Starting phenix.real_space_refine on Tue Nov 19 02:33:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hws_35063/11_2024/8hws_35063.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hws_35063/11_2024/8hws_35063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hws_35063/11_2024/8hws_35063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hws_35063/11_2024/8hws_35063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hws_35063/11_2024/8hws_35063.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hws_35063/11_2024/8hws_35063.cif" } resolution = 2.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8168 atoms to isotropic. 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 46 5.16 5 C 7244 2.51 5 N 1930 2.21 5 O 2291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11511 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1563 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 12, 'TRANS': 183} Chain: "H" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1617 Classifications: {'peptide': 219} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Chain: "L" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1632 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "D" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1662 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210} Chain: "E" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1634 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "I" Number of atoms: 1732 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 230, 1729 Classifications: {'peptide': 230} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 217} Conformer: "B" Number of residues, atoms: 230, 1729 Classifications: {'peptide': 230} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 217} bond proxies already assigned to first conformer: 1768 Chain: "J" Number of atoms: 1633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1630 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 214, 1630 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1659 Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} 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 Time building chain proxies: 9.64, per 1000 atoms: 0.84 Number of scatterers: 11511 At special positions: 0 Unit cell: (87.55, 113.9, 167.45, 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 46 16.00 O 2291 8.00 N 1930 7.00 C 7244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.04 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " distance=2.03 Simple disulfide: pdb=" SG CYS D 223 " - pdb=" SG CYS E 215 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 154 " - pdb=" SG CYS I 210 " distance=2.04 Simple disulfide: pdb=" SG CYS I 230 " - pdb=" SG CYS J 214 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.04 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG ACYS J 194 " distance=2.04 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG BCYS J 194 " distance=2.04 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 BETA1-4 " NAG B 1 " - " NAG B 2 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 2.0 seconds 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2768 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 36 sheets defined 9.7% alpha, 47.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.766A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.831A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.344A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.785A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.927A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 133 No H-bonds generated for 'chain 'H' and resid 131 through 133' Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.270A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 removed outlier: 3.546A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 187 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.514A pdb=" N SER D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.950A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 165 No H-bonds generated for 'chain 'D' and resid 163 through 165' Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 208 through 211 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.833A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.520A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 170 through 172 No H-bonds generated for 'chain 'I' and resid 170 through 172' Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'J' and resid 80 through 84 removed outlier: 3.912A pdb=" N PHE J 84 " --> pdb=" O PRO J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 126 Processing helix chain 'J' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.947A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.039A pdb=" N TYR H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.252A pdb=" N VAL H 106 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 124 through 128 removed outlier: 6.060A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 135 through 136 removed outlier: 6.060A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER H 181 " --> pdb=" O VAL H 173 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 155 through 158 removed outlier: 4.199A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6 removed outlier: 4.116A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.014A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.014A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.015A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR L 178 " --> pdb=" O GLN L 160 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN L 160 " --> pdb=" O THR L 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.308A pdb=" N ASP D 33 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET D 34 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.969A pdb=" N CYS D 95 " --> pdb=" O TRP D 110 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP D 110 " --> pdb=" O CYS D 95 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG D 97 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 127 through 131 removed outlier: 6.129A pdb=" N TYR D 183 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 138 through 139 removed outlier: 6.129A pdb=" N TYR D 183 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AC3, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.677A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.887A pdb=" N LEU E 11 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.887A pdb=" N LEU E 11 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR E 98 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 115 through 119 removed outlier: 5.783A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 145 through 151 Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.327A pdb=" N GLU I 10 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY I 33 " --> pdb=" O ASP I 99 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.327A pdb=" N GLU I 10 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N CYS I 96 " --> pdb=" O TRP I 117 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TRP I 117 " --> pdb=" O CYS I 96 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 134 through 138 removed outlier: 6.019A pdb=" N TYR I 190 " --> pdb=" O ASP I 158 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 134 through 138 removed outlier: 6.019A pdb=" N TYR I 190 " --> pdb=" O ASP I 158 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 165 through 168 removed outlier: 4.185A pdb=" N TYR I 208 " --> pdb=" O VAL I 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.864A pdb=" N LEU J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AD8, first strand: chain 'J' and resid 114 through 118 removed outlier: 6.347A pdb=" N TYR J 173 " --> pdb=" O ASN J 138 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 154 through 155 removed outlier: 4.677A pdb=" N TRP J 148 " --> pdb=" O GLN J 155 " (cutoff:3.500A) 511 hydrogen bonds defined for protein. 1271 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: 4.44 Time building geometry restraints manager: 3.45 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: 3687 1.34 - 1.47: 3032 1.47 - 1.59: 5009 1.59 - 1.71: 0 1.71 - 1.83: 55 Bond restraints: 11783 Sorted by residual: bond pdb=" N GLY I 113 " pdb=" CA GLY I 113 " ideal model delta sigma weight residual 1.453 1.442 0.011 8.60e-03 1.35e+04 1.65e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.62e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.06e+00 bond pdb=" CB PRO J 141 " pdb=" CG PRO J 141 " ideal model delta sigma weight residual 1.506 1.468 0.038 3.90e-02 6.57e+02 9.55e-01 ... (remaining 11778 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 15813 2.12 - 4.24: 189 4.24 - 6.36: 27 6.36 - 8.48: 1 8.48 - 10.60: 2 Bond angle restraints: 16032 Sorted by residual: angle pdb=" CA LEU I 192 " pdb=" CB LEU I 192 " pdb=" CG LEU I 192 " ideal model delta sigma weight residual 116.30 126.90 -10.60 3.50e+00 8.16e-02 9.16e+00 angle pdb=" CA TYR D 152 " pdb=" CB TYR D 152 " pdb=" CG TYR D 152 " ideal model delta sigma weight residual 113.90 118.74 -4.84 1.80e+00 3.09e-01 7.22e+00 angle pdb=" CA LEU D 115 " pdb=" CB LEU D 115 " pdb=" CG LEU D 115 " ideal model delta sigma weight residual 116.30 125.50 -9.20 3.50e+00 8.16e-02 6.91e+00 angle pdb=" CA LYS J 145 " pdb=" CB LYS J 145 " pdb=" CG LYS J 145 " ideal model delta sigma weight residual 114.10 119.16 -5.06 2.00e+00 2.50e-01 6.40e+00 angle pdb=" C VAL D 48 " pdb=" N SER D 49 " pdb=" CA SER D 49 " ideal model delta sigma weight residual 121.85 117.39 4.46 1.77e+00 3.19e-01 6.36e+00 ... (remaining 16027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 6195 17.07 - 34.14: 620 34.14 - 51.20: 193 51.20 - 68.27: 50 68.27 - 85.34: 17 Dihedral angle restraints: 7075 sinusoidal: 2724 harmonic: 4351 Sorted by residual: dihedral pdb=" CB CYS I 154 " pdb=" SG CYS I 154 " pdb=" SG CYS I 210 " pdb=" CB CYS I 210 " ideal model delta sinusoidal sigma weight residual 93.00 139.68 -46.68 1 1.00e+01 1.00e-02 3.01e+01 dihedral pdb=" CB CYS I 230 " pdb=" SG CYS I 230 " pdb=" SG CYS J 214 " pdb=" CB CYS J 214 " ideal model delta sinusoidal sigma weight residual -86.00 -125.91 39.91 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 95 " pdb=" CB CYS D 95 " ideal model delta sinusoidal sigma weight residual 93.00 55.96 37.04 1 1.00e+01 1.00e-02 1.94e+01 ... (remaining 7072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1068 0.030 - 0.059: 470 0.059 - 0.089: 133 0.089 - 0.118: 112 0.118 - 0.147: 20 Chirality restraints: 1803 Sorted by residual: chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CB THR A 430 " pdb=" CA THR A 430 " pdb=" OG1 THR A 430 " pdb=" CG2 THR A 430 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 1800 not shown) Planarity restraints: 2056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 100 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.18e+00 pdb=" N PRO E 101 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 101 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 101 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER J 7 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO J 8 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO J 8 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO J 8 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 162 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO I 163 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO I 163 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 163 " -0.021 5.00e-02 4.00e+02 ... (remaining 2053 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 495 2.72 - 3.26: 10143 3.26 - 3.81: 17777 3.81 - 4.35: 22144 4.35 - 4.90: 39420 Nonbonded interactions: 89979 Sorted by model distance: nonbonded pdb=" OG SER L 30 " pdb=" N SER L 31 " model vdw 2.174 3.120 nonbonded pdb=" OH TYR H 52 " pdb=" OD1 ASP L 94 " model vdw 2.237 3.040 nonbonded pdb=" O GLN L 124 " pdb=" OG SER L 127 " model vdw 2.240 3.040 nonbonded pdb=" OG SER J 64 " pdb=" OG1 THR J 75 " model vdw 2.240 3.040 nonbonded pdb=" O SER A 438 " pdb=" OG SER A 438 " model vdw 2.252 3.040 ... (remaining 89974 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 2 through 11 or resid 13 through 26 or resid 30 through 31 \ or resid 34 or resid 36 through 39 or resid 42 through 49 or resid 51 or resid \ 55 or resid 57 or resid 59 or resid 61 through 71 or resid 75 through 76 or resi \ d 78 through 82 or resid 84 through 87 or resid 89 through 97 or resid 99 or res \ id 102 or resid 104 or resid 108 or resid 110 through 114 or resid 117 through 2 \ 22)) selection = (chain 'H' and (resid 2 through 11 or resid 13 through 26 or resid 30 through 31 \ or resid 34 or resid 36 through 39 or resid 42 through 49 or resid 51 or resid \ 55 or resid 57 or resid 59 or resid 61 through 71 or resid 75 through 76 or resi \ d 78 through 82 or resid 84 through 87 or resid 89 through 98 or resid 100 or re \ sid 102 or resid 105 or resid 107 through 111 or resid 114 through 219)) } ncs_group { reference = (chain 'E' and (resid 2 or resid 5 through 9 or resid 11 through 13 or resid 15 \ through 27 or resid 29 or resid 31 or resid 33 or resid 35 through 44 or resid 4 \ 6 through 52 or resid 54 through 69 or resid 71 through 84 or resid 86 through 9 \ 0 or resid 94 or resid 97 through 100 or resid 102 through 104 or resid 107 thro \ ugh 214)) selection = (chain 'L' and (resid 2 or resid 5 through 9 or resid 11 through 13 or resid 15 \ through 27 or resid 29 or resid 31 or resid 33 or resid 35 through 44 or resid 4 \ 6 through 52 or resid 54 through 69 or resid 71 through 84 or resid 86 through 9 \ 0 or resid 93 or resid 96 through 99 or resid 101 through 103 or resid 106 throu \ gh 213)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.570 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 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:10.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 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 : 0.004 0.038 11783 Z= 0.232 Angle : 0.571 10.595 16032 Z= 0.289 Chirality : 0.043 0.147 1803 Planarity : 0.005 0.045 2055 Dihedral : 15.867 85.340 4250 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.26 % Allowed : 20.81 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.22), residues: 1496 helix: -1.86 (0.55), residues: 75 sheet: 1.33 (0.20), residues: 674 loop : -0.31 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 50 HIS 0.002 0.001 HIS J 92 PHE 0.017 0.001 PHE A 371 TYR 0.017 0.001 TYR A 473 ARG 0.007 0.000 ARG I 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 1.442 Fit side-chains outliers start: 42 outliers final: 38 residues processed: 221 average time/residue: 0.8966 time to fit residues: 222.0191 Evaluate side-chains 225 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 223 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain J residue 197 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.4980 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN H 175 GLN D 204 ASN E 6 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.0566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11783 Z= 0.329 Angle : 0.601 11.363 16032 Z= 0.308 Chirality : 0.044 0.151 1803 Planarity : 0.005 0.043 2055 Dihedral : 6.513 59.773 1748 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.96 % Allowed : 18.87 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1496 helix: -1.81 (0.58), residues: 69 sheet: 1.33 (0.20), residues: 679 loop : -0.35 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 110 HIS 0.004 0.001 HIS J 92 PHE 0.019 0.002 PHE E 99 TYR 0.023 0.002 TYR D 152 ARG 0.006 0.001 ARG I 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 205 time to evaluate : 1.292 Fit side-chains REVERT: L 55 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7136 (tp40) outliers start: 51 outliers final: 33 residues processed: 235 average time/residue: 0.8524 time to fit residues: 224.5147 Evaluate side-chains 221 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 223 CYS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 197 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 111 optimal weight: 0.0980 chunk 91 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 133 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 108 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 73 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN D 204 ASN D 207 HIS E 6 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11783 Z= 0.182 Angle : 0.544 11.135 16032 Z= 0.277 Chirality : 0.042 0.158 1803 Planarity : 0.005 0.041 2055 Dihedral : 5.528 52.513 1721 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.03 % Allowed : 19.80 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.22), residues: 1496 helix: -1.80 (0.57), residues: 69 sheet: 1.35 (0.20), residues: 680 loop : -0.25 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 50 HIS 0.002 0.000 HIS J 92 PHE 0.019 0.001 PHE A 371 TYR 0.024 0.001 TYR D 152 ARG 0.006 0.000 ARG I 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 1.280 Fit side-chains REVERT: A 420 ASP cc_start: 0.7050 (m-30) cc_final: 0.6826 (m-30) REVERT: I 89 ASP cc_start: 0.7430 (t0) cc_final: 0.7197 (t0) outliers start: 39 outliers final: 24 residues processed: 215 average time/residue: 0.9035 time to fit residues: 216.6205 Evaluate side-chains 207 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 223 CYS Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain J residue 70 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 14 optimal weight: 0.0370 chunk 64 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 143 optimal weight: 0.4980 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 0.2980 chunk 38 optimal weight: 0.0030 overall best weight: 0.2668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN E 6 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11783 Z= 0.143 Angle : 0.523 10.718 16032 Z= 0.263 Chirality : 0.042 0.223 1803 Planarity : 0.004 0.042 2055 Dihedral : 5.048 46.549 1713 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.95 % Allowed : 19.80 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.22), residues: 1496 helix: -1.76 (0.58), residues: 69 sheet: 1.38 (0.20), residues: 680 loop : -0.15 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 50 HIS 0.002 0.000 HIS J 92 PHE 0.015 0.001 PHE A 371 TYR 0.025 0.001 TYR D 152 ARG 0.006 0.000 ARG I 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 1.233 Fit side-chains REVERT: A 420 ASP cc_start: 0.7033 (m-30) cc_final: 0.6815 (m-30) REVERT: I 125 VAL cc_start: 0.7400 (m) cc_final: 0.7168 (p) REVERT: J 90 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7969 (tm-30) outliers start: 37 outliers final: 29 residues processed: 205 average time/residue: 0.9488 time to fit residues: 216.5891 Evaluate side-chains 214 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 223 CYS Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 109 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 128 optimal weight: 0.0470 chunk 36 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN H 76 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN D 204 ASN E 6 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11783 Z= 0.205 Angle : 0.540 10.858 16032 Z= 0.272 Chirality : 0.043 0.281 1803 Planarity : 0.004 0.042 2055 Dihedral : 5.042 47.726 1712 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.49 % Allowed : 19.72 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.22), residues: 1496 helix: -1.68 (0.58), residues: 69 sheet: 1.36 (0.20), residues: 684 loop : -0.14 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 50 HIS 0.002 0.000 HIS J 92 PHE 0.014 0.001 PHE A 371 TYR 0.025 0.001 TYR D 152 ARG 0.007 0.000 ARG I 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 1.322 Fit side-chains REVERT: A 420 ASP cc_start: 0.7063 (m-30) cc_final: 0.6848 (m-30) REVERT: I 125 VAL cc_start: 0.7433 (m) cc_final: 0.7214 (p) outliers start: 44 outliers final: 30 residues processed: 211 average time/residue: 0.8784 time to fit residues: 207.4731 Evaluate side-chains 220 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 223 CYS Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 109 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 143 optimal weight: 0.4980 chunk 118 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN D 204 ASN E 6 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11783 Z= 0.229 Angle : 0.556 10.901 16032 Z= 0.279 Chirality : 0.043 0.199 1803 Planarity : 0.004 0.042 2055 Dihedral : 4.911 48.214 1708 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.42 % Allowed : 19.80 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.22), residues: 1496 helix: -1.66 (0.59), residues: 69 sheet: 1.35 (0.20), residues: 684 loop : -0.17 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 110 HIS 0.002 0.001 HIS J 92 PHE 0.025 0.001 PHE A 371 TYR 0.026 0.001 TYR D 152 ARG 0.007 0.000 ARG I 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 1.240 Fit side-chains REVERT: A 420 ASP cc_start: 0.7090 (m-30) cc_final: 0.6872 (m-30) outliers start: 43 outliers final: 33 residues processed: 213 average time/residue: 0.8650 time to fit residues: 206.3382 Evaluate side-chains 217 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 223 CYS Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 109 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN D 204 ASN E 6 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11783 Z= 0.398 Angle : 0.621 11.275 16032 Z= 0.315 Chirality : 0.046 0.179 1803 Planarity : 0.005 0.042 2055 Dihedral : 5.055 45.265 1706 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.42 % Allowed : 19.95 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1496 helix: -1.63 (0.60), residues: 69 sheet: 1.30 (0.20), residues: 690 loop : -0.37 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 110 HIS 0.003 0.001 HIS E 190 PHE 0.027 0.002 PHE A 371 TYR 0.024 0.002 TYR D 152 ARG 0.006 0.000 ARG I 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 1.285 Fit side-chains REVERT: A 420 ASP cc_start: 0.7145 (m-30) cc_final: 0.6906 (m-30) REVERT: I 89 ASP cc_start: 0.7462 (t0) cc_final: 0.7237 (t0) outliers start: 43 outliers final: 37 residues processed: 211 average time/residue: 0.8838 time to fit residues: 208.5047 Evaluate side-chains 225 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 223 CYS Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 197 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN D 204 ASN E 6 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11783 Z= 0.265 Angle : 0.579 11.161 16032 Z= 0.293 Chirality : 0.044 0.156 1803 Planarity : 0.005 0.041 2055 Dihedral : 4.940 46.581 1706 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.49 % Allowed : 20.03 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1496 helix: -1.67 (0.59), residues: 69 sheet: 1.28 (0.20), residues: 688 loop : -0.34 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 110 HIS 0.003 0.001 HIS J 92 PHE 0.022 0.001 PHE A 371 TYR 0.026 0.002 TYR D 152 ARG 0.007 0.000 ARG I 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 1.358 Fit side-chains REVERT: A 420 ASP cc_start: 0.7152 (m-30) cc_final: 0.6910 (m-30) REVERT: I 89 ASP cc_start: 0.7428 (t0) cc_final: 0.7207 (t0) outliers start: 44 outliers final: 40 residues processed: 219 average time/residue: 0.8615 time to fit residues: 211.6827 Evaluate side-chains 229 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 223 CYS Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 197 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 104 optimal weight: 0.2980 chunk 40 optimal weight: 0.0980 chunk 120 optimal weight: 0.3980 chunk 125 optimal weight: 0.9980 chunk 87 optimal weight: 0.0070 chunk 140 optimal weight: 0.6980 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN D 204 ASN E 6 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11783 Z= 0.154 Angle : 0.537 10.574 16032 Z= 0.271 Chirality : 0.042 0.154 1803 Planarity : 0.004 0.041 2055 Dihedral : 4.725 47.537 1706 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.03 % Allowed : 20.65 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1496 helix: -1.69 (0.58), residues: 69 sheet: 1.34 (0.20), residues: 681 loop : -0.22 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 50 HIS 0.002 0.000 HIS J 92 PHE 0.018 0.001 PHE A 371 TYR 0.028 0.001 TYR D 152 ARG 0.007 0.000 ARG I 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 1.174 Fit side-chains REVERT: A 420 ASP cc_start: 0.7110 (m-30) cc_final: 0.6872 (m-30) REVERT: I 124 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.7982 (p) REVERT: I 125 VAL cc_start: 0.7441 (m) cc_final: 0.7223 (p) outliers start: 38 outliers final: 33 residues processed: 204 average time/residue: 0.9016 time to fit residues: 205.9385 Evaluate side-chains 211 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 223 CYS Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain J residue 48 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.2980 chunk 66 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 147 optimal weight: 0.0020 chunk 135 optimal weight: 0.2980 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 125 optimal weight: 0.1980 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN E 6 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11783 Z= 0.147 Angle : 0.532 10.260 16032 Z= 0.265 Chirality : 0.042 0.152 1803 Planarity : 0.004 0.042 2055 Dihedral : 4.573 48.106 1706 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.56 % Allowed : 21.58 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1496 helix: -1.63 (0.58), residues: 69 sheet: 1.40 (0.20), residues: 675 loop : -0.14 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 50 HIS 0.002 0.000 HIS J 92 PHE 0.018 0.001 PHE A 371 TYR 0.028 0.001 TYR D 152 ARG 0.007 0.000 ARG I 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 1.316 Fit side-chains REVERT: A 420 ASP cc_start: 0.7082 (m-30) cc_final: 0.6843 (m-30) REVERT: I 124 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7988 (p) outliers start: 32 outliers final: 27 residues processed: 195 average time/residue: 0.8984 time to fit residues: 195.6444 Evaluate side-chains 203 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 223 CYS Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 48 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 120 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN H 76 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN E 6 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.174453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.138724 restraints weight = 20914.085| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.96 r_work: 0.3717 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11783 Z= 0.242 Angle : 0.568 10.341 16032 Z= 0.284 Chirality : 0.043 0.153 1803 Planarity : 0.004 0.041 2055 Dihedral : 4.716 47.585 1706 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.64 % Allowed : 21.35 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1496 helix: -1.58 (0.59), residues: 69 sheet: 1.38 (0.20), residues: 684 loop : -0.19 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 110 HIS 0.003 0.001 HIS J 92 PHE 0.019 0.001 PHE A 371 TYR 0.012 0.001 TYR E 49 ARG 0.008 0.000 ARG J 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5071.42 seconds wall clock time: 91 minutes 44.60 seconds (5504.60 seconds total)