Starting phenix.real_space_refine on Sun Oct 25 05:29:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/44ab_82430/10_2026/44ab_82430.cif Found real_map, /net/cci-nas-00/data/ceres_data/44ab_82430/10_2026/44ab_82430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/44ab_82430/10_2026/44ab_82430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/44ab_82430/10_2026/44ab_82430.map" model { file = "/net/cci-nas-00/data/ceres_data/44ab_82430/10_2026/44ab_82430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/44ab_82430/10_2026/44ab_82430.cif" } resolution = 3.4 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 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= 0.001 sd= 0.038 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 9817 2.51 5 N 2652 2.21 5 O 2908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15451 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5017 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: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1340 Classifications: {'peptide': 164} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 154} 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: "H" 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: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 804 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 97} Chain: "P" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "Q" 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: "X" 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: "Y" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 782 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 96} 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 dihedrals: 9 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.41, per 1000 atoms: 0.22 Number of scatterers: 15451 At special positions: 0 Unit cell: (97.37, 110.21, 225.77, 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 2908 8.00 N 2652 7.00 C 9817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS E 20 " - pdb=" SG CYS E 40 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 97 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 90 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.03 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 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: 1.26 Conformation dependent library (CDL) restraints added in 727.2 milliseconds 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3650 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 27 sheets defined 29.1% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.836A 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 282 through 286 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 353 through 359 removed outlier: 4.236A pdb=" N ALA A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 436 through 454 removed outlier: 4.304A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 474 Processing helix chain 'A' and resid 480 through 494 Processing helix chain 'A' and resid 496 through 506 Processing helix chain 'A' and resid 507 through 509 No H-bonds generated for 'chain 'A' and resid 507 through 509' Processing helix chain 'A' and resid 515 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 102 through 113 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 130 through 145 removed outlier: 3.734A pdb=" N TRP B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 removed outlier: 4.117A pdb=" N THR B 175 " --> pdb=" O SER B 172 " (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: 3.637A pdb=" N PHE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 253 removed outlier: 4.051A pdb=" N ARG B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 81 removed outlier: 4.469A pdb=" N GLY C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' 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 52 through 56 removed outlier: 4.172A pdb=" N TYR D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 52 through 56' 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: 4.027A pdb=" N ASN D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.704A 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 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 'H' and resid 28 through 32 removed outlier: 3.686A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.541A pdb=" N GLN H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 102 through 108 removed outlier: 3.946A pdb=" N PHE H 106 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU H 107 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 33 removed outlier: 3.612A pdb=" N PHE L 33 " --> pdb=" O SER L 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 30 through 33' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'P' and resid 88 through 92 Processing helix chain 'Q' and resid 81 through 85 Processing helix chain 'X' and resid 28 through 32 Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'Y' and resid 79 through 83 removed outlier: 3.789A pdb=" N VAL Y 83 " --> pdb=" O PRO Y 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 92 removed outlier: 5.783A pdb=" N SER A 77 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU B 183 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ASN A 79 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL B 178 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA B 194 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE B 189 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 5.955A pdb=" N ILE A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL A 279 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 270 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 197 removed outlier: 3.628A pdb=" N THR A 209 " --> pdb=" O CYS A 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 528 Processing sheet with id=AA6, first strand: chain 'A' and resid 663 through 669 Processing sheet with id=AA7, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.056A pdb=" N LEU B 82 " --> pdb=" O GLY B 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 150 through 154 removed outlier: 3.515A pdb=" N VAL D 100 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N GLY B 161 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ARG D 102 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 12.005A pdb=" N ASP B 163 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR D 92 " --> pdb=" O SER D 72 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 150 through 154 removed outlier: 3.515A pdb=" N VAL D 100 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N GLY B 161 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ARG D 102 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 12.005A pdb=" N ASP B 163 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU D 88 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL D 77 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 50 removed outlier: 3.683A pdb=" N CYS C 49 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 7.004A 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: 4.715A pdb=" N THR E 106 " --> pdb=" O ARG E 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.852A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.229A pdb=" N GLY H 10 " --> pdb=" O THR H 121 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.229A pdb=" N GLY H 10 " --> pdb=" O THR H 121 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N CYS H 96 " --> pdb=" O TRP H 114 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TRP H 114 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS H 98 " --> pdb=" O ASP H 112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.503A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.639A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'P' and resid 10 through 12 removed outlier: 3.627A pdb=" N ALA P 51 " --> pdb=" O TRP P 38 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARG P 40 " --> pdb=" O TRP P 49 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TRP P 49 " --> pdb=" O ARG P 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Q' and resid 9 through 12 removed outlier: 6.674A pdb=" N VAL Q 10 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TRP Q 37 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Q' and resid 9 through 12 removed outlier: 6.674A pdb=" N VAL Q 10 " --> pdb=" O THR Q 110 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Q' and resid 18 through 23 Processing sheet with id=AC5, first strand: chain 'X' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'X' and resid 10 through 12 removed outlier: 3.684A pdb=" N ILE X 34 " --> pdb=" O ILE X 51 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ARG X 38 " --> pdb=" O TRP X 47 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TRP X 47 " --> pdb=" O ARG X 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'X' and resid 10 through 12 removed outlier: 4.226A pdb=" N ASP X 112 " --> pdb=" O ARG X 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Y' and resid 4 through 7 removed outlier: 3.526A pdb=" N VAL Y 19 " --> pdb=" O ILE Y 75 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N THR Y 69 " --> pdb=" O ALA Y 25 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N GLN Y 27 " --> pdb=" O SER Y 67 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N SER Y 67 " --> pdb=" O GLN Y 27 " (cutoff:3.500A) removed outlier: 11.684A pdb=" N ILE Y 29 " --> pdb=" O SER Y 65 " (cutoff:3.500A) removed outlier: 11.812A pdb=" N SER Y 65 " --> pdb=" O ILE Y 29 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Y' and resid 10 through 11 removed outlier: 4.039A pdb=" N ALA Y 84 " --> pdb=" O VAL Y 104 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLN Y 37 " --> pdb=" O LEU Y 46 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU Y 46 " --> pdb=" O GLN Y 37 " (cutoff:3.500A) 667 hydrogen bonds defined for protein. 1716 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: 2.62 Time building geometry restraints manager: 1.75 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: 5002 1.34 - 1.46: 3834 1.46 - 1.58: 6871 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 15811 Sorted by residual: bond pdb=" C1 NAG E 201 " pdb=" O5 NAG E 201 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.99e+00 bond pdb=" CB MET P 87 " pdb=" CG MET P 87 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.94e+00 bond pdb=" C1 NAG D 301 " pdb=" O5 NAG D 301 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.66e+00 bond pdb=" C1 NAG B 301 " pdb=" O5 NAG B 301 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.39e+00 bond pdb=" C1 NAG A 803 " pdb=" O5 NAG A 803 " ideal model delta sigma weight residual 1.406 1.428 -0.022 2.00e-02 2.50e+03 1.26e+00 ... (remaining 15806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 21218 2.28 - 4.55: 255 4.55 - 6.83: 13 6.83 - 9.11: 7 9.11 - 11.38: 1 Bond angle restraints: 21494 Sorted by residual: angle pdb=" N VAL B 73 " pdb=" CA VAL B 73 " pdb=" C VAL B 73 " ideal model delta sigma weight residual 112.43 108.70 3.73 9.20e-01 1.18e+00 1.65e+01 angle pdb=" CB MET P 87 " pdb=" CG MET P 87 " pdb=" SD MET P 87 " ideal model delta sigma weight residual 112.70 101.32 11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C THR B 130 " pdb=" N ALA B 131 " pdb=" CA ALA B 131 " ideal model delta sigma weight residual 120.97 126.39 -5.42 1.48e+00 4.57e-01 1.34e+01 angle pdb=" C MET P 87 " pdb=" N ASP P 88 " pdb=" CA ASP P 88 " ideal model delta sigma weight residual 122.40 129.53 -7.13 1.98e+00 2.55e-01 1.30e+01 angle pdb=" N ILE A 435 " pdb=" CA ILE A 435 " pdb=" C ILE A 435 " ideal model delta sigma weight residual 109.02 112.00 -2.98 9.30e-01 1.16e+00 1.03e+01 ... (remaining 21489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 8705 18.05 - 36.10: 636 36.10 - 54.14: 154 54.14 - 72.19: 26 72.19 - 90.24: 19 Dihedral angle restraints: 9540 sinusoidal: 3867 harmonic: 5673 Sorted by residual: 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 -176.76 -90.24 1 1.00e+01 1.00e-02 9.64e+01 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 -162.78 76.78 1 1.00e+01 1.00e-02 7.40e+01 dihedral pdb=" CB CYS A 195 " pdb=" SG CYS A 195 " pdb=" SG CYS A 211 " pdb=" CB CYS A 211 " ideal model delta sinusoidal sigma weight residual 93.00 137.78 -44.78 1 1.00e+01 1.00e-02 2.79e+01 ... (remaining 9537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1618 0.034 - 0.068: 552 0.068 - 0.102: 204 0.102 - 0.136: 60 0.136 - 0.170: 4 Chirality restraints: 2438 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 -2.23 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA PRO D 68 " pdb=" N PRO D 68 " pdb=" C PRO D 68 " pdb=" CB PRO D 68 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CB ILE A 196 " pdb=" CA ILE A 196 " pdb=" CG1 ILE A 196 " pdb=" CG2 ILE A 196 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 2435 not shown) Planarity restraints: 2746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 240 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO B 241 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 47 " -0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO B 48 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 48 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 48 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 313 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C LEU A 313 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU A 313 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 314 " -0.010 2.00e-02 2.50e+03 ... (remaining 2743 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 418 2.69 - 3.24: 15287 3.24 - 3.80: 24679 3.80 - 4.35: 32181 4.35 - 4.90: 54015 Nonbonded interactions: 126580 Sorted by model distance: nonbonded pdb=" OE2 GLU C 41 " pdb=" OH TYR C 65 " model vdw 2.140 3.040 nonbonded pdb=" OD1 ASP P 74 " pdb=" OG SER P 76 " model vdw 2.151 3.040 nonbonded pdb=" OH TYR D 113 " pdb=" OD1 ASP E 66 " model vdw 2.153 3.040 nonbonded pdb=" OH TYR A 589 " pdb=" O LEU A 698 " model vdw 2.154 3.040 nonbonded pdb=" O CYS C 96 " pdb=" ND2 ASN C 99 " model vdw 2.194 3.120 ... (remaining 126575 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 ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.150 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 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 0.042 15832 Z= 0.163 Angle : 0.633 11.384 21540 Z= 0.349 Chirality : 0.041 0.170 2438 Planarity : 0.004 0.054 2742 Dihedral : 13.804 89.078 5839 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.12 % Allowed : 8.98 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 1909 helix: 0.93 (0.25), residues: 439 sheet: 0.22 (0.23), residues: 521 loop : 0.10 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 117 TYR 0.014 0.001 TYR B 226 PHE 0.014 0.001 PHE L 72 TRP 0.014 0.001 TRP P 38 HIS 0.005 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (15811) covalent geometry : angle 0.63183 / 0.35 (21494) SS BOND : bond 0.00382 / 0.24 ( 17) SS BOND : angle 0.76813 / 0.44 ( 34) hydrogen bonds : bond 0.21059 / 13.43 ( 645) hydrogen bonds : angle 7.77251 / 5.60 ( 1716) link_NAG-ASN : bond 0.00154 / 0.07 ( 4) link_NAG-ASN : angle 1.27675 / 0.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.619 Fit side-chains REVERT: A 332 MET cc_start: 0.9112 (tpt) cc_final: 0.8809 (tpt) outliers start: 2 outliers final: 0 residues processed: 46 average time/residue: 0.1290 time to fit residues: 9.2957 Evaluate side-chains 45 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 621 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.036237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.031740 restraints weight = 120922.352| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.92 r_work: 0.2668 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 15832 Z= 0.271 Angle : 0.647 8.967 21540 Z= 0.336 Chirality : 0.044 0.163 2438 Planarity : 0.005 0.058 2742 Dihedral : 5.472 52.324 2268 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.76 % Allowed : 8.57 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.19), residues: 1909 helix: 0.92 (0.25), residues: 431 sheet: 0.06 (0.22), residues: 526 loop : -0.04 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 109 TYR 0.019 0.002 TYR X 95 PHE 0.019 0.002 PHE A 677 TRP 0.013 0.002 TRP P 38 HIS 0.007 0.002 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.27 (15811) covalent geometry : angle 0.64494 / 0.34 (21494) SS BOND : bond 0.00721 / 0.42 ( 17) SS BOND : angle 1.03254 / 0.61 ( 34) hydrogen bonds : bond 0.04595 / 2.99 ( 645) hydrogen bonds : angle 6.08700 / 4.32 ( 1716) link_NAG-ASN : bond 0.00401 / 0.19 ( 4) link_NAG-ASN : angle 2.01997 / 1.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 44 time to evaluate : 0.599 Fit side-chains REVERT: D 66 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8004 (m-80) REVERT: L 104 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8757 (tt) outliers start: 30 outliers final: 16 residues processed: 71 average time/residue: 0.1064 time to fit residues: 12.2514 Evaluate side-chains 59 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain X residue 48 MET Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [174, 15, 52, 71, 13, 72, 144, 66, 19, 149, 21] chunk 174 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.036178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.031694 restraints weight = 122255.688| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.94 r_work: 0.2665 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 15832 Z= 0.239 Angle : 0.612 8.419 21540 Z= 0.316 Chirality : 0.043 0.153 2438 Planarity : 0.005 0.067 2742 Dihedral : 5.431 53.130 2268 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.52 % Allowed : 9.22 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.19), residues: 1909 helix: 0.96 (0.25), residues: 427 sheet: 0.03 (0.23), residues: 517 loop : -0.13 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 109 TYR 0.020 0.002 TYR Y 49 PHE 0.016 0.002 PHE A 677 TRP 0.011 0.002 TRP A 438 HIS 0.006 0.002 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.24 (15811) covalent geometry : angle 0.60920 / 0.32 (21494) SS BOND : bond 0.00651 / 0.38 ( 17) SS BOND : angle 0.98136 / 0.58 ( 34) hydrogen bonds : bond 0.04219 / 2.76 ( 645) hydrogen bonds : angle 5.75620 / 4.06 ( 1716) link_NAG-ASN : bond 0.00311 / 0.15 ( 4) link_NAG-ASN : angle 1.97845 / 1.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 45 time to evaluate : 0.538 Fit side-chains REVERT: A 430 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8452 (t0) REVERT: A 449 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8436 (ttpt) REVERT: A 667 MET cc_start: 0.8310 (mmm) cc_final: 0.8094 (mmm) REVERT: D 66 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: H 28 THR cc_start: 0.9340 (OUTLIER) cc_final: 0.9098 (p) REVERT: L 104 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8734 (tt) outliers start: 43 outliers final: 26 residues processed: 84 average time/residue: 0.1081 time to fit residues: 14.8406 Evaluate side-chains 70 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 40 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain X residue 48 MET Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [58, 8, 30, 32, 180, 158, 106, 159, 171, 50, 37] chunk 58 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 159 optimal weight: 9.9990 chunk 171 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.036991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.032476 restraints weight = 120032.844| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 2.94 r_work: 0.2697 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15832 Z= 0.143 Angle : 0.540 7.852 21540 Z= 0.279 Chirality : 0.041 0.145 2438 Planarity : 0.004 0.067 2742 Dihedral : 5.120 54.679 2268 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.47 % Allowed : 11.22 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 1909 helix: 1.17 (0.25), residues: 427 sheet: 0.19 (0.23), residues: 517 loop : 0.00 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 117 TYR 0.014 0.001 TYR Y 49 PHE 0.011 0.001 PHE B 232 TRP 0.010 0.001 TRP A 438 HIS 0.005 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (15811) covalent geometry : angle 0.53805 / 0.28 (21494) SS BOND : bond 0.00422 / 0.24 ( 17) SS BOND : angle 0.82529 / 0.51 ( 34) hydrogen bonds : bond 0.03537 / 2.32 ( 645) hydrogen bonds : angle 5.38116 / 3.79 ( 1716) link_NAG-ASN : bond 0.00189 / 0.09 ( 4) link_NAG-ASN : angle 1.51835 / 0.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 47 time to evaluate : 0.581 Fit side-chains REVERT: A 96 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7354 (pt) REVERT: A 332 MET cc_start: 0.9064 (tpt) cc_final: 0.8848 (tpt) REVERT: A 430 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.8450 (t0) REVERT: A 449 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8394 (ttpt) REVERT: A 667 MET cc_start: 0.8310 (mmm) cc_final: 0.8024 (mmm) REVERT: D 66 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: H 28 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9063 (p) REVERT: L 104 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8685 (tt) outliers start: 25 outliers final: 11 residues processed: 70 average time/residue: 0.1091 time to fit residues: 12.4841 Evaluate side-chains 57 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain X residue 48 MET Chi-restraints excluded: chain X residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [137, 177, 52, 127, 17, 121, 7, 181, 3, 74, 58] chunk 137 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.036060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.031671 restraints weight = 121851.331| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.92 r_work: 0.2665 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 15832 Z= 0.242 Angle : 0.600 8.588 21540 Z= 0.309 Chirality : 0.043 0.171 2438 Planarity : 0.005 0.068 2742 Dihedral : 5.314 53.473 2268 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.23 % Allowed : 11.51 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.19), residues: 1909 helix: 1.06 (0.25), residues: 426 sheet: 0.13 (0.23), residues: 510 loop : -0.14 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 62 TYR 0.020 0.002 TYR Y 49 PHE 0.017 0.002 PHE D 147 TRP 0.011 0.002 TRP P 38 HIS 0.006 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.24 (15811) covalent geometry : angle 0.59809 / 0.31 (21494) SS BOND : bond 0.00650 / 0.38 ( 17) SS BOND : angle 0.95484 / 0.57 ( 34) hydrogen bonds : bond 0.03849 / 2.51 ( 645) hydrogen bonds : angle 5.48730 / 3.86 ( 1716) link_NAG-ASN : bond 0.00370 / 0.18 ( 4) link_NAG-ASN : angle 1.95361 / 1.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 41 time to evaluate : 0.612 Fit side-chains REVERT: A 96 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7499 (pt) REVERT: A 332 MET cc_start: 0.9067 (tpt) cc_final: 0.8843 (tpt) REVERT: A 430 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8241 (t0) REVERT: A 449 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8400 (ttpt) REVERT: A 667 MET cc_start: 0.8326 (mmm) cc_final: 0.8055 (mmm) REVERT: D 66 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: H 28 THR cc_start: 0.9335 (OUTLIER) cc_final: 0.9104 (p) REVERT: L 104 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8710 (tt) outliers start: 38 outliers final: 24 residues processed: 75 average time/residue: 0.1104 time to fit residues: 13.5659 Evaluate side-chains 69 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 40 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain X residue 48 MET Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain Y residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [4, 141, 113, 17, 3, 26, 16, 76, 45, 13, 127] chunk 4 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 GLN ** 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 = 0.2922 r_free = 0.2922 target = 0.036799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.032355 restraints weight = 120121.535| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.93 r_work: 0.2692 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15832 Z= 0.148 Angle : 0.540 8.260 21540 Z= 0.279 Chirality : 0.041 0.159 2438 Planarity : 0.004 0.065 2742 Dihedral : 5.138 55.060 2268 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.11 % Allowed : 12.10 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.20), residues: 1909 helix: 1.20 (0.25), residues: 427 sheet: 0.20 (0.23), residues: 513 loop : -0.02 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 117 TYR 0.015 0.001 TYR Y 49 PHE 0.011 0.001 PHE B 232 TRP 0.010 0.001 TRP A 438 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (15811) covalent geometry : angle 0.53786 / 0.28 (21494) SS BOND : bond 0.00424 / 0.25 ( 17) SS BOND : angle 0.82041 / 0.49 ( 34) hydrogen bonds : bond 0.03449 / 2.25 ( 645) hydrogen bonds : angle 5.28339 / 3.71 ( 1716) link_NAG-ASN : bond 0.00203 / 0.10 ( 4) link_NAG-ASN : angle 1.58992 / 0.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 41 time to evaluate : 0.539 Fit side-chains REVERT: A 96 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7433 (pt) REVERT: A 332 MET cc_start: 0.9046 (tpt) cc_final: 0.8833 (tpt) REVERT: A 430 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8369 (m-40) REVERT: A 449 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8379 (ttpt) REVERT: A 667 MET cc_start: 0.8289 (mmm) cc_final: 0.8040 (mmm) REVERT: D 66 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: H 28 THR cc_start: 0.9312 (OUTLIER) cc_final: 0.9090 (p) REVERT: L 104 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8672 (tt) REVERT: P 87 MET cc_start: 0.7204 (mmp) cc_final: 0.6876 (mmp) outliers start: 36 outliers final: 23 residues processed: 74 average time/residue: 0.1059 time to fit residues: 12.9589 Evaluate side-chains 68 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 40 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain X residue 48 MET Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [105, 57, 165, 67, 25, 120, 48, 128, 100, 79, 12] chunk 105 optimal weight: 0.0870 chunk 57 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** 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 = 0.2940 r_free = 0.2940 target = 0.037259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.032807 restraints weight = 119007.262| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.93 r_work: 0.2710 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15832 Z= 0.123 Angle : 0.517 8.123 21540 Z= 0.267 Chirality : 0.041 0.154 2438 Planarity : 0.004 0.065 2742 Dihedral : 4.922 55.017 2268 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.23 % Allowed : 12.27 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.20), residues: 1909 helix: 1.33 (0.26), residues: 426 sheet: 0.34 (0.23), residues: 514 loop : 0.05 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 117 TYR 0.013 0.001 TYR Y 49 PHE 0.011 0.001 PHE B 232 TRP 0.010 0.001 TRP B 134 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (15811) covalent geometry : angle 0.51526 / 0.27 (21494) SS BOND : bond 0.00342 / 0.20 ( 17) SS BOND : angle 0.73681 / 0.45 ( 34) hydrogen bonds : bond 0.03243 / 2.12 ( 645) hydrogen bonds : angle 5.11215 / 3.58 ( 1716) link_NAG-ASN : bond 0.00175 / 0.08 ( 4) link_NAG-ASN : angle 1.40793 / 0.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 42 time to evaluate : 0.521 Fit side-chains REVERT: A 91 HIS cc_start: 0.5700 (OUTLIER) cc_final: 0.5036 (m90) REVERT: A 96 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7436 (pt) REVERT: A 332 MET cc_start: 0.9058 (tpt) cc_final: 0.8856 (tpt) REVERT: A 430 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8315 (m-40) REVERT: A 449 LYS cc_start: 0.8812 (ttmt) cc_final: 0.8477 (ttpt) REVERT: A 667 MET cc_start: 0.8236 (mmm) cc_final: 0.7970 (mmm) REVERT: A 669 MET cc_start: 0.7258 (mmm) cc_final: 0.6869 (mmm) REVERT: D 66 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: H 28 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.9092 (p) REVERT: L 104 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8633 (tt) REVERT: P 87 MET cc_start: 0.7336 (mmp) cc_final: 0.7000 (mmp) outliers start: 38 outliers final: 22 residues processed: 78 average time/residue: 0.1016 time to fit residues: 13.1071 Evaluate side-chains 68 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 40 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain X residue 48 MET Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [36, 56, 25, 67, 189, 178, 93, 126, 87, 168, 46] chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 189 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** 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 = 0.2944 r_free = 0.2944 target = 0.037378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.032917 restraints weight = 119975.143| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.96 r_work: 0.2714 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15832 Z= 0.121 Angle : 0.511 8.084 21540 Z= 0.264 Chirality : 0.041 0.151 2438 Planarity : 0.004 0.064 2742 Dihedral : 4.841 54.749 2268 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.00 % Allowed : 12.27 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.20), residues: 1909 helix: 1.44 (0.26), residues: 421 sheet: 0.39 (0.23), residues: 514 loop : 0.13 (0.21), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 117 TYR 0.014 0.001 TYR Y 49 PHE 0.010 0.001 PHE B 232 TRP 0.009 0.001 TRP B 134 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (15811) covalent geometry : angle 0.51011 / 0.26 (21494) SS BOND : bond 0.00331 / 0.19 ( 17) SS BOND : angle 0.74369 / 0.45 ( 34) hydrogen bonds : bond 0.03192 / 2.10 ( 645) hydrogen bonds : angle 5.03446 / 3.53 ( 1716) link_NAG-ASN : bond 0.00171 / 0.08 ( 4) link_NAG-ASN : angle 1.37470 / 0.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 43 time to evaluate : 0.604 Fit side-chains REVERT: A 91 HIS cc_start: 0.5840 (OUTLIER) cc_final: 0.5097 (m90) REVERT: A 96 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7419 (pt) REVERT: A 117 ARG cc_start: 0.8789 (mtt90) cc_final: 0.8494 (mtm-85) REVERT: A 430 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8345 (m-40) REVERT: A 449 LYS cc_start: 0.8846 (ttmt) cc_final: 0.8498 (ttpt) REVERT: A 667 MET cc_start: 0.8227 (mmm) cc_final: 0.7974 (mmm) REVERT: D 66 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: H 28 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.9100 (p) REVERT: L 104 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8617 (tt) REVERT: P 87 MET cc_start: 0.7343 (mmp) cc_final: 0.6805 (mmt) outliers start: 34 outliers final: 25 residues processed: 75 average time/residue: 0.1013 time to fit residues: 12.5057 Evaluate side-chains 73 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 42 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain Y residue 5 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [53, 82, 123, 103, 140, 95, 69, 18, 148, 44, 34] chunk 53 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 140 optimal weight: 0.3980 chunk 95 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 GLN ** 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 = 0.2930 r_free = 0.2930 target = 0.037007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.032584 restraints weight = 119871.058| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.93 r_work: 0.2701 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15832 Z= 0.155 Angle : 0.536 10.259 21540 Z= 0.275 Chirality : 0.041 0.148 2438 Planarity : 0.004 0.064 2742 Dihedral : 4.917 54.380 2268 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.88 % Allowed : 12.27 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 1909 helix: 1.37 (0.26), residues: 421 sheet: 0.35 (0.23), residues: 521 loop : 0.08 (0.21), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 66 TYR 0.016 0.001 TYR Y 49 PHE 0.012 0.001 PHE D 147 TRP 0.008 0.001 TRP A 438 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (15811) covalent geometry : angle 0.53440 / 0.27 (21494) SS BOND : bond 0.00431 / 0.25 ( 17) SS BOND : angle 0.77470 / 0.47 ( 34) hydrogen bonds : bond 0.03338 / 2.19 ( 645) hydrogen bonds : angle 5.08505 / 3.56 ( 1716) link_NAG-ASN : bond 0.00213 / 0.10 ( 4) link_NAG-ASN : angle 1.54343 / 0.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 42 time to evaluate : 0.488 Fit side-chains REVERT: A 91 HIS cc_start: 0.5870 (OUTLIER) cc_final: 0.5108 (m90) REVERT: A 96 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7448 (pt) REVERT: A 430 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8388 (m-40) REVERT: A 449 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8521 (ttpt) REVERT: A 667 MET cc_start: 0.8254 (mmm) cc_final: 0.8002 (mmm) REVERT: A 669 MET cc_start: 0.7106 (mmm) cc_final: 0.6737 (mmm) REVERT: D 66 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: H 28 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9081 (p) REVERT: L 104 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8627 (tt) REVERT: P 87 MET cc_start: 0.7208 (mmp) cc_final: 0.6736 (mmt) outliers start: 32 outliers final: 24 residues processed: 72 average time/residue: 0.1035 time to fit residues: 12.3210 Evaluate side-chains 72 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 42 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain Y residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [75, 119, 99, 91, 107, 179, 169, 14, 102, 8, 55] chunk 75 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 179 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** 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 = 0.2951 r_free = 0.2951 target = 0.037572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.033110 restraints weight = 119530.797| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.95 r_work: 0.2721 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15832 Z= 0.111 Angle : 0.512 9.135 21540 Z= 0.263 Chirality : 0.041 0.150 2438 Planarity : 0.004 0.063 2742 Dihedral : 4.799 55.285 2268 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.82 % Allowed : 12.33 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.20), residues: 1909 helix: 1.45 (0.26), residues: 420 sheet: 0.39 (0.23), residues: 521 loop : 0.15 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 117 TYR 0.013 0.001 TYR Y 49 PHE 0.010 0.001 PHE D 147 TRP 0.010 0.001 TRP B 134 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (15811) covalent geometry : angle 0.51077 / 0.26 (21494) SS BOND : bond 0.00298 / 0.17 ( 17) SS BOND : angle 0.72436 / 0.44 ( 34) hydrogen bonds : bond 0.03142 / 2.06 ( 645) hydrogen bonds : angle 4.98589 / 3.49 ( 1716) link_NAG-ASN : bond 0.00174 / 0.08 ( 4) link_NAG-ASN : angle 1.33623 / 0.68 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 47 time to evaluate : 0.626 Fit side-chains REVERT: A 91 HIS cc_start: 0.5726 (OUTLIER) cc_final: 0.4975 (m90) REVERT: A 96 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7436 (pt) REVERT: A 430 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8458 (m-40) REVERT: A 449 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8459 (ttpt) REVERT: A 667 MET cc_start: 0.8248 (mmm) cc_final: 0.7980 (mmm) REVERT: D 66 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.7975 (m-80) REVERT: H 28 THR cc_start: 0.9312 (OUTLIER) cc_final: 0.9085 (p) REVERT: L 104 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8585 (tt) REVERT: P 87 MET cc_start: 0.7256 (mmp) cc_final: 0.6773 (mmt) outliers start: 31 outliers final: 22 residues processed: 77 average time/residue: 0.1016 time to fit residues: 13.0922 Evaluate side-chains 71 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 43 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [163, 189, 166, 159, 74, 83, 80, 115, 26, 51, 131] chunk 163 optimal weight: 0.1980 chunk 189 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** 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 = 0.2962 r_free = 0.2962 target = 0.037859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.033391 restraints weight = 118712.708| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.95 r_work: 0.2733 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15832 Z= 0.103 Angle : 0.509 10.008 21540 Z= 0.262 Chirality : 0.041 0.159 2438 Planarity : 0.004 0.060 2742 Dihedral : 4.699 55.008 2268 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.59 % Allowed : 12.86 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.20), residues: 1909 helix: 1.47 (0.26), residues: 420 sheet: 0.41 (0.23), residues: 521 loop : 0.21 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 117 TYR 0.012 0.001 TYR Y 49 PHE 0.009 0.001 PHE D 147 TRP 0.010 0.001 TRP B 134 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (15811) covalent geometry : angle 0.50795 / 0.26 (21494) SS BOND : bond 0.00277 / 0.16 ( 17) SS BOND : angle 0.70594 / 0.43 ( 34) hydrogen bonds : bond 0.03077 / 2.02 ( 645) hydrogen bonds : angle 4.92894 / 3.45 ( 1716) link_NAG-ASN : bond 0.00130 / 0.06 ( 4) link_NAG-ASN : angle 1.32816 / 0.67 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2563.81 seconds wall clock time: 45 minutes 10.01 seconds (2710.01 seconds total)