Starting phenix.real_space_refine on Mon Sep 30 00:47:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pby_20295/09_2024/6pby_20295.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pby_20295/09_2024/6pby_20295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pby_20295/09_2024/6pby_20295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pby_20295/09_2024/6pby_20295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pby_20295/09_2024/6pby_20295.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pby_20295/09_2024/6pby_20295.cif" } resolution = 3.67 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= 0.003 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 15412 2.51 5 N 3964 2.21 5 O 4328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 148 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23832 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5088 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 22, 'TRANS': 652} Chain breaks: 4 Unresolved non-hydrogen bonds: 379 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 9, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 228 Chain: "B" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 870 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 149 Restraints were copied for chains: C, E, G, D, F, H Time building chain proxies: 13.60, per 1000 atoms: 0.57 Number of scatterers: 23832 At special positions: 0 Unit cell: (155, 155, 143, 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 128 16.00 O 4328 8.00 N 3964 7.00 C 15412 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 - 3.00 Amino acid : True - 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: 5.82 Conformation dependent library (CDL) restraints added in 3.3 seconds 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6200 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 12 sheets defined 62.5% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.514A pdb=" N ILE A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 133 through 138 removed outlier: 3.884A pdb=" N GLN A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 175 through 194 removed outlier: 3.805A pdb=" N VAL A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 242 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 283 through 303 removed outlier: 4.041A pdb=" N LYS A 293 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N PHE A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 removed outlier: 4.196A pdb=" N VAL A 328 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 334 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 removed outlier: 3.799A pdb=" N LYS A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 379 removed outlier: 3.950A pdb=" N PHE A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 418 through 435 Processing helix chain 'A' and resid 446 through 499 removed outlier: 3.809A pdb=" N LEU A 462 " --> pdb=" O MET A 458 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN A 481 " --> pdb=" O GLN A 477 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 521 Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.930A pdb=" N CYS A 532 " --> pdb=" O VAL A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 545 Processing helix chain 'A' and resid 545 through 550 Processing helix chain 'A' and resid 559 through 568 Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 647 through 657 Processing helix chain 'A' and resid 657 through 668 removed outlier: 3.853A pdb=" N HIS A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 696 Processing helix chain 'A' and resid 707 through 720 removed outlier: 4.105A pdb=" N ARG A 712 " --> pdb=" O HIS A 708 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU A 713 " --> pdb=" O PRO A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 11 No H-bonds generated for 'chain 'B' and resid 9 through 11' Processing helix chain 'B' and resid 12 through 20 removed outlier: 3.704A pdb=" N ASP B 20 " --> pdb=" O PHE B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 40 Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.690A pdb=" N THR B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N MET B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 93 removed outlier: 3.609A pdb=" N GLU B 83 " --> pdb=" O THR B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 113 removed outlier: 3.565A pdb=" N GLY B 113 " --> pdb=" O MET B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.734A pdb=" N MET B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 11 No H-bonds generated for 'chain 'D' and resid 9 through 11' Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.704A pdb=" N ASP D 20 " --> pdb=" O PHE D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 40 Processing helix chain 'D' and resid 44 through 56 Processing helix chain 'D' and resid 65 through 75 removed outlier: 3.689A pdb=" N THR D 70 " --> pdb=" O PRO D 66 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N MET D 71 " --> pdb=" O GLU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 93 removed outlier: 3.609A pdb=" N GLU D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.565A pdb=" N GLY D 113 " --> pdb=" O MET D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.734A pdb=" N MET D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 11 No H-bonds generated for 'chain 'F' and resid 9 through 11' Processing helix chain 'F' and resid 12 through 20 removed outlier: 3.704A pdb=" N ASP F 20 " --> pdb=" O PHE F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 40 Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 65 through 75 removed outlier: 3.690A pdb=" N THR F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N MET F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 removed outlier: 3.609A pdb=" N GLU F 83 " --> pdb=" O THR F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 113 removed outlier: 3.566A pdb=" N GLY F 113 " --> pdb=" O MET F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 137 through 146 removed outlier: 3.735A pdb=" N MET F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 11 No H-bonds generated for 'chain 'H' and resid 9 through 11' Processing helix chain 'H' and resid 12 through 20 removed outlier: 3.704A pdb=" N ASP H 20 " --> pdb=" O PHE H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 40 Processing helix chain 'H' and resid 44 through 56 Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.690A pdb=" N THR H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N MET H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 removed outlier: 3.609A pdb=" N GLU H 83 " --> pdb=" O THR H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 113 removed outlier: 3.565A pdb=" N GLY H 113 " --> pdb=" O MET H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 137 through 146 removed outlier: 3.735A pdb=" N MET H 144 " --> pdb=" O GLU H 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 26 removed outlier: 3.514A pdb=" N ILE C 21 " --> pdb=" O PHE C 17 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN C 26 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 76 through 90 Processing helix chain 'C' and resid 133 through 138 removed outlier: 3.885A pdb=" N GLN C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 175 through 194 removed outlier: 3.805A pdb=" N VAL C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 242 Proline residue: C 236 - end of helix Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 283 through 303 removed outlier: 4.041A pdb=" N LYS C 293 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N PHE C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 335 removed outlier: 4.196A pdb=" N VAL C 328 " --> pdb=" O SER C 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 334 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.799A pdb=" N LYS C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 379 removed outlier: 3.949A pdb=" N PHE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 418 through 435 Processing helix chain 'C' and resid 446 through 499 removed outlier: 3.808A pdb=" N LEU C 462 " --> pdb=" O MET C 458 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN C 481 " --> pdb=" O GLN C 477 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR C 482 " --> pdb=" O MET C 478 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR C 485 " --> pdb=" O ASN C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 521 Processing helix chain 'C' and resid 524 through 532 removed outlier: 3.931A pdb=" N CYS C 532 " --> pdb=" O VAL C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 545 Processing helix chain 'C' and resid 545 through 550 Processing helix chain 'C' and resid 559 through 568 Processing helix chain 'C' and resid 620 through 625 Processing helix chain 'C' and resid 647 through 657 Processing helix chain 'C' and resid 657 through 668 removed outlier: 3.853A pdb=" N HIS C 662 " --> pdb=" O THR C 658 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 696 Processing helix chain 'C' and resid 707 through 720 removed outlier: 4.105A pdb=" N ARG C 712 " --> pdb=" O HIS C 708 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU C 713 " --> pdb=" O PRO C 709 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 26 removed outlier: 3.514A pdb=" N ILE E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN E 26 " --> pdb=" O VAL E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 76 through 90 Processing helix chain 'E' and resid 133 through 138 removed outlier: 3.885A pdb=" N GLN E 138 " --> pdb=" O THR E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 175 through 194 removed outlier: 3.805A pdb=" N VAL E 187 " --> pdb=" O ARG E 183 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 242 Proline residue: E 236 - end of helix Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 283 through 303 removed outlier: 4.041A pdb=" N LYS E 293 " --> pdb=" O MET E 289 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR E 294 " --> pdb=" O ASN E 290 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N PHE E 296 " --> pdb=" O LEU E 292 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL E 297 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 335 removed outlier: 4.196A pdb=" N VAL E 328 " --> pdb=" O SER E 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 334 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 removed outlier: 3.799A pdb=" N LYS E 340 " --> pdb=" O ARG E 336 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 379 removed outlier: 3.950A pdb=" N PHE E 379 " --> pdb=" O ASP E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 400 Processing helix chain 'E' and resid 418 through 435 Processing helix chain 'E' and resid 446 through 499 removed outlier: 3.810A pdb=" N LEU E 462 " --> pdb=" O MET E 458 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN E 481 " --> pdb=" O GLN E 477 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR E 482 " --> pdb=" O MET E 478 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR E 485 " --> pdb=" O ASN E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 521 Processing helix chain 'E' and resid 524 through 532 removed outlier: 3.931A pdb=" N CYS E 532 " --> pdb=" O VAL E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 545 Processing helix chain 'E' and resid 545 through 550 Processing helix chain 'E' and resid 559 through 568 Processing helix chain 'E' and resid 620 through 625 Processing helix chain 'E' and resid 647 through 657 Processing helix chain 'E' and resid 657 through 668 removed outlier: 3.853A pdb=" N HIS E 662 " --> pdb=" O THR E 658 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 696 Processing helix chain 'E' and resid 707 through 720 removed outlier: 4.105A pdb=" N ARG E 712 " --> pdb=" O HIS E 708 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU E 713 " --> pdb=" O PRO E 709 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 26 removed outlier: 3.514A pdb=" N ILE G 21 " --> pdb=" O PHE G 17 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN G 26 " --> pdb=" O VAL G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 54 Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'G' and resid 67 through 71 Processing helix chain 'G' and resid 76 through 90 Processing helix chain 'G' and resid 133 through 138 removed outlier: 3.884A pdb=" N GLN G 138 " --> pdb=" O THR G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 158 Processing helix chain 'G' and resid 175 through 194 removed outlier: 3.805A pdb=" N VAL G 187 " --> pdb=" O ARG G 183 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER G 192 " --> pdb=" O LEU G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 242 Proline residue: G 236 - end of helix Processing helix chain 'G' and resid 248 through 271 Processing helix chain 'G' and resid 283 through 303 removed outlier: 4.041A pdb=" N LYS G 293 " --> pdb=" O MET G 289 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N PHE G 296 " --> pdb=" O LEU G 292 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL G 297 " --> pdb=" O LYS G 293 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE G 298 " --> pdb=" O THR G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 335 removed outlier: 4.196A pdb=" N VAL G 328 " --> pdb=" O SER G 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU G 334 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 342 removed outlier: 3.799A pdb=" N LYS G 340 " --> pdb=" O ARG G 336 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP G 342 " --> pdb=" O ALA G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 347 through 379 removed outlier: 3.951A pdb=" N PHE G 379 " --> pdb=" O ASP G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 400 Processing helix chain 'G' and resid 418 through 435 Processing helix chain 'G' and resid 446 through 499 removed outlier: 3.809A pdb=" N LEU G 462 " --> pdb=" O MET G 458 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN G 481 " --> pdb=" O GLN G 477 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N THR G 482 " --> pdb=" O MET G 478 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR G 485 " --> pdb=" O ASN G 481 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 521 Processing helix chain 'G' and resid 524 through 532 removed outlier: 3.931A pdb=" N CYS G 532 " --> pdb=" O VAL G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 533 through 545 Processing helix chain 'G' and resid 545 through 550 Processing helix chain 'G' and resid 559 through 568 Processing helix chain 'G' and resid 620 through 625 Processing helix chain 'G' and resid 647 through 657 Processing helix chain 'G' and resid 657 through 668 removed outlier: 3.853A pdb=" N HIS G 662 " --> pdb=" O THR G 658 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER G 663 " --> pdb=" O ALA G 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 682 through 696 Processing helix chain 'G' and resid 707 through 720 removed outlier: 4.105A pdb=" N ARG G 712 " --> pdb=" O HIS G 708 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU G 713 " --> pdb=" O PRO G 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.475A pdb=" N LEU A 32 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER A 45 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N PHE A 30 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 29 " --> pdb=" O PHE A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 571 through 575 removed outlier: 6.831A pdb=" N HIS A 643 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL A 594 " --> pdb=" O HIS A 643 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE A 645 " --> pdb=" O CYS A 592 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N CYS A 592 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP A 615 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 672 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 606 through 611 removed outlier: 6.573A pdb=" N VAL A 601 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE A 610 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A 599 " --> pdb=" O ILE A 610 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.475A pdb=" N LEU C 32 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER C 45 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N PHE C 30 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 29 " --> pdb=" O PHE C 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 571 through 575 removed outlier: 6.831A pdb=" N HIS C 643 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL C 594 " --> pdb=" O HIS C 643 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE C 645 " --> pdb=" O CYS C 592 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N CYS C 592 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP C 615 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR C 672 " --> pdb=" O VAL C 616 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 606 through 611 removed outlier: 6.573A pdb=" N VAL C 601 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE C 610 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 599 " --> pdb=" O ILE C 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 42 through 45 removed outlier: 6.475A pdb=" N LEU E 32 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER E 45 " --> pdb=" O PHE E 30 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N PHE E 30 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN E 29 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 571 through 575 removed outlier: 6.830A pdb=" N HIS E 643 " --> pdb=" O VAL E 594 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL E 594 " --> pdb=" O HIS E 643 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE E 645 " --> pdb=" O CYS E 592 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N CYS E 592 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP E 615 " --> pdb=" O VAL E 594 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR E 672 " --> pdb=" O VAL E 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 606 through 611 removed outlier: 6.572A pdb=" N VAL E 601 " --> pdb=" O VAL E 608 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE E 610 " --> pdb=" O LEU E 599 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU E 599 " --> pdb=" O ILE E 610 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 45 removed outlier: 6.475A pdb=" N LEU G 32 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER G 45 " --> pdb=" O PHE G 30 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE G 30 " --> pdb=" O SER G 45 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN G 29 " --> pdb=" O PHE G 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 571 through 575 removed outlier: 6.831A pdb=" N HIS G 643 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL G 594 " --> pdb=" O HIS G 643 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE G 645 " --> pdb=" O CYS G 592 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N CYS G 592 " --> pdb=" O ILE G 645 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP G 615 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR G 672 " --> pdb=" O VAL G 616 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 606 through 611 removed outlier: 6.572A pdb=" N VAL G 601 " --> pdb=" O VAL G 608 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE G 610 " --> pdb=" O LEU G 599 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU G 599 " --> pdb=" O ILE G 610 " (cutoff:3.500A) 1512 hydrogen bonds defined for protein. 4332 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: 7.63 Time building geometry restraints manager: 6.74 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: 7427 1.34 - 1.46: 5499 1.46 - 1.58: 11250 1.58 - 1.70: 0 1.70 - 1.82: 196 Bond restraints: 24372 Sorted by residual: bond pdb=" CB ASN G 441 " pdb=" CG ASN G 441 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.91e+00 bond pdb=" CB ASN E 441 " pdb=" CG ASN E 441 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.83e+00 bond pdb=" CB ASN A 441 " pdb=" CG ASN A 441 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.83e+00 bond pdb=" CB ASN C 441 " pdb=" CG ASN C 441 " ideal model delta sigma weight residual 1.516 1.462 0.054 2.50e-02 1.60e+03 4.75e+00 bond pdb=" CG1 ILE E 456 " pdb=" CD1 ILE E 456 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.94e+00 ... (remaining 24367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 32520 2.57 - 5.15: 671 5.15 - 7.72: 93 7.72 - 10.30: 12 10.30 - 12.87: 12 Bond angle restraints: 33308 Sorted by residual: angle pdb=" CA ARG G 387 " pdb=" CB ARG G 387 " pdb=" CG ARG G 387 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CA ARG C 387 " pdb=" CB ARG C 387 " pdb=" CG ARG C 387 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CA ARG E 387 " pdb=" CB ARG E 387 " pdb=" CG ARG E 387 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CA ARG A 387 " pdb=" CB ARG A 387 " pdb=" CG ARG A 387 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CB MET A 366 " pdb=" CG MET A 366 " pdb=" SD MET A 366 " ideal model delta sigma weight residual 112.70 125.57 -12.87 3.00e+00 1.11e-01 1.84e+01 ... (remaining 33303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 12666 17.14 - 34.29: 1162 34.29 - 51.43: 236 51.43 - 68.57: 44 68.57 - 85.72: 12 Dihedral angle restraints: 14120 sinusoidal: 4560 harmonic: 9560 Sorted by residual: dihedral pdb=" CA ILE A 194 " pdb=" C ILE A 194 " pdb=" N LEU A 195 " pdb=" CA LEU A 195 " ideal model delta harmonic sigma weight residual 180.00 157.92 22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ILE C 194 " pdb=" C ILE C 194 " pdb=" N LEU C 195 " pdb=" CA LEU C 195 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ILE E 194 " pdb=" C ILE E 194 " pdb=" N LEU E 195 " pdb=" CA LEU E 195 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 14117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2750 0.052 - 0.103: 886 0.103 - 0.155: 240 0.155 - 0.206: 32 0.206 - 0.258: 20 Chirality restraints: 3928 Sorted by residual: chirality pdb=" CB ILE G 140 " pdb=" CA ILE G 140 " pdb=" CG1 ILE G 140 " pdb=" CG2 ILE G 140 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE C 140 " pdb=" CA ILE C 140 " pdb=" CG1 ILE C 140 " pdb=" CG2 ILE C 140 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE A 140 " pdb=" CA ILE A 140 " pdb=" CG1 ILE A 140 " pdb=" CG2 ILE A 140 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 3925 not shown) Planarity restraints: 4248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET E 366 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.97e+00 pdb=" C MET E 366 " -0.052 2.00e-02 2.50e+03 pdb=" O MET E 366 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA E 367 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 366 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C MET G 366 " 0.051 2.00e-02 2.50e+03 pdb=" O MET G 366 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA G 367 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 366 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.81e+00 pdb=" C MET A 366 " 0.051 2.00e-02 2.50e+03 pdb=" O MET A 366 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA A 367 " -0.018 2.00e-02 2.50e+03 ... (remaining 4245 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5864 2.78 - 3.31: 22799 3.31 - 3.84: 40975 3.84 - 4.37: 44736 4.37 - 4.90: 77811 Nonbonded interactions: 192185 Sorted by model distance: nonbonded pdb=" OH TYR A 198 " pdb=" OE1 GLU C 600 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR C 198 " pdb=" OE1 GLU E 600 " model vdw 2.257 3.040 nonbonded pdb=" OH TYR E 198 " pdb=" OE1 GLU G 600 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR G 446 " pdb=" OE1 GLU G 449 " model vdw 2.297 3.040 nonbonded pdb=" OG1 THR A 446 " pdb=" OE1 GLU A 449 " model vdw 2.298 3.040 ... (remaining 192180 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.010 Normalize map: mean=0, sd=1: 3.080 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: 0.030 Extract box with map and model: 0.970 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 51.470 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5656 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 : 0.008 0.077 24372 Z= 0.515 Angle : 0.927 12.870 33308 Z= 0.499 Chirality : 0.056 0.258 3928 Planarity : 0.007 0.055 4248 Dihedral : 14.382 85.718 7920 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.12), residues: 3220 helix: -2.06 (0.09), residues: 1788 sheet: -2.42 (0.28), residues: 228 loop : -2.36 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP E 222 HIS 0.010 0.002 HIS G 543 PHE 0.032 0.003 PHE E 475 TYR 0.039 0.003 TYR C 464 ARG 0.009 0.001 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 499 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 PHE cc_start: 0.8145 (t80) cc_final: 0.7903 (t80) REVERT: A 90 TYR cc_start: 0.7922 (m-80) cc_final: 0.7720 (m-10) REVERT: A 109 PHE cc_start: 0.7947 (m-80) cc_final: 0.7590 (m-10) REVERT: A 344 TYR cc_start: 0.4842 (m-80) cc_final: 0.4347 (m-80) REVERT: A 347 TYR cc_start: 0.4691 (m-80) cc_final: 0.4295 (t80) REVERT: A 376 TYR cc_start: 0.7854 (t80) cc_final: 0.7586 (t80) REVERT: A 519 MET cc_start: 0.7172 (ttm) cc_final: 0.6798 (tmm) REVERT: A 575 CYS cc_start: 0.6318 (m) cc_final: 0.5751 (p) REVERT: B 107 HIS cc_start: 0.6943 (t-90) cc_final: 0.6574 (t-170) REVERT: B 123 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7308 (tm-30) REVERT: D 107 HIS cc_start: 0.6469 (t-90) cc_final: 0.6266 (t70) REVERT: D 123 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7573 (tm-30) REVERT: D 127 GLU cc_start: 0.4810 (tt0) cc_final: 0.4575 (pt0) REVERT: H 123 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7255 (tm-30) REVERT: C 17 PHE cc_start: 0.8111 (t80) cc_final: 0.7869 (t80) REVERT: C 90 TYR cc_start: 0.7921 (m-80) cc_final: 0.7719 (m-10) REVERT: C 109 PHE cc_start: 0.7940 (m-80) cc_final: 0.7557 (m-10) REVERT: C 344 TYR cc_start: 0.4849 (m-80) cc_final: 0.4362 (m-80) REVERT: C 347 TYR cc_start: 0.4735 (m-80) cc_final: 0.4304 (t80) REVERT: C 398 ASP cc_start: 0.7699 (t70) cc_final: 0.7498 (t0) REVERT: C 519 MET cc_start: 0.7129 (ttm) cc_final: 0.6752 (tmm) REVERT: C 575 CYS cc_start: 0.6231 (m) cc_final: 0.5657 (p) REVERT: C 615 ASP cc_start: 0.7418 (m-30) cc_final: 0.7105 (m-30) REVERT: E 17 PHE cc_start: 0.8110 (t80) cc_final: 0.7868 (t80) REVERT: E 109 PHE cc_start: 0.7907 (m-80) cc_final: 0.7550 (m-10) REVERT: E 344 TYR cc_start: 0.4860 (m-80) cc_final: 0.4372 (m-80) REVERT: E 347 TYR cc_start: 0.4745 (m-80) cc_final: 0.4325 (t80) REVERT: E 519 MET cc_start: 0.7114 (ttm) cc_final: 0.6722 (tmm) REVERT: E 575 CYS cc_start: 0.6151 (m) cc_final: 0.5575 (p) REVERT: E 615 ASP cc_start: 0.7511 (m-30) cc_final: 0.7216 (m-30) REVERT: E 651 GLN cc_start: 0.7988 (mt0) cc_final: 0.7713 (mm-40) REVERT: G 17 PHE cc_start: 0.8119 (t80) cc_final: 0.7877 (t80) REVERT: G 109 PHE cc_start: 0.7905 (m-80) cc_final: 0.7544 (m-10) REVERT: G 344 TYR cc_start: 0.4850 (m-80) cc_final: 0.4361 (m-80) REVERT: G 347 TYR cc_start: 0.4740 (m-80) cc_final: 0.4325 (t80) REVERT: G 519 MET cc_start: 0.7102 (ttm) cc_final: 0.6709 (tmm) REVERT: G 575 CYS cc_start: 0.6162 (m) cc_final: 0.5580 (p) REVERT: G 615 ASP cc_start: 0.7461 (m-30) cc_final: 0.7150 (m-30) REVERT: G 651 GLN cc_start: 0.7988 (mt0) cc_final: 0.7715 (mm-40) outliers start: 0 outliers final: 0 residues processed: 499 average time/residue: 0.3458 time to fit residues: 267.7212 Evaluate side-chains 331 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 7.9990 chunk 245 optimal weight: 0.6980 chunk 136 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 165 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 253 optimal weight: 0.9980 chunk 98 optimal weight: 40.0000 chunk 154 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 ASN A 343 HIS A 545 ASN A 667 ASN B 107 HIS D 107 HIS F 107 HIS C 93 ASN C 343 HIS C 545 ASN C 667 ASN E 93 ASN E 343 HIS E 545 ASN E 667 ASN G 20 ASN G 93 ASN G 343 HIS G 545 ASN G 667 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5657 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24372 Z= 0.212 Angle : 0.616 12.922 33308 Z= 0.323 Chirality : 0.042 0.164 3928 Planarity : 0.004 0.043 4248 Dihedral : 5.031 15.956 3456 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.90 % Allowed : 14.63 % Favored : 83.47 % 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: -1.63 (0.13), residues: 3220 helix: -0.37 (0.11), residues: 1824 sheet: -2.05 (0.30), residues: 204 loop : -1.90 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 222 HIS 0.019 0.002 HIS D 107 PHE 0.014 0.001 PHE B 12 TYR 0.018 0.001 TYR A 464 ARG 0.003 0.000 ARG C 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 377 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 PHE cc_start: 0.8111 (t80) cc_final: 0.7898 (t80) REVERT: A 109 PHE cc_start: 0.7768 (m-80) cc_final: 0.7441 (m-10) REVERT: A 344 TYR cc_start: 0.4871 (m-80) cc_final: 0.4519 (m-80) REVERT: A 347 TYR cc_start: 0.4552 (m-80) cc_final: 0.4208 (t80) REVERT: A 519 MET cc_start: 0.7126 (ttm) cc_final: 0.6755 (tmm) REVERT: D 123 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7531 (tm-30) REVERT: D 127 GLU cc_start: 0.5045 (tt0) cc_final: 0.4754 (pt0) REVERT: C 17 PHE cc_start: 0.8113 (t80) cc_final: 0.7893 (t80) REVERT: C 229 PHE cc_start: 0.7181 (t80) cc_final: 0.6964 (m-10) REVERT: C 344 TYR cc_start: 0.4863 (m-80) cc_final: 0.4503 (m-80) REVERT: C 347 TYR cc_start: 0.4603 (m-80) cc_final: 0.4202 (t80) REVERT: C 442 ILE cc_start: 0.8122 (mm) cc_final: 0.7910 (mp) REVERT: C 519 MET cc_start: 0.7084 (ttm) cc_final: 0.6641 (tmm) REVERT: E 17 PHE cc_start: 0.8109 (t80) cc_final: 0.7881 (t80) REVERT: E 333 ARG cc_start: 0.7084 (mtt180) cc_final: 0.6879 (mtt90) REVERT: E 344 TYR cc_start: 0.4836 (m-80) cc_final: 0.4481 (m-80) REVERT: E 347 TYR cc_start: 0.4607 (m-80) cc_final: 0.4210 (t80) REVERT: E 442 ILE cc_start: 0.8161 (mm) cc_final: 0.7929 (mp) REVERT: E 487 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8116 (tp30) REVERT: E 519 MET cc_start: 0.7052 (ttm) cc_final: 0.6614 (tmm) REVERT: G 17 PHE cc_start: 0.8093 (t80) cc_final: 0.7875 (t80) REVERT: G 344 TYR cc_start: 0.4830 (m-80) cc_final: 0.4473 (m-80) REVERT: G 347 TYR cc_start: 0.4607 (m-80) cc_final: 0.4211 (t80) REVERT: G 442 ILE cc_start: 0.8169 (mm) cc_final: 0.7962 (mp) REVERT: G 519 MET cc_start: 0.7037 (ttm) cc_final: 0.6598 (tmm) outliers start: 42 outliers final: 15 residues processed: 400 average time/residue: 0.2934 time to fit residues: 194.2347 Evaluate side-chains 352 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 337 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 645 ILE Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 645 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 294 optimal weight: 10.0000 chunk 318 optimal weight: 5.9990 chunk 262 optimal weight: 10.0000 chunk 292 optimal weight: 4.9990 chunk 100 optimal weight: 30.0000 chunk 236 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS C 20 ASN C 643 HIS E 20 ASN E 643 HIS G 643 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5672 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 24372 Z= 0.418 Angle : 0.705 15.107 33308 Z= 0.359 Chirality : 0.045 0.216 3928 Planarity : 0.004 0.042 4248 Dihedral : 4.913 15.938 3456 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.72 % Allowed : 17.48 % Favored : 79.80 % 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: -0.88 (0.14), residues: 3220 helix: 0.24 (0.12), residues: 1820 sheet: -2.12 (0.33), residues: 160 loop : -1.53 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 517 HIS 0.010 0.002 HIS E 543 PHE 0.026 0.002 PHE G 261 TYR 0.022 0.002 TYR G 230 ARG 0.004 0.001 ARG E 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 330 time to evaluate : 2.639 Fit side-chains REVERT: A 347 TYR cc_start: 0.4625 (m-80) cc_final: 0.4295 (t80) REVERT: A 519 MET cc_start: 0.7120 (ttm) cc_final: 0.6735 (tmm) REVERT: C 347 TYR cc_start: 0.4697 (m-80) cc_final: 0.4330 (t80) REVERT: C 519 MET cc_start: 0.7056 (ttm) cc_final: 0.6671 (tmm) REVERT: E 264 ASP cc_start: 0.6854 (t0) cc_final: 0.6548 (t0) REVERT: E 347 TYR cc_start: 0.4705 (m-80) cc_final: 0.4338 (t80) REVERT: E 519 MET cc_start: 0.7040 (ttm) cc_final: 0.6634 (tmm) REVERT: G 347 TYR cc_start: 0.4703 (m-80) cc_final: 0.4338 (t80) REVERT: G 519 MET cc_start: 0.7020 (ttm) cc_final: 0.6610 (tmm) outliers start: 60 outliers final: 35 residues processed: 376 average time/residue: 0.3133 time to fit residues: 197.1481 Evaluate side-chains 325 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 290 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 645 ILE Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 592 CYS Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 645 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 295 optimal weight: 0.8980 chunk 313 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 280 optimal weight: 7.9990 chunk 84 optimal weight: 0.0070 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5657 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24372 Z= 0.192 Angle : 0.593 12.272 33308 Z= 0.307 Chirality : 0.041 0.159 3928 Planarity : 0.004 0.041 4248 Dihedral : 4.549 17.848 3456 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.08 % Allowed : 19.38 % Favored : 78.53 % 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: -0.38 (0.15), residues: 3220 helix: 0.69 (0.12), residues: 1836 sheet: -1.58 (0.34), residues: 180 loop : -1.46 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 222 HIS 0.006 0.001 HIS E 364 PHE 0.016 0.001 PHE C 429 TYR 0.016 0.001 TYR E 230 ARG 0.005 0.000 ARG E 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 348 time to evaluate : 2.878 Fit side-chains revert: symmetry clash REVERT: A 347 TYR cc_start: 0.4687 (m-80) cc_final: 0.4311 (t80) REVERT: A 519 MET cc_start: 0.7092 (ttm) cc_final: 0.6657 (tmm) REVERT: C 347 TYR cc_start: 0.4706 (m-80) cc_final: 0.4323 (t80) REVERT: C 442 ILE cc_start: 0.8076 (mm) cc_final: 0.7777 (mp) REVERT: C 519 MET cc_start: 0.7000 (ttm) cc_final: 0.6568 (tmm) REVERT: E 347 TYR cc_start: 0.4709 (m-80) cc_final: 0.4327 (t80) REVERT: E 442 ILE cc_start: 0.8067 (mm) cc_final: 0.7772 (mp) REVERT: E 519 MET cc_start: 0.6994 (ttm) cc_final: 0.6562 (tmm) REVERT: E 615 ASP cc_start: 0.7201 (m-30) cc_final: 0.6970 (m-30) REVERT: G 347 TYR cc_start: 0.4703 (m-80) cc_final: 0.4323 (t80) REVERT: G 442 ILE cc_start: 0.8104 (mm) cc_final: 0.7815 (mp) REVERT: G 519 MET cc_start: 0.6984 (ttm) cc_final: 0.6550 (tmm) outliers start: 46 outliers final: 23 residues processed: 379 average time/residue: 0.2841 time to fit residues: 181.0522 Evaluate side-chains 332 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 309 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 616 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 129 optimal weight: 20.0000 chunk 267 optimal weight: 3.9990 chunk 216 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 281 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN A 545 ASN ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5660 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24372 Z= 0.183 Angle : 0.585 10.770 33308 Z= 0.301 Chirality : 0.041 0.220 3928 Planarity : 0.003 0.039 4248 Dihedral : 4.344 16.815 3456 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.63 % Allowed : 20.15 % Favored : 77.22 % 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: -0.06 (0.15), residues: 3220 helix: 0.95 (0.12), residues: 1836 sheet: -1.38 (0.35), residues: 180 loop : -1.33 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 222 HIS 0.005 0.001 HIS A 364 PHE 0.016 0.001 PHE B 12 TYR 0.017 0.001 TYR A 230 ARG 0.004 0.000 ARG C 484 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 353 time to evaluate : 2.947 Fit side-chains revert: symmetry clash REVERT: A 347 TYR cc_start: 0.4691 (m-80) cc_final: 0.4311 (t80) REVERT: A 519 MET cc_start: 0.7071 (ttm) cc_final: 0.6641 (tmm) REVERT: C 347 TYR cc_start: 0.4712 (m-80) cc_final: 0.4316 (t80) REVERT: C 442 ILE cc_start: 0.8086 (mm) cc_final: 0.7569 (mp) REVERT: C 519 MET cc_start: 0.6987 (ttm) cc_final: 0.6553 (tmm) REVERT: E 347 TYR cc_start: 0.4725 (m-80) cc_final: 0.4340 (t80) REVERT: E 442 ILE cc_start: 0.8087 (mm) cc_final: 0.7558 (mp) REVERT: E 519 MET cc_start: 0.6983 (ttm) cc_final: 0.6546 (tmm) REVERT: E 615 ASP cc_start: 0.7298 (m-30) cc_final: 0.7015 (m-30) REVERT: G 347 TYR cc_start: 0.4711 (m-80) cc_final: 0.4333 (t80) REVERT: G 442 ILE cc_start: 0.8107 (mm) cc_final: 0.7633 (mp) REVERT: G 519 MET cc_start: 0.6974 (ttm) cc_final: 0.6537 (tmm) outliers start: 58 outliers final: 39 residues processed: 388 average time/residue: 0.2727 time to fit residues: 180.5417 Evaluate side-chains 353 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 314 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 552 HIS Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 530 GLN Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 530 GLN Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 686 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 5.9990 chunk 282 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 77 optimal weight: 20.0000 chunk 313 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 545 ASN E 545 ASN G 545 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5665 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24372 Z= 0.185 Angle : 0.572 11.161 33308 Z= 0.295 Chirality : 0.040 0.206 3928 Planarity : 0.003 0.038 4248 Dihedral : 4.219 16.097 3456 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.36 % Allowed : 22.28 % Favored : 75.36 % 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: 0.21 (0.15), residues: 3220 helix: 1.17 (0.12), residues: 1832 sheet: -1.28 (0.36), residues: 180 loop : -1.22 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 365 HIS 0.005 0.001 HIS G 364 PHE 0.022 0.001 PHE H 68 TYR 0.018 0.001 TYR D 138 ARG 0.004 0.000 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 346 time to evaluate : 2.685 Fit side-chains revert: symmetry clash REVERT: A 347 TYR cc_start: 0.4714 (m-80) cc_final: 0.4334 (t80) REVERT: A 519 MET cc_start: 0.6987 (ttm) cc_final: 0.6549 (tmm) REVERT: H 127 GLU cc_start: 0.6022 (mm-30) cc_final: 0.5549 (pt0) REVERT: C 347 TYR cc_start: 0.4721 (m-80) cc_final: 0.4327 (t80) REVERT: C 483 ASN cc_start: 0.7843 (p0) cc_final: 0.7579 (m110) REVERT: C 519 MET cc_start: 0.6978 (ttm) cc_final: 0.6551 (tmm) REVERT: E 347 TYR cc_start: 0.4731 (m-80) cc_final: 0.4337 (t80) REVERT: E 519 MET cc_start: 0.6976 (ttm) cc_final: 0.6549 (tmm) REVERT: E 615 ASP cc_start: 0.7328 (m-30) cc_final: 0.7021 (m-30) REVERT: G 347 TYR cc_start: 0.4711 (m-80) cc_final: 0.4326 (t80) REVERT: G 519 MET cc_start: 0.6972 (ttm) cc_final: 0.6543 (tmm) outliers start: 52 outliers final: 34 residues processed: 382 average time/residue: 0.2775 time to fit residues: 179.1847 Evaluate side-chains 345 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 311 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 530 GLN Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 530 GLN Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 686 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 178 optimal weight: 0.0970 chunk 228 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 312 optimal weight: 0.8980 chunk 195 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 HIS E 552 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5669 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24372 Z= 0.179 Angle : 0.566 10.153 33308 Z= 0.291 Chirality : 0.040 0.184 3928 Planarity : 0.003 0.039 4248 Dihedral : 4.124 16.273 3456 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.26 % Allowed : 24.00 % Favored : 73.73 % 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: 0.39 (0.15), residues: 3220 helix: 1.32 (0.12), residues: 1836 sheet: -1.13 (0.37), residues: 180 loop : -1.16 (0.19), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 365 HIS 0.008 0.001 HIS H 107 PHE 0.021 0.001 PHE E 109 TYR 0.017 0.001 TYR E 230 ARG 0.004 0.000 ARG E 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 358 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 TYR cc_start: 0.4727 (m-80) cc_final: 0.4344 (t80) REVERT: A 519 MET cc_start: 0.6982 (ttm) cc_final: 0.6554 (tmm) REVERT: F 144 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.7109 (ptp) REVERT: H 127 GLU cc_start: 0.5985 (mm-30) cc_final: 0.5428 (pt0) REVERT: C 347 TYR cc_start: 0.4637 (m-80) cc_final: 0.4223 (t80) REVERT: C 483 ASN cc_start: 0.7817 (p0) cc_final: 0.7531 (m110) REVERT: C 519 MET cc_start: 0.6973 (ttm) cc_final: 0.6543 (tmm) REVERT: E 347 TYR cc_start: 0.4645 (m-80) cc_final: 0.4232 (t80) REVERT: E 519 MET cc_start: 0.6973 (ttm) cc_final: 0.6541 (tmm) REVERT: E 615 ASP cc_start: 0.7308 (m-30) cc_final: 0.7004 (m-30) REVERT: G 347 TYR cc_start: 0.4629 (m-80) cc_final: 0.4222 (t80) REVERT: G 519 MET cc_start: 0.6967 (ttm) cc_final: 0.6542 (tmm) outliers start: 50 outliers final: 37 residues processed: 389 average time/residue: 0.2778 time to fit residues: 183.4345 Evaluate side-chains 362 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 324 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 616 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 212 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 245 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5673 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24372 Z= 0.191 Angle : 0.584 11.381 33308 Z= 0.299 Chirality : 0.040 0.184 3928 Planarity : 0.003 0.038 4248 Dihedral : 4.082 17.459 3456 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.58 % Allowed : 23.23 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 3220 helix: 1.43 (0.12), residues: 1836 sheet: -1.05 (0.37), residues: 180 loop : -1.15 (0.19), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 365 HIS 0.017 0.001 HIS H 107 PHE 0.024 0.001 PHE H 68 TYR 0.027 0.001 TYR E 230 ARG 0.006 0.000 ARG E 333 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 337 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 TYR cc_start: 0.4665 (m-80) cc_final: 0.4273 (t80) REVERT: A 519 MET cc_start: 0.6986 (ttm) cc_final: 0.6556 (tmm) REVERT: F 144 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.7116 (ptp) REVERT: H 127 GLU cc_start: 0.5879 (mm-30) cc_final: 0.5348 (pt0) REVERT: C 347 TYR cc_start: 0.4638 (m-80) cc_final: 0.4229 (t80) REVERT: C 483 ASN cc_start: 0.7818 (p0) cc_final: 0.7533 (m110) REVERT: C 519 MET cc_start: 0.7009 (ttm) cc_final: 0.6569 (tmm) REVERT: E 92 MET cc_start: 0.8547 (pmm) cc_final: 0.8271 (mtt) REVERT: E 347 TYR cc_start: 0.4654 (m-80) cc_final: 0.4241 (t80) REVERT: E 519 MET cc_start: 0.6977 (ttm) cc_final: 0.6543 (tmm) REVERT: E 615 ASP cc_start: 0.7332 (m-30) cc_final: 0.7007 (m-30) REVERT: G 347 TYR cc_start: 0.4661 (m-80) cc_final: 0.4258 (t80) REVERT: G 519 MET cc_start: 0.6945 (ttm) cc_final: 0.6522 (tmm) outliers start: 57 outliers final: 47 residues processed: 378 average time/residue: 0.2777 time to fit residues: 177.9170 Evaluate side-chains 374 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 326 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 530 GLN Chi-restraints excluded: chain E residue 648 ASP Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 530 GLN Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 648 ASP Chi-restraints excluded: chain G residue 686 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 6.9990 chunk 299 optimal weight: 0.5980 chunk 272 optimal weight: 0.0050 chunk 291 optimal weight: 9.9990 chunk 175 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 262 optimal weight: 5.9990 chunk 275 optimal weight: 0.4980 chunk 289 optimal weight: 0.7980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5672 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24372 Z= 0.176 Angle : 0.577 10.877 33308 Z= 0.296 Chirality : 0.040 0.219 3928 Planarity : 0.003 0.038 4248 Dihedral : 4.034 17.065 3456 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.49 % Allowed : 23.28 % Favored : 74.23 % 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: 0.65 (0.15), residues: 3220 helix: 1.51 (0.12), residues: 1844 sheet: -0.86 (0.38), residues: 180 loop : -1.07 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP G 365 HIS 0.004 0.001 HIS G 364 PHE 0.021 0.001 PHE E 359 TYR 0.027 0.001 TYR E 230 ARG 0.005 0.000 ARG E 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 347 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 TYR cc_start: 0.4676 (m-80) cc_final: 0.4264 (t80) REVERT: A 519 MET cc_start: 0.6977 (ttm) cc_final: 0.6553 (tmm) REVERT: F 144 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.7115 (ptp) REVERT: H 127 GLU cc_start: 0.5848 (mm-30) cc_final: 0.5299 (pt0) REVERT: C 347 TYR cc_start: 0.4735 (m-80) cc_final: 0.4327 (t80) REVERT: C 483 ASN cc_start: 0.7810 (p0) cc_final: 0.7526 (m110) REVERT: C 519 MET cc_start: 0.7000 (ttm) cc_final: 0.6562 (tmm) REVERT: E 347 TYR cc_start: 0.4752 (m-80) cc_final: 0.4338 (t80) REVERT: E 483 ASN cc_start: 0.7913 (p0) cc_final: 0.7626 (m110) REVERT: E 519 MET cc_start: 0.6954 (ttm) cc_final: 0.6526 (tmm) REVERT: E 615 ASP cc_start: 0.7338 (m-30) cc_final: 0.7005 (m-30) REVERT: G 347 TYR cc_start: 0.4642 (m-80) cc_final: 0.4238 (t80) REVERT: G 483 ASN cc_start: 0.7912 (p0) cc_final: 0.7626 (m110) REVERT: G 519 MET cc_start: 0.6925 (ttm) cc_final: 0.6503 (tmm) outliers start: 55 outliers final: 41 residues processed: 381 average time/residue: 0.2698 time to fit residues: 175.3062 Evaluate side-chains 367 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 325 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 458 MET Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 530 GLN Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 530 GLN Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 648 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 6.9990 chunk 307 optimal weight: 0.9980 chunk 187 optimal weight: 0.0060 chunk 145 optimal weight: 0.9980 chunk 213 optimal weight: 9.9990 chunk 322 optimal weight: 6.9990 chunk 297 optimal weight: 0.4980 chunk 257 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 198 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5675 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24372 Z= 0.173 Angle : 0.605 10.457 33308 Z= 0.304 Chirality : 0.041 0.229 3928 Planarity : 0.003 0.037 4248 Dihedral : 3.991 16.609 3456 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.26 % Allowed : 23.82 % Favored : 73.91 % 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: 0.76 (0.15), residues: 3220 helix: 1.60 (0.12), residues: 1844 sheet: -0.75 (0.38), residues: 180 loop : -1.04 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP G 365 HIS 0.005 0.001 HIS G 364 PHE 0.027 0.001 PHE H 68 TYR 0.026 0.001 TYR E 230 ARG 0.004 0.000 ARG E 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 356 time to evaluate : 4.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7755 (mtm) cc_final: 0.7327 (ptp) REVERT: A 347 TYR cc_start: 0.4804 (m-80) cc_final: 0.4391 (t80) REVERT: A 519 MET cc_start: 0.6946 (ttm) cc_final: 0.6529 (tmm) REVERT: A 569 GLU cc_start: 0.7709 (mp0) cc_final: 0.7504 (mp0) REVERT: F 144 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.7021 (ptp) REVERT: H 127 GLU cc_start: 0.5889 (mm-30) cc_final: 0.5349 (pt0) REVERT: C 347 TYR cc_start: 0.4791 (m-80) cc_final: 0.4380 (t80) REVERT: C 483 ASN cc_start: 0.7809 (p0) cc_final: 0.7526 (m110) REVERT: C 519 MET cc_start: 0.6938 (ttm) cc_final: 0.6515 (tmm) REVERT: E 347 TYR cc_start: 0.4801 (m-80) cc_final: 0.4386 (t80) REVERT: E 483 ASN cc_start: 0.7920 (p0) cc_final: 0.7632 (m110) REVERT: E 519 MET cc_start: 0.6925 (ttm) cc_final: 0.6504 (tmm) REVERT: E 615 ASP cc_start: 0.7337 (m-30) cc_final: 0.7002 (m-30) REVERT: G 347 TYR cc_start: 0.4664 (m-80) cc_final: 0.4259 (t80) REVERT: G 483 ASN cc_start: 0.7919 (p0) cc_final: 0.7632 (m110) REVERT: G 519 MET cc_start: 0.6925 (ttm) cc_final: 0.6501 (tmm) outliers start: 50 outliers final: 41 residues processed: 387 average time/residue: 0.2847 time to fit residues: 188.9791 Evaluate side-chains 382 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 340 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 648 ASP Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 530 GLN Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 648 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 10.0000 chunk 273 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 71 optimal weight: 6.9990 chunk 257 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.140692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.109169 restraints weight = 51517.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.108382 restraints weight = 37296.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.108720 restraints weight = 29795.305| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 24372 Z= 0.258 Angle : 0.630 11.394 33308 Z= 0.320 Chirality : 0.042 0.295 3928 Planarity : 0.004 0.040 4248 Dihedral : 4.094 16.753 3456 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.63 % Allowed : 23.96 % Favored : 73.41 % 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: 0.74 (0.15), residues: 3220 helix: 1.59 (0.12), residues: 1848 sheet: -0.93 (0.38), residues: 180 loop : -1.03 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 365 HIS 0.005 0.001 HIS E 543 PHE 0.020 0.001 PHE G 359 TYR 0.025 0.002 TYR E 230 ARG 0.004 0.001 ARG C 537 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4506.66 seconds wall clock time: 81 minutes 18.17 seconds (4878.17 seconds total)