Starting phenix.real_space_refine (version: dev) on Thu Feb 23 02:14:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo9_7121/02_2023/6bo9_7121.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo9_7121/02_2023/6bo9_7121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo9_7121/02_2023/6bo9_7121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo9_7121/02_2023/6bo9_7121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo9_7121/02_2023/6bo9_7121.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo9_7121/02_2023/6bo9_7121.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 Process input model Symmetric amino acids flipped Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 621": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 621": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C ARG 589": "NH1" <-> "NH2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C ARG 621": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D ARG 589": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 621": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 19048 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "B" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "C" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "D" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Time building chain proxies: 10.64, per 1000 atoms: 0.56 Number of scatterers: 19048 At special positions: 0 Unit cell: (140.14, 140.14, 125.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 3368 8.00 N 3220 7.00 C 12304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.14 Conformation dependent library (CDL) restraints added in 2.9 seconds 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 63.2% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 3.753A pdb=" N ARG A 33 " --> pdb=" O TRP A 29 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 40 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.642A pdb=" N ASP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 66 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 4.374A pdb=" N GLU A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.586A pdb=" N ALA A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 209 through 220 removed outlier: 4.175A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 224 removed outlier: 4.105A pdb=" N ARG A 224 " --> pdb=" O SER A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 224' Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.716A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.624A pdb=" N ALA A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 325 through 349 removed outlier: 3.738A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 403 removed outlier: 3.860A pdb=" N ILE A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 446 Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.717A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.725A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 493 through 512 removed outlier: 4.220A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 4.032A pdb=" N PHE A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR A 524 " --> pdb=" O GLY A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.846A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.760A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 588 removed outlier: 3.519A pdb=" N LEU A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 606 Processing helix chain 'B' and resid 29 through 47 removed outlier: 3.754A pdb=" N ARG B 33 " --> pdb=" O TRP B 29 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.642A pdb=" N ASP B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 66 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 4.374A pdb=" N GLU B 100 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.586A pdb=" N ALA B 135 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 209 through 220 removed outlier: 4.174A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 224 removed outlier: 4.105A pdb=" N ARG B 224 " --> pdb=" O SER B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 224' Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.716A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.624A pdb=" N ALA B 304 " --> pdb=" O LYS B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 325 through 349 removed outlier: 3.739A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 349 " --> pdb=" O MET B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 403 removed outlier: 3.861A pdb=" N ILE B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 446 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.717A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.725A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 493 through 512 removed outlier: 4.220A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 524 removed outlier: 4.032A pdb=" N PHE B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 524' Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.847A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.759A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 588 removed outlier: 3.520A pdb=" N LEU B 573 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 606 Processing helix chain 'C' and resid 29 through 47 removed outlier: 3.754A pdb=" N ARG C 33 " --> pdb=" O TRP C 29 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.643A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 4.374A pdb=" N GLU C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.586A pdb=" N ALA C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 209 through 220 removed outlier: 4.174A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 224 removed outlier: 4.104A pdb=" N ARG C 224 " --> pdb=" O SER C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 224' Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.716A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.624A pdb=" N ALA C 304 " --> pdb=" O LYS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 Processing helix chain 'C' and resid 325 through 349 removed outlier: 3.738A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR C 349 " --> pdb=" O MET C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 403 removed outlier: 3.861A pdb=" N ILE C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 446 Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.716A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.726A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 493 through 512 removed outlier: 4.220A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 524 removed outlier: 4.032A pdb=" N PHE C 523 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR C 524 " --> pdb=" O GLY C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 524' Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.847A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.760A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 588 removed outlier: 3.519A pdb=" N LEU C 573 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 606 Processing helix chain 'D' and resid 29 through 47 removed outlier: 3.754A pdb=" N ARG D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN D 40 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.643A pdb=" N ASP D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 4.373A pdb=" N GLU D 100 " --> pdb=" O MET D 96 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.587A pdb=" N ALA D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 209 through 220 removed outlier: 4.174A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 224 removed outlier: 4.104A pdb=" N ARG D 224 " --> pdb=" O SER D 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 221 through 224' Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.716A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 Processing helix chain 'D' and resid 301 through 309 removed outlier: 3.624A pdb=" N ALA D 304 " --> pdb=" O LYS D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 Processing helix chain 'D' and resid 325 through 349 removed outlier: 3.738A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR D 349 " --> pdb=" O MET D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 403 removed outlier: 3.861A pdb=" N ILE D 384 " --> pdb=" O PRO D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 446 Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.716A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.726A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 493 through 512 removed outlier: 4.220A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 524 removed outlier: 4.031A pdb=" N PHE D 523 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR D 524 " --> pdb=" O GLY D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 524' Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.847A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.760A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 588 removed outlier: 3.519A pdb=" N LEU D 573 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 606 Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AA3, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AA4, first strand: chain 'D' and resid 269 through 270 960 hydrogen bonds defined for protein. 2760 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: 5.45 Time building geometry restraints manager: 7.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6070 1.34 - 1.46: 4285 1.46 - 1.58: 8865 1.58 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 19484 Sorted by residual: bond pdb=" C ILE A 565 " pdb=" N ALA A 566 " ideal model delta sigma weight residual 1.332 1.301 0.032 1.40e-02 5.10e+03 5.09e+00 bond pdb=" C ILE B 565 " pdb=" N ALA B 566 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 4.95e+00 bond pdb=" C ILE C 565 " pdb=" N ALA C 566 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 4.95e+00 bond pdb=" C ILE D 565 " pdb=" N ALA D 566 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 4.93e+00 bond pdb=" CA VAL D 404 " pdb=" CB VAL D 404 " ideal model delta sigma weight residual 1.534 1.548 -0.014 6.80e-03 2.16e+04 4.14e+00 ... (remaining 19479 not shown) Histogram of bond angle deviations from ideal: 98.02 - 105.33: 443 105.33 - 112.63: 10225 112.63 - 119.93: 7055 119.93 - 127.23: 8429 127.23 - 134.54: 288 Bond angle restraints: 26440 Sorted by residual: angle pdb=" N SER B 112 " pdb=" CA SER B 112 " pdb=" C SER B 112 " ideal model delta sigma weight residual 108.79 117.21 -8.42 1.53e+00 4.27e-01 3.03e+01 angle pdb=" N SER C 112 " pdb=" CA SER C 112 " pdb=" C SER C 112 " ideal model delta sigma weight residual 108.79 117.17 -8.38 1.53e+00 4.27e-01 3.00e+01 angle pdb=" N SER A 112 " pdb=" CA SER A 112 " pdb=" C SER A 112 " ideal model delta sigma weight residual 108.79 117.16 -8.37 1.53e+00 4.27e-01 2.99e+01 angle pdb=" N SER D 112 " pdb=" CA SER D 112 " pdb=" C SER D 112 " ideal model delta sigma weight residual 108.79 117.14 -8.35 1.53e+00 4.27e-01 2.98e+01 angle pdb=" N LEU B 352 " pdb=" CA LEU B 352 " pdb=" C LEU B 352 " ideal model delta sigma weight residual 110.91 117.17 -6.26 1.17e+00 7.31e-01 2.86e+01 ... (remaining 26435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 10904 15.36 - 30.73: 591 30.73 - 46.09: 177 46.09 - 61.45: 4 61.45 - 76.82: 12 Dihedral angle restraints: 11688 sinusoidal: 4728 harmonic: 6960 Sorted by residual: dihedral pdb=" CA ASN C 129 " pdb=" C ASN C 129 " pdb=" N MET C 130 " pdb=" CA MET C 130 " ideal model delta harmonic sigma weight residual 180.00 144.34 35.66 0 5.00e+00 4.00e-02 5.09e+01 dihedral pdb=" CA ASN D 129 " pdb=" C ASN D 129 " pdb=" N MET D 130 " pdb=" CA MET D 130 " ideal model delta harmonic sigma weight residual 180.00 144.35 35.65 0 5.00e+00 4.00e-02 5.08e+01 dihedral pdb=" CA ASN B 129 " pdb=" C ASN B 129 " pdb=" N MET B 130 " pdb=" CA MET B 130 " ideal model delta harmonic sigma weight residual 180.00 144.35 35.65 0 5.00e+00 4.00e-02 5.08e+01 ... (remaining 11685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1969 0.049 - 0.097: 827 0.097 - 0.146: 168 0.146 - 0.195: 36 0.195 - 0.244: 12 Chirality restraints: 3012 Sorted by residual: chirality pdb=" CA THR A 311 " pdb=" N THR A 311 " pdb=" C THR A 311 " pdb=" CB THR A 311 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA THR D 311 " pdb=" N THR D 311 " pdb=" C THR D 311 " pdb=" CB THR D 311 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA THR B 311 " pdb=" N THR B 311 " pdb=" C THR B 311 " pdb=" CB THR B 311 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 3009 not shown) Planarity restraints: 3336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 323 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C ARG D 323 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG D 323 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR D 324 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 323 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C ARG A 323 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG A 323 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR A 324 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 323 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C ARG B 323 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG B 323 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR B 324 " -0.013 2.00e-02 2.50e+03 ... (remaining 3333 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 4393 2.78 - 3.31: 19040 3.31 - 3.84: 31753 3.84 - 4.37: 38142 4.37 - 4.90: 61257 Nonbonded interactions: 154585 Sorted by model distance: nonbonded pdb=" O VAL A 427 " pdb=" OG1 THR A 431 " model vdw 2.245 2.440 nonbonded pdb=" O VAL C 427 " pdb=" OG1 THR C 431 " model vdw 2.245 2.440 nonbonded pdb=" O VAL D 427 " pdb=" OG1 THR D 431 " model vdw 2.245 2.440 nonbonded pdb=" O VAL B 427 " pdb=" OG1 THR B 431 " model vdw 2.245 2.440 nonbonded pdb=" OH TYR C 339 " pdb=" O THR C 392 " model vdw 2.259 2.440 ... (remaining 154580 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 12304 2.51 5 N 3220 2.21 5 O 3368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.710 Check model and map are aligned: 0.290 Process input model: 46.750 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.160 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5891 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 0.059 19484 Z= 0.428 Angle : 1.168 18.238 26440 Z= 0.658 Chirality : 0.055 0.244 3012 Planarity : 0.007 0.046 3336 Dihedral : 10.847 76.817 7184 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.34 (0.14), residues: 2356 helix: -2.49 (0.10), residues: 1348 sheet: -5.71 (0.21), residues: 56 loop : -3.13 (0.19), residues: 952 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 930 time to evaluate : 2.274 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 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: 20 outliers final: 2 residues processed: 942 average time/residue: 0.3207 time to fit residues: 446.7789 Evaluate side-chains 536 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 534 time to evaluate : 2.262 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1651 time to fit residues: 3.7272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 71 optimal weight: 0.0670 chunk 112 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 214 optimal weight: 0.0870 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 HIS A 165 HIS A 257 GLN A 357 ASN A 365 ASN A 464 ASN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 365 ASN B 522 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS C 174 ASN C 257 GLN C 265 HIS C 267 GLN C 357 ASN C 365 ASN C 464 ASN C 522 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS D 257 GLN D 267 GLN D 464 ASN D 572 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 19484 Z= 0.207 Angle : 0.800 12.574 26440 Z= 0.391 Chirality : 0.044 0.246 3012 Planarity : 0.005 0.037 3336 Dihedral : 5.899 27.884 2596 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.30 % Favored : 90.66 % Rotamer Outliers : 3.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.16), residues: 2356 helix: -0.55 (0.12), residues: 1388 sheet: -4.65 (0.31), residues: 56 loop : -2.74 (0.20), residues: 912 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 625 time to evaluate : 2.010 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 30 residues processed: 671 average time/residue: 0.2876 time to fit residues: 297.5076 Evaluate side-chains 534 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 504 time to evaluate : 2.187 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1717 time to fit residues: 12.8810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 212 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 172 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN A 267 GLN A 464 ASN A 522 HIS A 572 ASN B 31 GLN B 41 GLN B 118 GLN ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 267 GLN B 357 ASN B 464 ASN B 572 ASN C 31 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 19484 Z= 0.255 Angle : 0.775 12.860 26440 Z= 0.378 Chirality : 0.045 0.290 3012 Planarity : 0.004 0.049 3336 Dihedral : 5.349 25.699 2596 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.17), residues: 2356 helix: 0.38 (0.14), residues: 1384 sheet: -3.59 (0.42), residues: 56 loop : -2.55 (0.21), residues: 916 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 537 time to evaluate : 2.281 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: 76 outliers final: 31 residues processed: 579 average time/residue: 0.2708 time to fit residues: 247.1335 Evaluate side-chains 503 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 472 time to evaluate : 2.086 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1631 time to fit residues: 12.6012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 228 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 ASN ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN A 464 ASN ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN C 306 GLN ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN D 265 HIS ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.6043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 19484 Z= 0.202 Angle : 0.758 14.657 26440 Z= 0.360 Chirality : 0.044 0.221 3012 Planarity : 0.004 0.045 3336 Dihedral : 5.146 26.870 2596 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.18), residues: 2356 helix: 0.65 (0.14), residues: 1388 sheet: -2.60 (0.53), residues: 56 loop : -2.42 (0.21), residues: 912 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 500 time to evaluate : 2.367 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 revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 23 residues processed: 532 average time/residue: 0.2849 time to fit residues: 237.7045 Evaluate side-chains 477 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 454 time to evaluate : 2.420 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1791 time to fit residues: 10.8504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 3 optimal weight: 0.0970 chunk 169 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 157 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 0.0050 chunk 204 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN A 267 GLN A 306 GLN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN B 596 GLN ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN D 464 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.6387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 19484 Z= 0.181 Angle : 0.745 14.471 26440 Z= 0.351 Chirality : 0.043 0.221 3012 Planarity : 0.004 0.034 3336 Dihedral : 4.938 23.582 2596 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.18), residues: 2356 helix: 0.80 (0.14), residues: 1408 sheet: -2.00 (0.60), residues: 56 loop : -2.34 (0.21), residues: 892 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 494 time to evaluate : 2.343 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: 57 outliers final: 21 residues processed: 523 average time/residue: 0.2829 time to fit residues: 232.7234 Evaluate side-chains 465 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 444 time to evaluate : 2.427 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1722 time to fit residues: 9.6836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 133 optimal weight: 0.0980 chunk 56 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 464 ASN B 41 GLN ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 197 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.6779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 19484 Z= 0.212 Angle : 0.754 14.044 26440 Z= 0.356 Chirality : 0.043 0.200 3012 Planarity : 0.004 0.033 3336 Dihedral : 4.867 22.436 2596 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.18), residues: 2356 helix: 0.76 (0.14), residues: 1424 sheet: -1.87 (0.56), residues: 56 loop : -2.32 (0.22), residues: 876 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 482 time to evaluate : 2.289 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: 60 outliers final: 24 residues processed: 510 average time/residue: 0.2821 time to fit residues: 226.0745 Evaluate side-chains 464 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 440 time to evaluate : 2.198 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1766 time to fit residues: 10.9287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 129 optimal weight: 20.0000 chunk 192 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 227 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.7524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 19484 Z= 0.316 Angle : 0.839 16.027 26440 Z= 0.403 Chirality : 0.047 0.244 3012 Planarity : 0.004 0.036 3336 Dihedral : 5.182 25.263 2596 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 2356 helix: 0.59 (0.14), residues: 1408 sheet: -2.03 (0.56), residues: 56 loop : -2.36 (0.22), residues: 892 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 489 time to evaluate : 2.271 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 outliers start: 53 outliers final: 17 residues processed: 520 average time/residue: 0.2822 time to fit residues: 230.7679 Evaluate side-chains 463 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 446 time to evaluate : 2.296 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1748 time to fit residues: 8.8457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 HIS ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 197 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.7879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 19484 Z= 0.275 Angle : 0.831 16.175 26440 Z= 0.393 Chirality : 0.046 0.233 3012 Planarity : 0.004 0.040 3336 Dihedral : 5.069 26.070 2596 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.76 % Favored : 90.20 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.18), residues: 2356 helix: 0.59 (0.14), residues: 1416 sheet: -2.03 (0.56), residues: 56 loop : -2.42 (0.22), residues: 884 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 459 time to evaluate : 2.188 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 outliers start: 33 outliers final: 17 residues processed: 477 average time/residue: 0.2855 time to fit residues: 214.9647 Evaluate side-chains 450 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 433 time to evaluate : 2.109 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1815 time to fit residues: 8.6907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 0.3980 chunk 198 optimal weight: 0.8980 chunk 211 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 92 optimal weight: 0.1980 chunk 166 optimal weight: 0.7980 chunk 65 optimal weight: 20.0000 chunk 191 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 306 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.8040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 19484 Z= 0.212 Angle : 0.850 16.301 26440 Z= 0.395 Chirality : 0.045 0.296 3012 Planarity : 0.004 0.038 3336 Dihedral : 5.027 28.914 2596 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.18), residues: 2356 helix: 0.72 (0.14), residues: 1392 sheet: -1.93 (0.60), residues: 56 loop : -2.42 (0.21), residues: 908 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 491 time to evaluate : 2.364 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 outliers start: 22 outliers final: 10 residues processed: 501 average time/residue: 0.2902 time to fit residues: 227.0784 Evaluate side-chains 456 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 446 time to evaluate : 2.177 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1809 time to fit residues: 6.4168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 6.9990 chunk 106 optimal weight: 0.1980 chunk 155 optimal weight: 4.9990 chunk 235 optimal weight: 10.0000 chunk 216 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 19 optimal weight: 0.0670 chunk 144 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 148 optimal weight: 0.9980 chunk 199 optimal weight: 5.9990 overall best weight: 1.4520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN C 185 HIS C 197 ASN C 257 GLN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 197 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.8183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 19484 Z= 0.235 Angle : 0.868 15.810 26440 Z= 0.402 Chirality : 0.046 0.361 3012 Planarity : 0.004 0.038 3336 Dihedral : 4.983 28.170 2596 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.18), residues: 2356 helix: 0.74 (0.14), residues: 1404 sheet: -1.92 (0.59), residues: 56 loop : -2.38 (0.21), residues: 896 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 463 time to evaluate : 2.433 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 outliers start: 11 outliers final: 5 residues processed: 468 average time/residue: 0.2807 time to fit residues: 209.1006 Evaluate side-chains 445 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 440 time to evaluate : 2.206 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1743 time to fit residues: 4.5549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 8.9990 chunk 172 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.0070 chunk 164 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 HIS ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 257 GLN ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 197 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.147915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119552 restraints weight = 38411.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121590 restraints weight = 25067.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122729 restraints weight = 18651.013| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.8345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 19484 Z= 0.265 Angle : 0.892 15.611 26440 Z= 0.415 Chirality : 0.047 0.350 3012 Planarity : 0.004 0.040 3336 Dihedral : 5.020 30.134 2596 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.02 (0.18), residues: 2356 helix: 0.56 (0.14), residues: 1444 sheet: -2.01 (0.58), residues: 56 loop : -2.81 (0.21), residues: 856 =============================================================================== Job complete usr+sys time: 4461.73 seconds wall clock time: 81 minutes 2.06 seconds (4862.06 seconds total)