Starting phenix.real_space_refine on Thu Mar 13 02:27:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e8f_31017/03_2025/7e8f_31017.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e8f_31017/03_2025/7e8f_31017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e8f_31017/03_2025/7e8f_31017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e8f_31017/03_2025/7e8f_31017.map" model { file = "/net/cci-nas-00/data/ceres_data/7e8f_31017/03_2025/7e8f_31017.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e8f_31017/03_2025/7e8f_31017.cif" } resolution = 3.18 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 5569 2.51 5 N 1468 2.21 5 O 1694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8768 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2079 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 243} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "C" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "B" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "D" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 874 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "R" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1498 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain breaks: 1 Time building chain proxies: 5.85, per 1000 atoms: 0.67 Number of scatterers: 8768 At special positions: 0 Unit cell: (133.604, 78.9, 99.94, 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 37 16.00 O 1694 8.00 N 1468 7.00 C 5569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.06 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 26 sheets defined 5.7% alpha, 42.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'H' and resid 27 through 32 removed outlier: 3.546A pdb=" N SER H 30 " --> pdb=" O PHE H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 103 through 108 removed outlier: 4.672A pdb=" N SER H 108 " --> pdb=" O SER H 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 removed outlier: 3.582A pdb=" N ASP L 29 " --> pdb=" O LYS L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.900A pdb=" N GLU L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.783A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'R' and resid 365 through 370 removed outlier: 3.797A pdb=" N ASN R 370 " --> pdb=" O SER R 366 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.567A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 removed outlier: 3.526A pdb=" N SER R 443 " --> pdb=" O ASN R 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.458A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.004A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 160 removed outlier: 9.840A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.101A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 10.282A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.113A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 160 removed outlier: 9.840A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.101A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 10.282A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.113A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.664A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.039A pdb=" N VAL H 114 " --> pdb=" O THR H 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.838A pdb=" N VAL L 10 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA L 83 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.838A pdb=" N VAL L 10 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA L 83 " --> pdb=" O LEU L 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.587A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 12 removed outlier: 5.871A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ALA C 40 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C 45 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.807A pdb=" N CYS C 96 " --> pdb=" O TRP C 115 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TRP C 115 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS C 98 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.514A pdb=" N GLU B 110 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU B 38 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR B 54 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP B 40 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AC1, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.496A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR D 33 " --> pdb=" O ASP D 98 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL D 106 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU D 99 " --> pdb=" O MET D 104 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N MET D 104 " --> pdb=" O LEU D 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.496A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR D 33 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.578A pdb=" N LEU E 11 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.515A pdb=" N LYS R 378 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.707A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'R' and resid 473 through 474 326 hydrogen bonds defined for protein. 801 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: 3.30 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2807 1.35 - 1.48: 2512 1.48 - 1.61: 3611 1.61 - 1.74: 0 1.74 - 1.87: 49 Bond restraints: 8979 Sorted by residual: bond pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 1.808 1.873 -0.065 3.30e-02 9.18e+02 3.84e+00 bond pdb=" CA CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sigma weight residual 1.536 1.500 0.036 2.08e-02 2.31e+03 3.03e+00 bond pdb=" CB PRO L 8 " pdb=" CG PRO L 8 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.01e+00 bond pdb=" C GLN B 47 " pdb=" N SER B 48 " ideal model delta sigma weight residual 1.340 1.258 0.082 5.87e-02 2.90e+02 1.95e+00 bond pdb=" CG LEU R 461 " pdb=" CD1 LEU R 461 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.86e+00 ... (remaining 8974 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 12007 2.22 - 4.44: 168 4.44 - 6.65: 17 6.65 - 8.87: 3 8.87 - 11.09: 2 Bond angle restraints: 12197 Sorted by residual: angle pdb=" CA CYS R 432 " pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 114.40 125.49 -11.09 2.30e+00 1.89e-01 2.32e+01 angle pdb=" CA PRO L 8 " pdb=" N PRO L 8 " pdb=" CD PRO L 8 " ideal model delta sigma weight residual 112.00 105.50 6.50 1.40e+00 5.10e-01 2.16e+01 angle pdb=" CA CYS A 166 " pdb=" CB CYS A 166 " pdb=" SG CYS A 166 " ideal model delta sigma weight residual 114.40 124.20 -9.80 2.30e+00 1.89e-01 1.82e+01 angle pdb=" C ILE E 29 " pdb=" N SER E 30 " pdb=" CA SER E 30 " ideal model delta sigma weight residual 121.54 128.44 -6.90 1.91e+00 2.74e-01 1.31e+01 angle pdb=" N SER E 30 " pdb=" CA SER E 30 " pdb=" C SER E 30 " ideal model delta sigma weight residual 110.80 118.40 -7.60 2.13e+00 2.20e-01 1.27e+01 ... (remaining 12192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 4761 18.09 - 36.19: 418 36.19 - 54.28: 64 54.28 - 72.38: 9 72.38 - 90.47: 7 Dihedral angle restraints: 5259 sinusoidal: 2015 harmonic: 3244 Sorted by residual: dihedral pdb=" CA HIS B 31 " pdb=" C HIS B 31 " pdb=" N SER B 32 " pdb=" CA SER B 32 " ideal model delta harmonic sigma weight residual 180.00 143.72 36.28 0 5.00e+00 4.00e-02 5.27e+01 dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual 93.00 42.44 50.56 1 1.00e+01 1.00e-02 3.50e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 45.01 47.99 1 1.00e+01 1.00e-02 3.17e+01 ... (remaining 5256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 958 0.045 - 0.089: 273 0.089 - 0.134: 92 0.134 - 0.178: 3 0.178 - 0.223: 3 Chirality restraints: 1329 Sorted by residual: chirality pdb=" CA CYS A 166 " pdb=" N CYS A 166 " pdb=" C CYS A 166 " pdb=" CB CYS A 166 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA CYS R 432 " pdb=" N CYS R 432 " pdb=" C CYS R 432 " pdb=" CB CYS R 432 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA THR B 99 " pdb=" N THR B 99 " pdb=" C THR B 99 " pdb=" CB THR B 99 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 8.03e-01 ... (remaining 1326 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 7 " -0.085 5.00e-02 4.00e+02 1.26e-01 2.54e+01 pdb=" N PRO L 8 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 14 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.65e+00 pdb=" N PRO B 15 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 15 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 15 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 347 " 0.017 2.00e-02 2.50e+03 1.72e-02 5.15e+00 pdb=" CG PHE R 347 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE R 347 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE R 347 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE R 347 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 347 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE R 347 " 0.001 2.00e-02 2.50e+03 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 313 2.71 - 3.25: 8172 3.25 - 3.80: 13819 3.80 - 4.35: 18791 4.35 - 4.90: 31839 Nonbonded interactions: 72934 Sorted by model distance: nonbonded pdb=" OH TYR C 107 " pdb=" OG SER B 32 " model vdw 2.157 3.040 nonbonded pdb=" OG SER E 30 " pdb=" OE1 GLN R 498 " model vdw 2.170 3.040 nonbonded pdb=" OE1 GLN L 36 " pdb=" OH TYR L 85 " model vdw 2.186 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR A 144 " pdb=" OE2 GLU A 156 " model vdw 2.207 3.040 ... (remaining 72929 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 25.530 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.005 0.087 8979 Z= 0.334 Angle : 0.682 11.089 12197 Z= 0.377 Chirality : 0.046 0.223 1329 Planarity : 0.005 0.126 1569 Dihedral : 13.858 90.470 3171 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.24), residues: 1112 helix: -4.20 (0.58), residues: 27 sheet: -0.58 (0.25), residues: 419 loop : -1.30 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 47 HIS 0.005 0.001 HIS B 31 PHE 0.039 0.002 PHE R 347 TYR 0.014 0.002 TYR R 505 ARG 0.009 0.001 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.927 Fit side-chains REVERT: H 56 SER cc_start: 0.8477 (p) cc_final: 0.8251 (p) REVERT: D 19 ARG cc_start: 0.7236 (ttp-170) cc_final: 0.6939 (ttp-170) REVERT: D 61 ASP cc_start: 0.7102 (m-30) cc_final: 0.6892 (p0) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2345 time to fit residues: 51.8705 Evaluate side-chains 142 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 ASN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.118112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.098941 restraints weight = 10647.557| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.54 r_work: 0.2921 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8979 Z= 0.235 Angle : 0.634 12.204 12197 Z= 0.338 Chirality : 0.045 0.194 1329 Planarity : 0.005 0.077 1569 Dihedral : 5.544 38.275 1241 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.52 % Allowed : 6.80 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.25), residues: 1112 helix: -4.47 (0.42), residues: 33 sheet: -0.27 (0.25), residues: 432 loop : -1.06 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 47 HIS 0.005 0.001 HIS B 31 PHE 0.024 0.002 PHE A 79 TYR 0.014 0.001 TYR R 505 ARG 0.006 0.001 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 167 time to evaluate : 1.097 Fit side-chains REVERT: C 77 ASN cc_start: 0.8353 (m110) cc_final: 0.8138 (m110) REVERT: B 110 GLU cc_start: 0.7522 (pt0) cc_final: 0.7299 (pt0) REVERT: D 19 ARG cc_start: 0.7385 (ttp-170) cc_final: 0.6998 (ttp-170) REVERT: D 21 SER cc_start: 0.8636 (m) cc_final: 0.8411 (t) REVERT: D 46 GLU cc_start: 0.8395 (tt0) cc_final: 0.8130 (tt0) REVERT: R 444 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7862 (ttmt) outliers start: 5 outliers final: 3 residues processed: 170 average time/residue: 0.2474 time to fit residues: 57.0451 Evaluate side-chains 153 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 61 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.117309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.098045 restraints weight = 10960.730| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.57 r_work: 0.2879 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8979 Z= 0.251 Angle : 0.613 10.788 12197 Z= 0.325 Chirality : 0.045 0.209 1329 Planarity : 0.004 0.065 1569 Dihedral : 5.400 37.257 1241 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.36 % Allowed : 9.83 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.25), residues: 1112 helix: -4.59 (0.35), residues: 33 sheet: -0.10 (0.25), residues: 450 loop : -1.02 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 47 HIS 0.005 0.001 HIS B 31 PHE 0.024 0.002 PHE A 79 TYR 0.012 0.001 TYR R 505 ARG 0.005 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.920 Fit side-chains REVERT: D 3 GLN cc_start: 0.8033 (tt0) cc_final: 0.7830 (tt0) REVERT: D 19 ARG cc_start: 0.7343 (ttp-170) cc_final: 0.6987 (ttp-170) REVERT: E 31 SER cc_start: 0.8048 (m) cc_final: 0.7510 (p) REVERT: R 444 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7823 (ttmt) outliers start: 13 outliers final: 8 residues processed: 167 average time/residue: 0.2234 time to fit residues: 50.3829 Evaluate side-chains 155 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain R residue 382 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 76 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 41 optimal weight: 0.0870 chunk 25 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.118739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.099440 restraints weight = 10707.568| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.63 r_work: 0.2912 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8979 Z= 0.200 Angle : 0.591 12.035 12197 Z= 0.313 Chirality : 0.044 0.242 1329 Planarity : 0.004 0.060 1569 Dihedral : 5.193 36.087 1241 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.36 % Allowed : 11.09 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.25), residues: 1112 helix: -5.13 (0.19), residues: 26 sheet: 0.01 (0.25), residues: 443 loop : -0.94 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 47 HIS 0.005 0.001 HIS A 207 PHE 0.018 0.001 PHE H 29 TYR 0.012 0.001 TYR A 265 ARG 0.008 0.001 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 1.019 Fit side-chains REVERT: D 3 GLN cc_start: 0.8019 (tt0) cc_final: 0.7814 (tt0) REVERT: D 19 ARG cc_start: 0.7270 (ttp-170) cc_final: 0.6933 (ttp-170) REVERT: E 31 SER cc_start: 0.7715 (m) cc_final: 0.7216 (p) REVERT: R 444 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7834 (ttmt) outliers start: 13 outliers final: 9 residues processed: 166 average time/residue: 0.2584 time to fit residues: 60.0477 Evaluate side-chains 158 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain R residue 382 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 218 GLN E 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.116104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.096780 restraints weight = 10803.765| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.56 r_work: 0.2850 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 8979 Z= 0.328 Angle : 0.653 11.892 12197 Z= 0.344 Chirality : 0.046 0.261 1329 Planarity : 0.004 0.057 1569 Dihedral : 5.488 37.573 1241 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.51 % Allowed : 11.61 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.25), residues: 1112 helix: -4.64 (0.34), residues: 33 sheet: -0.07 (0.25), residues: 443 loop : -0.94 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 47 HIS 0.006 0.002 HIS A 207 PHE 0.023 0.002 PHE H 29 TYR 0.016 0.002 TYR R 505 ARG 0.006 0.001 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.889 Fit side-chains REVERT: B 22 SER cc_start: 0.7949 (t) cc_final: 0.7731 (m) REVERT: D 109 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: E 31 SER cc_start: 0.7784 (m) cc_final: 0.7232 (p) REVERT: R 444 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7741 (ttmt) outliers start: 24 outliers final: 14 residues processed: 163 average time/residue: 0.2029 time to fit residues: 45.8890 Evaluate side-chains 159 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain R residue 382 VAL Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 0.0170 chunk 51 optimal weight: 3.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.119022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.099850 restraints weight = 10651.855| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.60 r_work: 0.2940 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8979 Z= 0.182 Angle : 0.580 12.256 12197 Z= 0.307 Chirality : 0.044 0.271 1329 Planarity : 0.004 0.037 1569 Dihedral : 5.138 35.575 1241 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.67 % Allowed : 12.97 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.93 (0.25), residues: 1112 helix: -5.04 (0.21), residues: 26 sheet: 0.08 (0.25), residues: 437 loop : -0.91 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 47 HIS 0.005 0.001 HIS A 207 PHE 0.016 0.001 PHE H 29 TYR 0.012 0.001 TYR A 265 ARG 0.008 0.001 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 1.139 Fit side-chains REVERT: C 77 ASN cc_start: 0.8296 (m110) cc_final: 0.8032 (m110) REVERT: D 19 ARG cc_start: 0.7076 (ttp-170) cc_final: 0.6831 (ttp-170) REVERT: R 444 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7841 (ttmt) outliers start: 16 outliers final: 11 residues processed: 164 average time/residue: 0.2845 time to fit residues: 63.9106 Evaluate side-chains 157 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 95 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 14 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.116545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.097199 restraints weight = 10827.774| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.58 r_work: 0.2929 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8979 Z= 0.306 Angle : 0.644 12.989 12197 Z= 0.338 Chirality : 0.046 0.296 1329 Planarity : 0.004 0.037 1569 Dihedral : 5.413 37.239 1241 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.30 % Allowed : 12.97 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.91 (0.25), residues: 1112 helix: -5.07 (0.21), residues: 26 sheet: 0.11 (0.25), residues: 435 loop : -0.91 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 47 HIS 0.008 0.002 HIS A 207 PHE 0.022 0.002 PHE H 29 TYR 0.016 0.002 TYR R 505 ARG 0.006 0.001 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.908 Fit side-chains REVERT: B 22 SER cc_start: 0.7930 (t) cc_final: 0.7697 (m) REVERT: R 444 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7828 (ttmt) outliers start: 22 outliers final: 15 residues processed: 164 average time/residue: 0.2007 time to fit residues: 45.8555 Evaluate side-chains 159 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain R residue 382 VAL Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 42 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 0.0040 chunk 98 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.117124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.097931 restraints weight = 10868.692| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.56 r_work: 0.2927 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8979 Z= 0.278 Angle : 0.637 13.714 12197 Z= 0.334 Chirality : 0.046 0.308 1329 Planarity : 0.004 0.035 1569 Dihedral : 5.448 36.768 1241 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.62 % Allowed : 13.70 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.99 (0.25), residues: 1112 helix: -5.06 (0.21), residues: 26 sheet: 0.05 (0.25), residues: 448 loop : -0.97 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 47 HIS 0.009 0.002 HIS A 207 PHE 0.020 0.002 PHE H 29 TYR 0.014 0.002 TYR R 505 ARG 0.005 0.001 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 1.178 Fit side-chains REVERT: A 40 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.6236 (p0) REVERT: R 444 LYS cc_start: 0.8235 (ttmt) cc_final: 0.7818 (ttmt) outliers start: 25 outliers final: 16 residues processed: 166 average time/residue: 0.2377 time to fit residues: 56.2018 Evaluate side-chains 163 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 98 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 207 HIS H 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.115101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.095679 restraints weight = 10915.005| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.54 r_work: 0.2871 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 8979 Z= 0.407 Angle : 0.715 14.907 12197 Z= 0.374 Chirality : 0.049 0.332 1329 Planarity : 0.005 0.037 1569 Dihedral : 5.876 39.068 1241 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.62 % Allowed : 14.02 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.25), residues: 1112 helix: -4.67 (0.36), residues: 33 sheet: 0.09 (0.25), residues: 431 loop : -1.13 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 47 HIS 0.010 0.002 HIS A 207 PHE 0.025 0.002 PHE H 29 TYR 0.020 0.002 TYR R 489 ARG 0.005 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.945 Fit side-chains REVERT: A 290 ASP cc_start: 0.5855 (OUTLIER) cc_final: 0.5372 (t0) REVERT: D 61 ASP cc_start: 0.8092 (m-30) cc_final: 0.7573 (p0) REVERT: E 5 THR cc_start: 0.8278 (m) cc_final: 0.7873 (p) REVERT: E 31 SER cc_start: 0.7773 (m) cc_final: 0.7224 (p) REVERT: R 444 LYS cc_start: 0.8149 (ttmt) cc_final: 0.7760 (ttmt) REVERT: R 478 THR cc_start: 0.7689 (m) cc_final: 0.7214 (p) outliers start: 25 outliers final: 15 residues processed: 163 average time/residue: 0.2063 time to fit residues: 47.0702 Evaluate side-chains 161 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 96 optimal weight: 0.0040 chunk 90 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 173 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.120826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.101576 restraints weight = 10778.442| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.62 r_work: 0.2914 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8979 Z= 0.158 Angle : 0.582 14.109 12197 Z= 0.305 Chirality : 0.044 0.280 1329 Planarity : 0.004 0.040 1569 Dihedral : 5.145 34.083 1241 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.05 % Allowed : 15.59 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.94 (0.25), residues: 1112 helix: -4.97 (0.25), residues: 26 sheet: 0.12 (0.25), residues: 442 loop : -0.96 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.008 0.001 HIS A 207 PHE 0.012 0.001 PHE H 29 TYR 0.013 0.001 TYR A 265 ARG 0.007 0.000 ARG R 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 1.011 Fit side-chains REVERT: C 77 ASN cc_start: 0.8227 (m110) cc_final: 0.7932 (m110) REVERT: E 5 THR cc_start: 0.8229 (m) cc_final: 0.7841 (p) REVERT: R 334 ASN cc_start: 0.5112 (t0) cc_final: 0.4887 (m110) REVERT: R 478 THR cc_start: 0.7841 (m) cc_final: 0.7497 (p) outliers start: 10 outliers final: 7 residues processed: 160 average time/residue: 0.2068 time to fit residues: 46.1175 Evaluate side-chains 154 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain R residue 432 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.120177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.100966 restraints weight = 10822.246| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.55 r_work: 0.3032 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8979 Z= 0.186 Angle : 0.586 13.843 12197 Z= 0.307 Chirality : 0.044 0.279 1329 Planarity : 0.004 0.051 1569 Dihedral : 5.128 34.571 1241 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.36 % Allowed : 15.59 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.84 (0.25), residues: 1112 helix: -4.95 (0.27), residues: 26 sheet: 0.26 (0.25), residues: 429 loop : -0.94 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 47 HIS 0.008 0.002 HIS A 207 PHE 0.016 0.001 PHE H 29 TYR 0.012 0.001 TYR A 265 ARG 0.009 0.001 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4661.90 seconds wall clock time: 82 minutes 36.33 seconds (4956.33 seconds total)