Starting phenix.real_space_refine on Mon Mar 18 02:17:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hws_35063/03_2024/8hws_35063.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hws_35063/03_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_35063/03_2024/8hws_35063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hws_35063/03_2024/8hws_35063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hws_35063/03_2024/8hws_35063.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hws_35063/03_2024/8hws_35063.pdb" } 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 Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 171": "OD1" <-> "OD2" Residue "I TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.56, per 1000 atoms: 0.66 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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: 4.29 Conformation dependent library (CDL) restraints added in 2.8 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: 1.59 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: 4.07 Time building geometry restraints manager: 4.63 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: 99.05 - 106.05: 285 106.05 - 113.06: 6370 113.06 - 120.06: 3802 120.06 - 127.07: 5443 127.07 - 134.07: 132 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 2.520 nonbonded pdb=" OH TYR H 52 " pdb=" OD1 ASP L 94 " model vdw 2.237 2.440 nonbonded pdb=" O GLN L 124 " pdb=" OG SER L 127 " model vdw 2.240 2.440 nonbonded pdb=" OG SER J 64 " pdb=" OG1 THR J 75 " model vdw 2.240 2.440 nonbonded pdb=" O SER A 438 " pdb=" OG SER A 438 " model vdw 2.252 2.440 ... (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 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 9.920 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 35.050 Find NCS groups from input model: 0.620 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: 0.010 Load rotamer database and sin/cos tables:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.990 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 42 poor density : 181 time to evaluate : 1.209 Fit side-chains outliers start: 42 outliers final: 38 residues processed: 221 average time/residue: 0.8064 time to fit residues: 199.4622 Evaluate side-chains 225 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 187 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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: 0.9980 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** L 100 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: 0.7451 moved from start: 0.0497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11783 Z= 0.315 Angle : 0.584 11.365 16032 Z= 0.297 Chirality : 0.044 0.150 1803 Planarity : 0.005 0.043 2055 Dihedral : 6.507 54.027 1748 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.27 % Allowed : 19.18 % Favored : 76.55 % 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: -1.58 (0.60), residues: 68 sheet: 1.32 (0.20), residues: 680 loop : -0.36 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 110 HIS 0.003 0.001 HIS J 92 PHE 0.019 0.002 PHE E 99 TYR 0.022 0.002 TYR D 152 ARG 0.006 0.000 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 253 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 198 time to evaluate : 1.248 Fit side-chains REVERT: L 55 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7134 (tp40) outliers start: 55 outliers final: 35 residues processed: 233 average time/residue: 0.7945 time to fit residues: 207.6355 Evaluate side-chains 224 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 188 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR 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 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 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 33 ASP Chi-restraints excluded: chain D residue 56 ASP 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 33 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 169 SER 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 211 ASN 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: 0.0040 chunk 41 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 133 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 175 GLN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 100 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.0593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11783 Z= 0.213 Angle : 0.548 11.437 16032 Z= 0.276 Chirality : 0.043 0.158 1803 Planarity : 0.005 0.041 2055 Dihedral : 5.711 54.608 1726 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.57 % Allowed : 20.11 % 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: 0.62 (0.22), residues: 1496 helix: -1.52 (0.60), residues: 68 sheet: 1.39 (0.20), residues: 675 loop : -0.31 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 50 HIS 0.002 0.001 HIS J 92 PHE 0.021 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 238 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 192 time to evaluate : 1.354 Fit side-chains REVERT: L 30 SER cc_start: 0.7554 (OUTLIER) cc_final: 0.7275 (p) outliers start: 46 outliers final: 29 residues processed: 222 average time/residue: 0.7993 time to fit residues: 199.2433 Evaluate side-chains 217 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 187 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR 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 30 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 33 ASP Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 118 VAL 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 69 THR Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 109 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 64 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** ** L 100 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: 0.7427 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11783 Z= 0.202 Angle : 0.539 11.293 16032 Z= 0.270 Chirality : 0.043 0.195 1803 Planarity : 0.004 0.041 2055 Dihedral : 5.314 54.982 1719 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.73 % Allowed : 20.11 % Favored : 76.16 % 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: -1.45 (0.61), residues: 68 sheet: 1.40 (0.20), residues: 668 loop : -0.29 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 50 HIS 0.003 0.000 HIS J 92 PHE 0.016 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 234 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 187 time to evaluate : 1.323 Fit side-chains REVERT: L 30 SER cc_start: 0.7531 (OUTLIER) cc_final: 0.7256 (p) outliers start: 47 outliers final: 33 residues processed: 217 average time/residue: 0.8231 time to fit residues: 200.4135 Evaluate side-chains 217 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 183 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 73 ASN 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 30 SER Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 138 ASN 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 33 ASP Chi-restraints excluded: chain D residue 56 ASP 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 69 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 115 ASP 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 I residue 211 ASN Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 197 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 106 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 chunk 0 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 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 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** 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: 0.7435 moved from start: 0.0747 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= 0.238 Angle : 0.547 11.493 16032 Z= 0.275 Chirality : 0.043 0.310 1803 Planarity : 0.004 0.042 2055 Dihedral : 5.321 56.615 1718 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.74 % Allowed : 19.72 % Favored : 75.54 % 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: 0.60 (0.22), residues: 1496 helix: -1.42 (0.61), residues: 68 sheet: 1.33 (0.20), residues: 686 loop : -0.30 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 50 HIS 0.003 0.001 HIS J 92 PHE 0.015 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 240 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 180 time to evaluate : 1.032 Fit side-chains REVERT: L 30 SER cc_start: 0.7544 (OUTLIER) cc_final: 0.7260 (p) REVERT: E 4 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8270 (mmm) outliers start: 60 outliers final: 41 residues processed: 222 average time/residue: 0.7705 time to fit residues: 192.9267 Evaluate side-chains 230 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 187 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 18 LEU 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 30 SER 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 138 ASN 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 33 ASP Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 100 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 4 MET 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 69 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 115 ASP 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 I residue 211 ASN Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 197 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 100 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: 0.7444 moved from start: 0.0819 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= 0.276 Angle : 0.564 11.665 16032 Z= 0.283 Chirality : 0.044 0.222 1803 Planarity : 0.004 0.041 2055 Dihedral : 5.415 59.311 1718 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.50 % Allowed : 19.80 % Favored : 75.70 % 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: 0.59 (0.22), residues: 1496 helix: -1.42 (0.61), residues: 68 sheet: 1.32 (0.20), residues: 689 loop : -0.32 (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 0.026 0.002 PHE A 371 TYR 0.025 0.002 TYR D 152 ARG 0.006 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 247 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 190 time to evaluate : 1.225 Fit side-chains REVERT: A 420 ASP cc_start: 0.7072 (m-30) cc_final: 0.6843 (m-30) REVERT: L 30 SER cc_start: 0.7569 (OUTLIER) cc_final: 0.7280 (p) outliers start: 57 outliers final: 43 residues processed: 228 average time/residue: 0.7616 time to fit residues: 195.6009 Evaluate side-chains 227 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 183 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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 57 THR 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 H residue 181 SER Chi-restraints excluded: chain L residue 30 SER 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 138 ASN 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 33 ASP Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 100 SER 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 I residue 211 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 120 optimal weight: 0.0870 chunk 79 optimal weight: 4.9990 chunk 142 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 100 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: 0.7427 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11783 Z= 0.203 Angle : 0.541 11.314 16032 Z= 0.271 Chirality : 0.042 0.155 1803 Planarity : 0.004 0.041 2055 Dihedral : 5.292 58.536 1716 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.11 % Allowed : 20.57 % Favored : 75.31 % 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: 0.62 (0.22), residues: 1496 helix: -1.42 (0.61), residues: 68 sheet: 1.36 (0.20), residues: 676 loop : -0.29 (0.22), residues: 752 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 0.022 0.001 PHE A 371 TYR 0.027 0.001 TYR D 152 ARG 0.007 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 237 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 185 time to evaluate : 1.331 Fit side-chains REVERT: A 420 ASP cc_start: 0.7068 (m-30) cc_final: 0.6845 (m-30) REVERT: L 30 SER cc_start: 0.7521 (OUTLIER) cc_final: 0.7236 (p) outliers start: 52 outliers final: 40 residues processed: 219 average time/residue: 0.7655 time to fit residues: 189.5185 Evaluate side-chains 229 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 188 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 57 THR 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 30 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 138 ASN 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 33 ASP Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 100 SER 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 I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR 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 I residue 211 ASN Chi-restraints excluded: chain J residue 48 LEU 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: 1.9990 chunk 85 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 90 optimal weight: 0.0770 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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: 0.7427 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11783 Z= 0.212 Angle : 0.544 11.261 16032 Z= 0.272 Chirality : 0.043 0.160 1803 Planarity : 0.004 0.041 2055 Dihedral : 5.115 58.643 1712 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.04 % Allowed : 20.81 % Favored : 75.16 % 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: 0.62 (0.22), residues: 1496 helix: -1.39 (0.61), residues: 68 sheet: 1.36 (0.20), residues: 676 loop : -0.27 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 50 HIS 0.002 0.001 HIS J 92 PHE 0.020 0.001 PHE A 371 TYR 0.027 0.001 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 232 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 181 time to evaluate : 1.293 Fit side-chains REVERT: A 420 ASP cc_start: 0.7081 (m-30) cc_final: 0.6856 (m-30) REVERT: L 30 SER cc_start: 0.7521 (OUTLIER) cc_final: 0.7235 (p) REVERT: D 214 VAL cc_start: 0.6447 (p) cc_final: 0.6087 (m) outliers start: 51 outliers final: 43 residues processed: 216 average time/residue: 0.7806 time to fit residues: 190.1127 Evaluate side-chains 231 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 187 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 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 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 30 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 138 ASN 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 33 ASP Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 100 SER 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 E residue 159 ASN 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 I residue 211 ASN Chi-restraints excluded: chain J residue 48 LEU 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: 0.6980 chunk 124 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 80 optimal weight: 0.0570 chunk 57 optimal weight: 5.9990 chunk 104 optimal weight: 0.4980 chunk 40 optimal weight: 0.2980 chunk 120 optimal weight: 0.0170 chunk 125 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.2936 ------------------------------------------------------------------------------- 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: 0.7402 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11783 Z= 0.145 Angle : 0.513 10.704 16032 Z= 0.256 Chirality : 0.042 0.155 1803 Planarity : 0.004 0.041 2055 Dihedral : 4.789 59.046 1710 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.80 % Allowed : 21.89 % Favored : 75.31 % 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: -1.37 (0.61), residues: 68 sheet: 1.36 (0.20), residues: 679 loop : -0.20 (0.23), residues: 749 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 0.017 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 225 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 190 time to evaluate : 1.306 Fit side-chains REVERT: A 420 ASP cc_start: 0.7060 (m-30) cc_final: 0.6836 (m-30) REVERT: I 124 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7999 (p) outliers start: 35 outliers final: 30 residues processed: 212 average time/residue: 0.7979 time to fit residues: 190.3578 Evaluate side-chains 216 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 185 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU 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 H residue 173 VAL Chi-restraints excluded: chain H residue 181 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 56 ASP 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 68 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 48 LEU Chi-restraints excluded: chain J residue 197 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 0.0970 chunk 71 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** 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: 0.7430 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11783 Z= 0.255 Angle : 0.564 10.959 16032 Z= 0.279 Chirality : 0.043 0.157 1803 Planarity : 0.004 0.042 2055 Dihedral : 4.867 57.844 1708 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.03 % Allowed : 21.66 % Favored : 75.31 % 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: 0.66 (0.22), residues: 1496 helix: -1.34 (0.61), residues: 68 sheet: 1.32 (0.20), residues: 687 loop : -0.21 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 50 HIS 0.003 0.001 HIS J 92 PHE 0.019 0.001 PHE A 371 TYR 0.027 0.002 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 225 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 187 time to evaluate : 1.443 Fit side-chains REVERT: A 420 ASP cc_start: 0.7084 (m-30) cc_final: 0.6857 (m-30) outliers start: 38 outliers final: 35 residues processed: 214 average time/residue: 0.7895 time to fit residues: 190.3455 Evaluate side-chains 220 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 185 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain H residue 6 GLU 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 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 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 56 ASP 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 E residue 159 ASN Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR 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 48 LEU Chi-restraints excluded: chain J residue 197 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.176424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.141084 restraints weight = 20724.052| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.94 r_work: 0.3705 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11783 Z= 0.271 Angle : 0.575 11.071 16032 Z= 0.285 Chirality : 0.044 0.158 1803 Planarity : 0.004 0.041 2055 Dihedral : 4.911 56.914 1708 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.03 % Allowed : 21.66 % Favored : 75.31 % 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: -1.33 (0.62), residues: 68 sheet: 1.31 (0.20), residues: 687 loop : -0.24 (0.23), residues: 741 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 0.026 0.002 TYR D 152 ARG 0.007 0.000 ARG I 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4781.22 seconds wall clock time: 85 minutes 3.40 seconds (5103.40 seconds total)