Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 18:56:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4q_25685/04_2023/7t4q_25685.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4q_25685/04_2023/7t4q_25685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4q_25685/04_2023/7t4q_25685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4q_25685/04_2023/7t4q_25685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4q_25685/04_2023/7t4q_25685.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4q_25685/04_2023/7t4q_25685.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.025 sd= 0.591 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 74 5.16 5 C 9825 2.51 5 N 2658 2.21 5 O 2916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 15473 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5018 Classifications: {'peptide': 623} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 591} Chain breaks: 6 Chain: "B" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1843 Classifications: {'peptide': 233} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 213} Chain: "C" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 999 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "D" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1335 Classifications: {'peptide': 164} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 153} Chain: "E" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 917 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "F" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 962 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "G" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 828 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "H" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Chain: "I" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 960 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 924 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "K" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 790 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 97} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLU C 136 " occ=0.97 ... (7 atoms not shown) pdb=" OE2 GLU C 136 " occ=0.97 residue: pdb=" N ASP C 138 " occ=0.99 ... (6 atoms not shown) pdb=" OD2 ASP C 138 " occ=0.99 Time building chain proxies: 8.30, per 1000 atoms: 0.54 Number of scatterers: 15473 At special positions: 0 Unit cell: (176.83, 124.259, 169.662, 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 74 16.00 O 2916 8.00 N 2658 7.00 C 9825 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS B 54 " distance=2.03 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS B 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 624 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 111 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 83 " distance=2.03 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 207 " distance=2.01 Simple disulfide: pdb=" SG CYS E 20 " - pdb=" SG CYS E 40 " distance=2.03 Simple disulfide: pdb=" SG CYS F 45 " - pdb=" SG CYS F 120 " distance=2.03 Simple disulfide: pdb=" SG CYS G 45 " - pdb=" SG CYS G 113 " distance=2.03 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 112 " distance=2.04 Simple disulfide: pdb=" SG CYS I 45 " - pdb=" SG CYS I 119 " distance=2.04 Simple disulfide: pdb=" SG CYS J 45 " - pdb=" SG CYS J 119 " distance=2.03 Simple disulfide: pdb=" SG CYS K 46 " - pdb=" SG CYS K 111 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 803 " - " ASN A 192 " " NAG B 301 " - " ASN B 74 " " NAG D 301 " - " ASN D 201 " " NAG E 201 " - " ASN E 81 " Time building additional restraints: 6.31 Conformation dependent library (CDL) restraints added in 2.5 seconds 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 28 sheets defined 29.0% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.511A pdb=" N GLU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 283 through 287 removed outlier: 4.364A pdb=" N ASN A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 283 through 287' Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 334 through 353 Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 362 through 385 Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.547A pdb=" N LEU A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 436 through 454 removed outlier: 3.816A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 removed outlier: 4.056A pdb=" N HIS A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 495 removed outlier: 3.668A pdb=" N CYS A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 506 Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 681 through 684 Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 130 through 145 removed outlier: 3.916A pdb=" N TRP B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 236 removed outlier: 3.656A pdb=" N PHE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 253 removed outlier: 4.080A pdb=" N ARG B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 82 removed outlier: 4.345A pdb=" N GLY C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N HIS C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 145 through 156 Processing helix chain 'D' and resid 53 through 57 removed outlier: 4.007A pdb=" N TYR D 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 104 through 118 removed outlier: 4.189A pdb=" N ASN D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.697A pdb=" N GLN D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'E' and resid 21 through 26 removed outlier: 3.842A pdb=" N GLU E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 41 Processing helix chain 'E' and resid 45 through 69 Processing helix chain 'E' and resid 76 through 80 Processing helix chain 'E' and resid 81 through 95 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'G' and resid 104 through 108 Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 103 through 107 removed outlier: 3.712A pdb=" N PHE H 107 " --> pdb=" O PRO H 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 55 Processing helix chain 'I' and resid 110 through 114 Processing helix chain 'I' and resid 125 through 131 removed outlier: 3.582A pdb=" N TRP I 128 " --> pdb=" O TYR I 125 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE I 129 " --> pdb=" O LEU I 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 55 removed outlier: 3.508A pdb=" N TYR J 55 " --> pdb=" O PHE J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 88 Processing helix chain 'J' and resid 110 through 114 Processing helix chain 'K' and resid 102 through 106 removed outlier: 3.744A pdb=" N VAL K 106 " --> pdb=" O PRO K 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 92 removed outlier: 6.033A pdb=" N SER A 77 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU B 183 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ASN A 79 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL B 178 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA B 194 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE B 189 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 126 removed outlier: 4.847A pdb=" N VAL A 281 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 270 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 279 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ILE A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A 136 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 126 removed outlier: 4.847A pdb=" N VAL A 281 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 197 Processing sheet with id=AA6, first strand: chain 'A' and resid 527 through 528 removed outlier: 3.831A pdb=" N PHE A 578 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 663 through 666 Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 83 removed outlier: 5.996A pdb=" N LEU B 82 " --> pdb=" O GLY B 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 150 through 155 removed outlier: 5.523A pdb=" N GLY B 161 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ARG D 102 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ASP B 163 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU D 88 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ARG D 76 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU D 90 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE D 74 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR D 92 " --> pdb=" O SER D 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 50 removed outlier: 6.771A pdb=" N THR C 53 " --> pdb=" O CYS C 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 109 through 111 Processing sheet with id=AB3, first strand: chain 'C' and resid 130 through 132 removed outlier: 4.577A pdb=" N THR E 106 " --> pdb=" O ARG E 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 26 through 29 Processing sheet with id=AB5, first strand: chain 'F' and resid 33 through 35 removed outlier: 3.502A pdb=" N ALA F 74 " --> pdb=" O TRP F 61 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ARG F 63 " --> pdb=" O TRP F 72 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N TRP F 72 " --> pdb=" O ARG F 63 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 33 through 35 Processing sheet with id=AB7, first strand: chain 'G' and resid 32 through 35 removed outlier: 6.682A pdb=" N VAL G 33 " --> pdb=" O THR G 133 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL G 58 " --> pdb=" O TYR G 74 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR G 74 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TRP G 60 " --> pdb=" O LEU G 72 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 32 through 35 removed outlier: 6.682A pdb=" N VAL G 33 " --> pdb=" O THR G 133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 41 through 46 Processing sheet with id=AC1, first strand: chain 'H' and resid 27 through 30 Processing sheet with id=AC2, first strand: chain 'H' and resid 33 through 36 removed outlier: 6.342A pdb=" N LEU H 34 " --> pdb=" O GLU H 128 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU H 57 " --> pdb=" O TYR H 73 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TYR H 73 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP H 59 " --> pdb=" O LEU H 71 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 26 through 30 Processing sheet with id=AC4, first strand: chain 'I' and resid 33 through 35 removed outlier: 6.739A pdb=" N MET I 57 " --> pdb=" O VAL I 73 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL I 73 " --> pdb=" O MET I 57 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP I 59 " --> pdb=" O VAL I 71 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 33 through 35 removed outlier: 3.726A pdb=" N TYR I 136 " --> pdb=" O LYS I 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 26 through 29 Processing sheet with id=AC7, first strand: chain 'J' and resid 33 through 35 removed outlier: 6.774A pdb=" N ILE J 57 " --> pdb=" O ILE J 73 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE J 73 " --> pdb=" O ILE J 57 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP J 59 " --> pdb=" O MET J 71 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 33 through 35 removed outlier: 3.870A pdb=" N ASP J 135 " --> pdb=" O ARG J 121 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 27 through 30 removed outlier: 5.806A pdb=" N THR K 92 " --> pdb=" O ALA K 48 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N GLN K 50 " --> pdb=" O SER K 90 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N SER K 90 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 11.599A pdb=" N ILE K 52 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 11.675A pdb=" N SER K 88 " --> pdb=" O ILE K 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 33 through 34 removed outlier: 6.535A pdb=" N TRP K 58 " --> pdb=" O LEU K 70 " (cutoff:3.500A) 676 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.46 Time building geometry restraints manager: 6.85 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: 5005 1.34 - 1.46: 3898 1.46 - 1.59: 6826 1.59 - 1.71: 0 1.71 - 1.83: 104 Bond restraints: 15833 Sorted by residual: bond pdb=" N ASN A 55 " pdb=" CA ASN A 55 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.31e-02 5.83e+03 4.45e+00 bond pdb=" N GLU A 54 " pdb=" CA GLU A 54 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.31e-02 5.83e+03 4.09e+00 bond pdb=" C1 NAG B 301 " pdb=" O5 NAG B 301 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" C1 NAG A 801 " pdb=" O5 NAG A 801 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C1 NAG A 803 " pdb=" O5 NAG A 803 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 ... (remaining 15828 not shown) Histogram of bond angle deviations from ideal: 98.61 - 105.70: 377 105.70 - 112.79: 8388 112.79 - 119.87: 5241 119.87 - 126.96: 7309 126.96 - 134.04: 209 Bond angle restraints: 21524 Sorted by residual: angle pdb=" CA ARG C 42 " pdb=" CB ARG C 42 " pdb=" CG ARG C 42 " ideal model delta sigma weight residual 114.10 121.57 -7.47 2.00e+00 2.50e-01 1.39e+01 angle pdb=" C GLU A 73 " pdb=" CA GLU A 73 " pdb=" CB GLU A 73 " ideal model delta sigma weight residual 109.62 115.88 -6.26 1.79e+00 3.12e-01 1.22e+01 angle pdb=" CA MET A 667 " pdb=" CB MET A 667 " pdb=" CG MET A 667 " ideal model delta sigma weight residual 114.10 120.88 -6.78 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N ASN A 55 " pdb=" CA ASN A 55 " pdb=" C ASN A 55 " ideal model delta sigma weight residual 113.18 109.21 3.97 1.21e+00 6.83e-01 1.07e+01 angle pdb=" N PRO A 389 " pdb=" CD PRO A 389 " pdb=" CG PRO A 389 " ideal model delta sigma weight residual 103.20 98.61 4.59 1.50e+00 4.44e-01 9.35e+00 ... (remaining 21519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8764 17.93 - 35.85: 526 35.85 - 53.78: 96 53.78 - 71.71: 29 71.71 - 89.63: 21 Dihedral angle restraints: 9436 sinusoidal: 3754 harmonic: 5682 Sorted by residual: dihedral pdb=" CB CYS A 330 " pdb=" SG CYS A 330 " pdb=" SG CYS A 383 " pdb=" CB CYS A 383 " ideal model delta sinusoidal sigma weight residual -86.00 -175.63 89.63 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS C 162 " pdb=" CB CYS C 162 " ideal model delta sinusoidal sigma weight residual 93.00 176.37 -83.37 1 1.00e+01 1.00e-02 8.49e+01 dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS B 54 " pdb=" CB CYS B 54 " ideal model delta sinusoidal sigma weight residual -86.00 -140.12 54.12 1 1.00e+01 1.00e-02 3.97e+01 ... (remaining 9433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2085 0.058 - 0.116: 305 0.116 - 0.173: 48 0.173 - 0.231: 1 0.231 - 0.289: 1 Chirality restraints: 2440 Sorted by residual: chirality pdb=" C1 NAG B 301 " pdb=" ND2 ASN B 74 " pdb=" C2 NAG B 301 " pdb=" O5 NAG B 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA GLU A 54 " pdb=" N GLU A 54 " pdb=" C GLU A 54 " pdb=" CB GLU A 54 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" CA ILE K 71 " pdb=" N ILE K 71 " pdb=" C ILE K 71 " pdb=" CB ILE K 71 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 2437 not shown) Planarity restraints: 2752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 544 " -0.050 5.00e-02 4.00e+02 7.52e-02 9.04e+00 pdb=" N PRO A 545 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 545 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 545 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 468 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C TYR A 468 " 0.038 2.00e-02 2.50e+03 pdb=" O TYR A 468 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 469 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 270 " 0.171 9.50e-02 1.11e+02 7.69e-02 3.77e+00 pdb=" NE ARG A 270 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 270 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 270 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 270 " 0.004 2.00e-02 2.50e+03 ... (remaining 2749 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 833 2.73 - 3.27: 16078 3.27 - 3.81: 25164 3.81 - 4.36: 32105 4.36 - 4.90: 54511 Nonbonded interactions: 128691 Sorted by model distance: nonbonded pdb=" NH1 ARG A 72 " pdb=" O GLU A 73 " model vdw 2.184 2.520 nonbonded pdb=" ND2 ASN C 97 " pdb=" O ARG E 32 " model vdw 2.243 2.520 nonbonded pdb=" ND1 HIS A 275 " pdb=" OH TYR A 306 " model vdw 2.244 2.520 nonbonded pdb=" NH2 ARG A 365 " pdb=" OD2 ASP A 368 " model vdw 2.259 2.520 nonbonded pdb=" N LEU I 123 " pdb=" OD2 ASP I 132 " model vdw 2.262 2.520 ... (remaining 128686 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.97 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.450 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 42.050 Find NCS groups from input model: 0.510 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: 0.000 Load rotamer database and sin/cos tables:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.003 0.053 15833 Z= 0.217 Angle : 0.618 7.468 21524 Z= 0.329 Chirality : 0.044 0.289 2440 Planarity : 0.007 0.077 2748 Dihedral : 12.956 88.592 5726 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.18), residues: 1912 helix: -0.89 (0.23), residues: 415 sheet: 0.13 (0.22), residues: 515 loop : -0.37 (0.19), residues: 982 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 1.3023 time to fit residues: 533.0013 Evaluate side-chains 275 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.824 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 57 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 271 GLN A 370 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN D 123 GLN E 19 GLN F 109 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN J 29 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 15833 Z= 0.277 Angle : 0.664 9.792 21524 Z= 0.345 Chirality : 0.046 0.179 2440 Planarity : 0.005 0.052 2748 Dihedral : 5.542 23.251 2146 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % 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: 0.24 (0.19), residues: 1912 helix: 0.47 (0.24), residues: 421 sheet: 0.19 (0.22), residues: 510 loop : 0.15 (0.20), residues: 981 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 305 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 15 residues processed: 320 average time/residue: 1.2834 time to fit residues: 453.7911 Evaluate side-chains 288 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 273 time to evaluate : 1.805 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 5 residues processed: 10 average time/residue: 0.6436 time to fit residues: 10.0681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 187 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS D 123 GLN E 62 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 15833 Z= 0.328 Angle : 0.656 9.902 21524 Z= 0.337 Chirality : 0.046 0.204 2440 Planarity : 0.005 0.057 2748 Dihedral : 5.353 22.479 2146 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 3.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 1912 helix: 0.64 (0.25), residues: 434 sheet: 0.11 (0.22), residues: 517 loop : 0.16 (0.20), residues: 961 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 289 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 32 residues processed: 319 average time/residue: 1.2756 time to fit residues: 449.3955 Evaluate side-chains 307 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 275 time to evaluate : 1.866 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 18 residues processed: 14 average time/residue: 0.8666 time to fit residues: 16.3286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN E 62 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 15833 Z= 0.216 Angle : 0.595 9.388 21524 Z= 0.305 Chirality : 0.043 0.176 2440 Planarity : 0.004 0.057 2748 Dihedral : 5.076 21.888 2146 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 3.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 1912 helix: 0.92 (0.25), residues: 435 sheet: 0.16 (0.22), residues: 526 loop : 0.19 (0.20), residues: 951 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 301 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 32 residues processed: 330 average time/residue: 1.2711 time to fit residues: 464.8866 Evaluate side-chains 304 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 272 time to evaluate : 1.816 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 19 residues processed: 13 average time/residue: 0.5852 time to fit residues: 11.6794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 0.0370 chunk 104 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 chunk 137 optimal weight: 0.1980 chunk 76 optimal weight: 3.9990 chunk 157 optimal weight: 0.2980 chunk 127 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 165 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 overall best weight: 0.2858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 15833 Z= 0.151 Angle : 0.565 8.905 21524 Z= 0.287 Chirality : 0.042 0.172 2440 Planarity : 0.004 0.056 2748 Dihedral : 4.748 20.788 2146 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 3.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 1912 helix: 1.13 (0.25), residues: 434 sheet: 0.25 (0.22), residues: 545 loop : 0.29 (0.21), residues: 933 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 299 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 22 residues processed: 335 average time/residue: 1.2032 time to fit residues: 447.8564 Evaluate side-chains 303 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 281 time to evaluate : 1.959 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 4 average time/residue: 0.5714 time to fit residues: 5.3843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 0.0020 chunk 166 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 15 optimal weight: 0.2980 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN E 62 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN I 100 ASN ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 15833 Z= 0.238 Angle : 0.603 11.852 21524 Z= 0.306 Chirality : 0.043 0.265 2440 Planarity : 0.004 0.056 2748 Dihedral : 4.799 20.668 2146 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 4.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % 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: 0.57 (0.19), residues: 1912 helix: 1.09 (0.24), residues: 436 sheet: 0.26 (0.22), residues: 544 loop : 0.27 (0.21), residues: 932 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 284 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 40 residues processed: 324 average time/residue: 1.2762 time to fit residues: 457.4547 Evaluate side-chains 312 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 272 time to evaluate : 1.703 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 27 residues processed: 13 average time/residue: 0.4261 time to fit residues: 9.5972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 165 HIS A 315 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 15833 Z= 0.361 Angle : 0.687 11.388 21524 Z= 0.348 Chirality : 0.046 0.236 2440 Planarity : 0.005 0.056 2748 Dihedral : 5.088 23.655 2146 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 3.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % 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: 0.33 (0.19), residues: 1912 helix: 0.85 (0.24), residues: 442 sheet: 0.24 (0.22), residues: 543 loop : 0.04 (0.21), residues: 927 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 284 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 43 residues processed: 322 average time/residue: 1.3131 time to fit residues: 469.0037 Evaluate side-chains 317 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 274 time to evaluate : 1.804 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 34 residues processed: 10 average time/residue: 0.7763 time to fit residues: 11.5085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 0.9980 chunk 73 optimal weight: 0.0980 chunk 109 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 chunk 36 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 15833 Z= 0.187 Angle : 0.628 14.507 21524 Z= 0.317 Chirality : 0.043 0.244 2440 Planarity : 0.004 0.056 2748 Dihedral : 4.866 27.834 2146 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % 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: 0.41 (0.19), residues: 1912 helix: 1.00 (0.25), residues: 434 sheet: 0.30 (0.22), residues: 547 loop : 0.04 (0.21), residues: 931 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 288 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 37 residues processed: 323 average time/residue: 1.2478 time to fit residues: 447.3065 Evaluate side-chains 304 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 267 time to evaluate : 1.986 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 29 residues processed: 8 average time/residue: 0.5350 time to fit residues: 7.9509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 0.5980 chunk 176 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 15833 Z= 0.396 Angle : 0.716 14.533 21524 Z= 0.361 Chirality : 0.047 0.248 2440 Planarity : 0.005 0.056 2748 Dihedral : 5.186 27.121 2146 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 3.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % 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: 0.23 (0.19), residues: 1912 helix: 0.85 (0.25), residues: 427 sheet: 0.19 (0.22), residues: 546 loop : -0.07 (0.20), residues: 939 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 270 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 37 residues processed: 305 average time/residue: 1.2937 time to fit residues: 436.8181 Evaluate side-chains 300 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 263 time to evaluate : 1.886 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 29 residues processed: 8 average time/residue: 0.7052 time to fit residues: 9.1736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.8980 chunk 181 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 190 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 15833 Z= 0.222 Angle : 0.656 13.431 21524 Z= 0.331 Chirality : 0.044 0.241 2440 Planarity : 0.005 0.056 2748 Dihedral : 4.965 25.249 2146 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % 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: 0.26 (0.19), residues: 1912 helix: 0.84 (0.25), residues: 434 sheet: 0.27 (0.22), residues: 546 loop : -0.08 (0.21), residues: 932 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 272 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 33 residues processed: 302 average time/residue: 1.3083 time to fit residues: 438.4120 Evaluate side-chains 296 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 263 time to evaluate : 1.722 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 29 residues processed: 5 average time/residue: 0.2266 time to fit residues: 4.2545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 151 optimal weight: 0.0020 chunk 63 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN F 122 HIS ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.118588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.095361 restraints weight = 29756.055| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.27 r_work: 0.3091 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 15833 Z= 0.198 Angle : 0.638 12.425 21524 Z= 0.322 Chirality : 0.044 0.281 2440 Planarity : 0.004 0.056 2748 Dihedral : 4.828 26.143 2146 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.91 % 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: 0.35 (0.19), residues: 1912 helix: 1.00 (0.25), residues: 432 sheet: 0.29 (0.22), residues: 546 loop : -0.06 (0.21), residues: 934 =============================================================================== Job complete usr+sys time: 7131.94 seconds wall clock time: 126 minutes 34.79 seconds (7594.79 seconds total)