS C 757 " --> pdb=" O LEU C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 4 through 6 Processing sheet with id= T, first strand: chain 'D' and resid 21 through 25 removed outlier: 3.567A pdb=" N THR D 21 " --> pdb=" O VAL D 86 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 43 through 46 Processing sheet with id= V, first strand: chain 'D' and resid 487 through 489 removed outlier: 6.432A pdb=" N VAL D 352 " --> pdb=" O ILE D 488 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU D 351 " --> pdb=" O PHE D 467 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE D 419 " --> pdb=" O PHE D 466 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 520 through 522 removed outlier: 6.110A pdb=" N ARG D 567 " --> pdb=" O GLU D 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'D' and resid 613 through 618 removed outlier: 3.629A pdb=" N GLU D 613 " --> pdb=" O HIS D 666 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL D 617 " --> pdb=" O ASP D 662 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP D 662 " --> pdb=" O VAL D 617 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 705 through 707 removed outlier: 4.445A pdb=" N GLU D 705 " --> pdb=" O MET D 713 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 732 through 736 removed outlier: 6.458A pdb=" N GLU D 755 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU D 735 " --> pdb=" O GLU D 755 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS D 757 " --> pdb=" O LEU D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'E' and resid 21 through 23 removed outlier: 4.055A pdb=" N THR E 21 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL E 86 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU E 87 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL E 71 " --> pdb=" O GLU E 87 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 65 through 67 Processing sheet with id= AC, first strand: chain 'E' and resid 487 through 490 removed outlier: 6.615A pdb=" N VAL E 352 " --> pdb=" O ILE E 488 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE E 490 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL E 354 " --> pdb=" O ILE E 490 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N LEU E 353 " --> pdb=" O PHE E 467 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR E 469 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N GLY E 355 " --> pdb=" O THR E 469 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA E 471 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE E 419 " --> pdb=" O PHE E 466 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS E 377 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 420 " --> pdb=" O HIS E 377 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 520 through 522 removed outlier: 5.787A pdb=" N ARG E 567 " --> pdb=" O GLU E 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'E' and resid 613 through 618 removed outlier: 3.783A pdb=" N VAL E 617 " --> pdb=" O ASP E 662 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL E 665 " --> pdb=" O SER E 624 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 700 through 702 removed outlier: 5.962A pdb=" N LYS E 732 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLU E 755 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU E 735 " --> pdb=" O GLU E 755 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS E 757 " --> pdb=" O LEU E 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'F' and resid 21 through 23 removed outlier: 3.956A pdb=" N THR F 21 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL F 86 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLN F 68 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ARG F 91 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY F 66 " --> pdb=" O ARG F 91 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 352 through 354 removed outlier: 9.048A pdb=" N LEU F 353 " --> pdb=" O PHE F 467 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR F 469 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE F 419 " --> pdb=" O PHE F 466 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP F 422 " --> pdb=" O ILE F 379 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 520 through 522 removed outlier: 5.775A pdb=" N ARG F 567 " --> pdb=" O GLU F 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'F' and resid 596 through 600 removed outlier: 3.811A pdb=" N HIS F 664 " --> pdb=" O ALA F 615 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 732 through 736 removed outlier: 6.156A pdb=" N GLU F 755 " --> pdb=" O ILE F 733 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU F 735 " --> pdb=" O GLU F 755 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS F 757 " --> pdb=" O LEU F 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK 1259 hydrogen bonds defined for protein. 3684 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.89 Time building geometry restraints manager: 14.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 12503 1.36 - 1.51: 9595 1.51 - 1.65: 14776 1.65 - 1.80: 183 1.80 - 1.95: 71 Bond restraints: 37128 Sorted by residual: bond pdb=" C ASP D 51 " pdb=" N PRO D 52 " ideal model delta sigma weight residual 1.330 1.389 -0.059 1.19e-02 7.06e+03 2.48e+01 bond pdb=" C ILE A 477 " pdb=" N PRO A 478 " ideal model delta sigma weight residual 1.331 1.374 -0.043 1.20e-02 6.94e+03 1.30e+01 bond pdb=" C ASP C 51 " pdb=" N PRO C 52 " ideal model delta sigma weight residual 1.332 1.379 -0.047 1.33e-02 5.65e+03 1.26e+01 bond pdb=" CA MET B 516 " pdb=" CB MET B 516 " ideal model delta sigma weight residual 1.528 1.573 -0.045 1.47e-02 4.63e+03 9.44e+00 bond pdb=" N ILE B 419 " pdb=" CA ILE B 419 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.24e-02 6.50e+03 8.95e+00 ... (remaining 37123 not shown) Histogram of bond angle deviations from ideal: 92.99 - 101.97: 124 101.97 - 110.95: 12797 110.95 - 119.93: 21109 119.93 - 128.91: 16039 128.91 - 137.89: 255 Bond angle restraints: 50324 Sorted by residual: angle pdb=" CB MET A 439 " pdb=" CG MET A 439 " pdb=" SD MET A 439 " ideal model delta sigma weight residual 112.70 134.77 -22.07 3.00e+00 1.11e-01 5.41e+01 angle pdb=" N THR B 576 " pdb=" CA THR B 576 " pdb=" C THR B 576 " ideal model delta sigma weight residual 114.62 107.02 7.60 1.14e+00 7.69e-01 4.45e+01 angle pdb=" CA GLU D 204 " pdb=" CB GLU D 204 " pdb=" CG GLU D 204 " ideal model delta sigma weight residual 114.10 127.11 -13.01 2.00e+00 2.50e-01 4.23e+01 angle pdb=" N GLN A 229 " pdb=" CA GLN A 229 " pdb=" CB GLN A 229 " ideal model delta sigma weight residual 110.16 119.49 -9.33 1.48e+00 4.57e-01 3.97e+01 angle pdb=" CA ARG F 227 " pdb=" CB ARG F 227 " pdb=" CG ARG F 227 " ideal model delta sigma weight residual 114.10 126.51 -12.41 2.00e+00 2.50e-01 3.85e+01 ... (remaining 50319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.17: 21997 25.17 - 50.34: 867 50.34 - 75.50: 72 75.50 - 100.67: 16 100.67 - 125.84: 2 Dihedral angle restraints: 22954 sinusoidal: 9574 harmonic: 13380 Sorted by residual: dihedral pdb=" CA ALA D 601 " pdb=" C ALA D 601 " pdb=" N TRP D 602 " pdb=" CA TRP D 602 " ideal model delta harmonic sigma weight residual 180.00 150.16 29.84 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA ASP E 386 " pdb=" C ASP E 386 " pdb=" N GLU E 387 " pdb=" CA GLU E 387 " ideal model delta harmonic sigma weight residual 180.00 150.19 29.81 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA VAL D 706 " pdb=" C VAL D 706 " pdb=" N SER D 707 " pdb=" CA SER D 707 " ideal model delta harmonic sigma weight residual 180.00 150.36 29.64 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 22951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4920 0.096 - 0.192: 735 0.192 - 0.288: 61 0.288 - 0.383: 15 0.383 - 0.479: 5 Chirality restraints: 5736 Sorted by residual: chirality pdb=" CG LEU E 249 " pdb=" CB LEU E 249 " pdb=" CD1 LEU E 249 " pdb=" CD2 LEU E 249 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CB ILE C 468 " pdb=" CA ILE C 468 " pdb=" CG1 ILE C 468 " pdb=" CG2 ILE C 468 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" CB ILE F 415 " pdb=" CA ILE F 415 " pdb=" CG1 ILE F 415 " pdb=" CG2 ILE F 415 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.88e+00 ... (remaining 5733 not shown) Planarity restraints: 6548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 534 " 0.045 2.00e-02 2.50e+03 2.99e-02 1.79e+01 pdb=" CG TYR C 534 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR C 534 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 534 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 534 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 534 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 534 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR C 534 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 203 " 0.034 2.00e-02 2.50e+03 2.82e-02 1.39e+01 pdb=" CG PHE F 203 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE F 203 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE F 203 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 203 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 203 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE F 203 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 602 " -0.026 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP B 602 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP B 602 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP B 602 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 602 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 602 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 602 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 602 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 602 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 602 " -0.009 2.00e-02 2.50e+03 ... (remaining 6545 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 88 2.37 - 3.00: 17965 3.00 - 3.63: 60234 3.63 - 4.27: 89066 4.27 - 4.90: 139388 Nonbonded interactions: 306741 Sorted by model distance: nonbonded pdb=" O TYR B 320 " pdb=" OH TYR B 493 " model vdw 1.737 2.440 nonbonded pdb=" CD2 TYR B 320 " pdb=" CE2 TYR B 493 " model vdw 2.012 3.640 nonbonded pdb=" OG1 THR E 626 " pdb=" O VAL E 665 " model vdw 2.209 2.440 nonbonded pdb=" OG1 THR D 603 " pdb=" O GLY D 606 " model vdw 2.239 2.440 nonbonded pdb=" O LEU A 290 " pdb=" OG1 THR A 294 " model vdw 2.248 2.440 ... (remaining 306736 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 774) selection = (chain 'B' and resid 2 through 774) selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 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: 13.880 Check model and map are aligned: 0.530 Set scattering table: 0.320 Process input model: 96.250 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.210 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 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 : 0.007 0.098 37128 Z= 0.487 Angle : 1.260 22.072 50324 Z= 0.691 Chirality : 0.068 0.479 5736 Planarity : 0.008 0.074 6548 Dihedral : 13.340 125.839 14338 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.92 % Favored : 93.06 % Rotamer: Outliers : 0.13 % Allowed : 0.95 % Favored : 98.92 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.11), residues: 4626 helix: -1.84 (0.10), residues: 1977 sheet: -2.15 (0.22), residues: 470 loop : -1.89 (0.12), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP B 602 HIS 0.020 0.003 HIS C 407 PHE 0.065 0.004 PHE F 203 TYR 0.070 0.004 TYR C 534 ARG 0.036 0.002 ARG D 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 296 time to evaluate : 3.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 300 average time/residue: 0.5298 time to fit residues: 259.8970 Evaluate side-chains 237 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 235 time to evaluate : 4.257 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3523 time to fit residues: 7.7225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 390 optimal weight: 0.5980 chunk 350 optimal weight: 20.0000 chunk 194 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 236 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 362 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 220 optimal weight: 3.9990 chunk 269 optimal weight: 3.9990 chunk 419 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 HIS ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 GLN C 83 GLN ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5915 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37128 Z= 0.194 Angle : 0.694 12.930 50324 Z= 0.352 Chirality : 0.045 0.188 5736 Planarity : 0.005 0.063 6548 Dihedral : 7.297 127.384 5140 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.49 % Allowed : 7.50 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.12), residues: 4626 helix: -0.88 (0.11), residues: 1954 sheet: -2.00 (0.22), residues: 508 loop : -1.75 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 431 HIS 0.008 0.001 HIS E 666 PHE 0.032 0.002 PHE F 203 TYR 0.028 0.002 TYR B 320 ARG 0.007 0.000 ARG D 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 255 time to evaluate : 3.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 263 average time/residue: 0.5090 time to fit residues: 220.7902 Evaluate side-chains 238 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 225 time to evaluate : 3.927 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3737 time to fit residues: 14.5801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 30.0000 chunk 130 optimal weight: 4.9990 chunk 349 optimal weight: 9.9990 chunk 285 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 420 optimal weight: 9.9990 chunk 454 optimal weight: 6.9990 chunk 374 optimal weight: 5.9990 chunk 416 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 337 optimal weight: 0.8980 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN A 407 HIS ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN C 659 ASN C 664 HIS D 499 GLN ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 37128 Z= 0.276 Angle : 0.727 12.286 50324 Z= 0.367 Chirality : 0.045 0.175 5736 Planarity : 0.006 0.071 6548 Dihedral : 7.061 122.014 5140 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 27.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.26 % Allowed : 10.50 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.95 (0.12), residues: 4626 helix: -0.62 (0.11), residues: 1971 sheet: -2.10 (0.22), residues: 517 loop : -1.65 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 431 HIS 0.011 0.002 HIS E 666 PHE 0.028 0.002 PHE D 203 TYR 0.020 0.002 TYR C 768 ARG 0.011 0.001 ARG D 552 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 246 time to evaluate : 4.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 21 residues processed: 277 average time/residue: 0.4916 time to fit residues: 227.1182 Evaluate side-chains 250 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 229 time to evaluate : 4.300 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3403 time to fit residues: 19.5941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 50.0000 chunk 316 optimal weight: 50.0000 chunk 218 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 200 optimal weight: 7.9990 chunk 282 optimal weight: 10.0000 chunk 421 optimal weight: 3.9990 chunk 446 optimal weight: 30.0000 chunk 220 optimal weight: 0.7980 chunk 399 optimal weight: 40.0000 chunk 120 optimal weight: 0.8980 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS A 411 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 ASN ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 37128 Z= 0.248 Angle : 0.687 11.377 50324 Z= 0.347 Chirality : 0.044 0.222 5736 Planarity : 0.005 0.066 6548 Dihedral : 6.921 122.823 5140 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 26.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.38 % Favored : 93.60 % Rotamer: Outliers : 1.41 % Allowed : 13.02 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.81 (0.12), residues: 4626 helix: -0.43 (0.11), residues: 1962 sheet: -2.14 (0.22), residues: 523 loop : -1.62 (0.13), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 431 HIS 0.009 0.002 HIS E 666 PHE 0.021 0.002 PHE F 203 TYR 0.021 0.002 TYR D 534 ARG 0.006 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 235 time to evaluate : 4.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 28 residues processed: 276 average time/residue: 0.4918 time to fit residues: 228.8495 Evaluate side-chains 246 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 218 time to evaluate : 4.236 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3472 time to fit residues: 23.5593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 371 optimal weight: 0.7980 chunk 253 optimal weight: 0.6980 chunk 6 optimal weight: 50.0000 chunk 332 optimal weight: 20.0000 chunk 184 optimal weight: 3.9990 chunk 381 optimal weight: 20.0000 chunk 308 optimal weight: 60.0000 chunk 0 optimal weight: 90.0000 chunk 228 optimal weight: 9.9990 chunk 400 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 ASN ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37128 Z= 0.229 Angle : 0.677 12.148 50324 Z= 0.338 Chirality : 0.044 0.195 5736 Planarity : 0.005 0.066 6548 Dihedral : 6.788 121.699 5140 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 26.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 1.13 % Allowed : 14.82 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.66 (0.12), residues: 4626 helix: -0.29 (0.11), residues: 1964 sheet: -2.14 (0.22), residues: 518 loop : -1.54 (0.14), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 431 HIS 0.008 0.001 HIS A 666 PHE 0.018 0.001 PHE F 203 TYR 0.023 0.002 TYR D 225 ARG 0.007 0.000 ARG D 374 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 233 time to evaluate : 4.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 21 residues processed: 267 average time/residue: 0.4840 time to fit residues: 215.5226 Evaluate side-chains 244 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 223 time to evaluate : 4.079 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3381 time to fit residues: 19.1504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 3.9990 chunk 402 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 262 optimal weight: 0.1980 chunk 110 optimal weight: 10.0000 chunk 447 optimal weight: 20.0000 chunk 371 optimal weight: 8.9990 chunk 206 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 234 optimal weight: 30.0000 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 GLN ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 GLN ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 37128 Z= 0.230 Angle : 0.673 11.902 50324 Z= 0.337 Chirality : 0.044 0.190 5736 Planarity : 0.005 0.069 6548 Dihedral : 6.713 121.654 5140 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 27.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.92 % Favored : 93.06 % Rotamer: Outliers : 1.49 % Allowed : 15.64 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.38 % Twisted General : 0.02 % 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: -1.57 (0.12), residues: 4626 helix: -0.17 (0.11), residues: 1968 sheet: -2.01 (0.22), residues: 503 loop : -1.56 (0.14), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 431 HIS 0.009 0.001 HIS E 666 PHE 0.016 0.001 PHE F 203 TYR 0.018 0.002 TYR C 332 ARG 0.025 0.000 ARG D 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 232 time to evaluate : 4.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 28 residues processed: 278 average time/residue: 0.5028 time to fit residues: 230.6163 Evaluate side-chains 251 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 223 time to evaluate : 4.072 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3676 time to fit residues: 23.9275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 430 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 254 optimal weight: 0.8980 chunk 326 optimal weight: 50.0000 chunk 252 optimal weight: 8.9990 chunk 376 optimal weight: 10.0000 chunk 249 optimal weight: 50.0000 chunk 445 optimal weight: 8.9990 chunk 278 optimal weight: 10.0000 chunk 271 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37128 Z= 0.210 Angle : 0.671 12.637 50324 Z= 0.333 Chirality : 0.044 0.228 5736 Planarity : 0.005 0.071 6548 Dihedral : 6.492 116.245 5140 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 26.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.00 % Allowed : 16.54 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.50 (0.12), residues: 4626 helix: -0.10 (0.12), residues: 1969 sheet: -1.98 (0.22), residues: 524 loop : -1.54 (0.14), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 602 HIS 0.008 0.001 HIS A 666 PHE 0.015 0.001 PHE F 203 TYR 0.019 0.001 TYR C 332 ARG 0.011 0.000 ARG D 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 229 time to evaluate : 4.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 21 residues processed: 258 average time/residue: 0.5168 time to fit residues: 223.8117 Evaluate side-chains 245 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 224 time to evaluate : 4.526 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4036 time to fit residues: 21.3670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 275 optimal weight: 10.0000 chunk 177 optimal weight: 0.9990 chunk 265 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 87 optimal weight: 40.0000 chunk 86 optimal weight: 9.9990 chunk 283 optimal weight: 9.9990 chunk 303 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 41 optimal weight: 30.0000 chunk 350 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 GLN ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37128 Z= 0.205 Angle : 0.667 12.471 50324 Z= 0.330 Chirality : 0.044 0.205 5736 Planarity : 0.005 0.065 6548 Dihedral : 6.434 110.009 5140 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 26.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.82 % Allowed : 16.87 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.42 (0.12), residues: 4626 helix: -0.03 (0.12), residues: 1969 sheet: -1.88 (0.22), residues: 502 loop : -1.53 (0.14), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 602 HIS 0.008 0.001 HIS C 664 PHE 0.014 0.001 PHE F 203 TYR 0.020 0.001 TYR C 332 ARG 0.011 0.000 ARG D 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 228 time to evaluate : 4.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 249 average time/residue: 0.4834 time to fit residues: 202.8775 Evaluate side-chains 238 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 223 time to evaluate : 4.141 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3542 time to fit residues: 16.1820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 405 optimal weight: 10.0000 chunk 426 optimal weight: 8.9990 chunk 389 optimal weight: 50.0000 chunk 414 optimal weight: 0.9980 chunk 249 optimal weight: 50.0000 chunk 180 optimal weight: 5.9990 chunk 325 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 374 optimal weight: 7.9990 chunk 392 optimal weight: 50.0000 chunk 413 optimal weight: 4.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 GLN ** F 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 37128 Z= 0.285 Angle : 0.754 12.646 50324 Z= 0.376 Chirality : 0.046 0.217 5736 Planarity : 0.005 0.056 6548 Dihedral : 6.727 110.585 5140 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 33.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.69 % Allowed : 17.49 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.12), residues: 4626 helix: -0.24 (0.11), residues: 1947 sheet: -2.02 (0.22), residues: 511 loop : -1.58 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 602 HIS 0.008 0.002 HIS C 664 PHE 0.026 0.002 PHE F 451 TYR 0.023 0.002 TYR C 332 ARG 0.018 0.001 ARG B 697 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 231 time to evaluate : 4.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 251 average time/residue: 0.4938 time to fit residues: 210.1088 Evaluate side-chains 238 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 223 time to evaluate : 4.127 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4271 time to fit residues: 17.4437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 272 optimal weight: 9.9990 chunk 438 optimal weight: 30.0000 chunk 267 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 305 optimal weight: 4.9990 chunk 460 optimal weight: 8.9990 chunk 423 optimal weight: 10.0000 chunk 366 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 283 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37128 Z= 0.224 Angle : 0.701 12.455 50324 Z= 0.348 Chirality : 0.045 0.242 5736 Planarity : 0.005 0.049 6548 Dihedral : 6.588 112.599 5140 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 28.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.39 % Allowed : 18.05 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.54 (0.12), residues: 4626 helix: -0.12 (0.12), residues: 1950 sheet: -1.92 (0.22), residues: 518 loop : -1.58 (0.14), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 602 HIS 0.009 0.001 HIS C 664 PHE 0.016 0.001 PHE D 467 TYR 0.020 0.001 TYR C 332 ARG 0.008 0.000 ARG D 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 229 time to evaluate : 4.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 237 average time/residue: 0.5160 time to fit residues: 206.8452 Evaluate side-chains 231 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 222 time to evaluate : 4.450 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3585 time to fit residues: 12.2688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 291 optimal weight: 0.0770 chunk 390 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 337 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 101 optimal weight: 0.5980 chunk 367 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 chunk 376 optimal weight: 10.0000 chunk 46 optimal weight: 0.0980 chunk 67 optimal weight: 9.9990 overall best weight: 2.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 HIS ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.116718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.083632 restraints weight = 124493.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.081510 restraints weight = 176405.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.081033 restraints weight = 225282.266| |-----------------------------------------------------------------------------| r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37128 Z= 0.202 Angle : 0.696 15.013 50324 Z= 0.342 Chirality : 0.045 0.203 5736 Planarity : 0.005 0.049 6548 Dihedral : 6.501 110.285 5140 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 27.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.05 % Allowed : 18.36 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.45 (0.12), residues: 4626 helix: -0.04 (0.12), residues: 1945 sheet: -1.90 (0.22), residues: 512 loop : -1.54 (0.14), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 602 HIS 0.009 0.001 HIS C 664 PHE 0.014 0.001 PHE B 132 TYR 0.020 0.001 TYR C 332 ARG 0.007 0.000 ARG D 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6834.28 seconds wall clock time: 126 minutes 29.60 seconds (7589.60 seconds total)