Starting phenix.real_space_refine on Fri Jul 19 10:58:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh7_36258/07_2024/8jh7_36258.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh7_36258/07_2024/8jh7_36258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh7_36258/07_2024/8jh7_36258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh7_36258/07_2024/8jh7_36258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh7_36258/07_2024/8jh7_36258.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh7_36258/07_2024/8jh7_36258.cif" } resolution = 3.2 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= 0.022 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 40 5.16 5 C 4911 2.51 5 N 1273 2.21 5 O 1439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "D TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7663 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1682 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1624 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 3436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3436 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 12, 'TRANS': 418} Chain breaks: 3 Time building chain proxies: 5.11, per 1000 atoms: 0.67 Number of scatterers: 7663 At special positions: 0 Unit cell: (66.56, 100.672, 157.248, 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 40 16.00 O 1439 8.00 N 1273 7.00 C 4911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 181 " distance=2.03 Simple disulfide: pdb=" SG CYS D 185 " - pdb=" SG CYS D 260 " distance=2.03 Simple disulfide: pdb=" SG CYS D 282 " - pdb=" SG CYS D 357 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.5 seconds 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1834 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 35.1% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'H' and resid 65 through 68 removed outlier: 3.626A pdb=" N LYS H 68 " --> pdb=" O ASP H 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 65 through 68' Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.605A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 200 through 205 removed outlier: 3.646A pdb=" N GLY H 204 " --> pdb=" O SER H 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 129 removed outlier: 3.821A pdb=" N LEU L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS L 128 " --> pdb=" O ASP L 124 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 123 through 129' Processing helix chain 'L' and resid 185 through 189 removed outlier: 3.552A pdb=" N GLU L 189 " --> pdb=" O LYS L 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 185 through 189' Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.526A pdb=" N GLY D 177 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 211 removed outlier: 4.390A pdb=" N GLU D 196 " --> pdb=" O SER D 192 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE D 208 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 224 removed outlier: 3.625A pdb=" N LEU D 221 " --> pdb=" O PHE D 217 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP D 223 " --> pdb=" O THR D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 231 Processing helix chain 'D' and resid 232 through 255 removed outlier: 3.908A pdb=" N TYR D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR D 248 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 312 removed outlier: 3.669A pdb=" N LEU D 289 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE D 291 " --> pdb=" O MET D 287 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE D 292 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 322 Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'D' and resid 333 through 342 Processing helix chain 'D' and resid 364 through 371 removed outlier: 3.815A pdb=" N ARG D 368 " --> pdb=" O LEU D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 395 Processing helix chain 'D' and resid 1002 through 1024 Processing helix chain 'D' and resid 1029 through 1049 removed outlier: 3.758A pdb=" N ASP D1033 " --> pdb=" O ALA D1029 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR D1049 " --> pdb=" O ALA D1045 " (cutoff:3.500A) Processing helix chain 'D' and resid 1064 through 1085 Processing helix chain 'D' and resid 1089 through 1098 Processing helix chain 'D' and resid 1098 through 1105 removed outlier: 4.256A pdb=" N THR D1102 " --> pdb=" O GLN D1098 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA D1105 " --> pdb=" O THR D1101 " (cutoff:3.500A) Processing helix chain 'D' and resid 1107 through 1118 Processing helix chain 'D' and resid 410 through 440 removed outlier: 3.740A pdb=" N VAL D 426 " --> pdb=" O GLY D 422 " (cutoff:3.500A) Proline residue: D 427 - end of helix Processing helix chain 'D' and resid 441 through 453 Processing helix chain 'D' and resid 472 through 486 removed outlier: 4.152A pdb=" N PHE D 476 " --> pdb=" O GLU D 472 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET D 477 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D 484 " --> pdb=" O TYR D 480 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 486 " --> pdb=" O MET D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 489 No H-bonds generated for 'chain 'D' and resid 487 through 489' Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.632A pdb=" N THR H 72 " --> pdb=" O GLN H 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.508A pdb=" N THR H 121 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER H 62 " --> pdb=" O TYR H 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 134 through 138 removed outlier: 3.998A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER H 194 " --> pdb=" O CYS H 154 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 138 removed outlier: 3.998A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER H 194 " --> pdb=" O CYS H 154 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 165 through 168 removed outlier: 3.879A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.973A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.631A pdb=" N GLY K 10 " --> pdb=" O GLN K 116 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR K 118 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.712A pdb=" N ASP L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.445A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.553A pdb=" N GLN L 91 " --> pdb=" O THR L 99 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 118 through 120 removed outlier: 3.781A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 146 through 151 Processing sheet with id=AB4, first strand: chain 'D' and resid 260 through 261 removed outlier: 3.741A pdb=" N ASN D 261 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR D 272 " --> pdb=" O ASN D 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 348 through 349 365 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 3.18 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: 2403 1.34 - 1.46: 1992 1.46 - 1.58: 3396 1.58 - 1.70: 0 1.70 - 1.82: 55 Bond restraints: 7846 Sorted by residual: bond pdb=" CA GLY D 255 " pdb=" C GLY D 255 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.04e-02 9.25e+03 2.51e+00 bond pdb=" CB PRO D 427 " pdb=" CG PRO D 427 " ideal model delta sigma weight residual 1.492 1.425 0.067 5.00e-02 4.00e+02 1.81e+00 bond pdb=" CB ASN K 77 " pdb=" CG ASN K 77 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.80e+00 bond pdb=" N GLY D 255 " pdb=" CA GLY D 255 " ideal model delta sigma weight residual 1.464 1.449 0.015 1.12e-02 7.97e+03 1.77e+00 bond pdb=" N THR H 205 " pdb=" CA THR H 205 " ideal model delta sigma weight residual 1.460 1.477 -0.017 1.54e-02 4.22e+03 1.21e+00 ... (remaining 7841 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.54: 138 105.54 - 112.66: 4042 112.66 - 119.79: 2567 119.79 - 126.92: 3793 126.92 - 134.04: 117 Bond angle restraints: 10657 Sorted by residual: angle pdb=" CA LEU D 176 " pdb=" CB LEU D 176 " pdb=" CG LEU D 176 " ideal model delta sigma weight residual 116.30 128.71 -12.41 3.50e+00 8.16e-02 1.26e+01 angle pdb=" C MET D 345 " pdb=" N ASN D 346 " pdb=" CA ASN D 346 " ideal model delta sigma weight residual 122.82 127.53 -4.71 1.42e+00 4.96e-01 1.10e+01 angle pdb=" CB MET D 294 " pdb=" CG MET D 294 " pdb=" SD MET D 294 " ideal model delta sigma weight residual 112.70 122.47 -9.77 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C ARG D 225 " pdb=" N ARG D 226 " pdb=" CA ARG D 226 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C TYR D 463 " pdb=" N GLN D 464 " pdb=" CA GLN D 464 " ideal model delta sigma weight residual 122.61 127.58 -4.97 1.56e+00 4.11e-01 1.02e+01 ... (remaining 10652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 4139 16.00 - 31.99: 373 31.99 - 47.99: 90 47.99 - 63.98: 18 63.98 - 79.98: 8 Dihedral angle restraints: 4628 sinusoidal: 1765 harmonic: 2863 Sorted by residual: dihedral pdb=" CB CYS D 282 " pdb=" SG CYS D 282 " pdb=" SG CYS D 357 " pdb=" CB CYS D 357 " ideal model delta sinusoidal sigma weight residual -86.00 -136.09 50.09 1 1.00e+01 1.00e-02 3.44e+01 dihedral pdb=" CB CYS D 185 " pdb=" SG CYS D 185 " pdb=" SG CYS D 260 " pdb=" CB CYS D 260 " ideal model delta sinusoidal sigma weight residual 93.00 133.22 -40.22 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CA PRO D 230 " pdb=" C PRO D 230 " pdb=" N GLU D 231 " pdb=" CA GLU D 231 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 4625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 833 0.043 - 0.086: 275 0.086 - 0.129: 73 0.129 - 0.172: 10 0.172 - 0.216: 3 Chirality restraints: 1194 Sorted by residual: chirality pdb=" CB THR H 94 " pdb=" CA THR H 94 " pdb=" OG1 THR H 94 " pdb=" CG2 THR H 94 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB VAL D 426 " pdb=" CA VAL D 426 " pdb=" CG1 VAL D 426 " pdb=" CG2 VAL D 426 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ASN D 346 " pdb=" N ASN D 346 " pdb=" C ASN D 346 " pdb=" CB ASN D 346 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.75e-01 ... (remaining 1191 not shown) Planarity restraints: 1340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN K 77 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.65e+00 pdb=" C ASN K 77 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN K 77 " -0.018 2.00e-02 2.50e+03 pdb=" N THR K 78 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN K 13 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO K 14 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO K 14 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO K 14 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 182 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.34e+00 pdb=" N PRO D 183 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 183 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 183 " 0.037 5.00e-02 4.00e+02 ... (remaining 1337 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1343 2.77 - 3.30: 7131 3.30 - 3.84: 12285 3.84 - 4.37: 14088 4.37 - 4.90: 24610 Nonbonded interactions: 59457 Sorted by model distance: nonbonded pdb=" OG SER K 35 " pdb=" OH TYR K 108 " model vdw 2.240 2.440 nonbonded pdb=" OG1 THR D 167 " pdb=" OE1 GLN D 180 " model vdw 2.250 2.440 nonbonded pdb=" O TYR L 50 " pdb=" OG SER L 54 " model vdw 2.263 2.440 nonbonded pdb=" O TYR L 188 " pdb=" OH TYR L 194 " model vdw 2.273 2.440 nonbonded pdb=" OD2 ASP D 351 " pdb=" OH TYR D 480 " model vdw 2.294 2.440 ... (remaining 59452 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.470 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.770 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 7846 Z= 0.224 Angle : 0.770 12.414 10657 Z= 0.397 Chirality : 0.047 0.216 1194 Planarity : 0.006 0.068 1340 Dihedral : 13.568 79.981 2770 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.48 (0.26), residues: 974 helix: -1.26 (0.27), residues: 291 sheet: 0.11 (0.33), residues: 265 loop : -1.40 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 445 HIS 0.005 0.001 HIS L 191 PHE 0.018 0.002 PHE H 114 TYR 0.027 0.002 TYR H 53 ARG 0.004 0.000 ARG K 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: H 23 LEU cc_start: 0.7979 (mp) cc_final: 0.7778 (mt) REVERT: H 76 ASP cc_start: 0.7945 (p0) cc_final: 0.7588 (p0) REVERT: H 122 LEU cc_start: 0.8677 (tp) cc_final: 0.8437 (tt) REVERT: H 131 LYS cc_start: 0.7700 (ptmm) cc_final: 0.7323 (ptmm) REVERT: H 184 LEU cc_start: 0.8301 (mt) cc_final: 0.8087 (mt) REVERT: L 47 LEU cc_start: 0.8757 (tt) cc_final: 0.8375 (tp) REVERT: L 62 ARG cc_start: 0.7809 (ptt-90) cc_final: 0.7207 (ptt180) REVERT: L 73 THR cc_start: 0.8279 (m) cc_final: 0.8020 (p) REVERT: L 83 ASP cc_start: 0.7740 (m-30) cc_final: 0.6768 (m-30) REVERT: D 238 SER cc_start: 0.7868 (p) cc_final: 0.7491 (t) REVERT: D 1032 LYS cc_start: 0.8117 (ttmt) cc_final: 0.7824 (mtpt) REVERT: D 1033 ASP cc_start: 0.7150 (m-30) cc_final: 0.6755 (m-30) REVERT: D 1088 LYS cc_start: 0.8154 (mttp) cc_final: 0.7877 (mttm) REVERT: D 417 ILE cc_start: 0.8641 (tp) cc_final: 0.8364 (tt) REVERT: D 423 LEU cc_start: 0.8446 (mp) cc_final: 0.8239 (mt) REVERT: D 438 GLU cc_start: 0.6787 (mm-30) cc_final: 0.6579 (mm-30) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1779 time to fit residues: 44.1622 Evaluate side-chains 170 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.0030 chunk 57 optimal weight: 0.0050 chunk 88 optimal weight: 2.9990 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 169 ASN H 211 ASN H 213 ASN K 77 ASN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 ASN D1018 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7846 Z= 0.221 Angle : 0.619 8.251 10657 Z= 0.318 Chirality : 0.042 0.159 1194 Planarity : 0.005 0.062 1340 Dihedral : 4.603 22.175 1068 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.53 % Allowed : 8.30 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.27), residues: 974 helix: 0.21 (0.30), residues: 285 sheet: 0.30 (0.34), residues: 243 loop : -1.17 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 445 HIS 0.003 0.001 HIS L 200 PHE 0.017 0.001 PHE D 358 TYR 0.020 0.002 TYR D 237 ARG 0.003 0.000 ARG K 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: H 131 LYS cc_start: 0.8002 (ptmm) cc_final: 0.7624 (ptmm) REVERT: H 191 SER cc_start: 0.8323 (p) cc_final: 0.7850 (m) REVERT: L 62 ARG cc_start: 0.7875 (ptt-90) cc_final: 0.7272 (ptt180) REVERT: L 83 ASP cc_start: 0.7777 (m-30) cc_final: 0.6856 (m-30) REVERT: D 250 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.8027 (mt) REVERT: D 353 ILE cc_start: 0.8096 (mp) cc_final: 0.7719 (mt) REVERT: D 1032 LYS cc_start: 0.8036 (ttmt) cc_final: 0.7815 (mtpt) REVERT: D 1091 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6962 (tm-30) REVERT: D 1110 TYR cc_start: 0.7722 (t80) cc_final: 0.7314 (t80) REVERT: D 438 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6538 (mm-30) outliers start: 21 outliers final: 13 residues processed: 176 average time/residue: 0.1798 time to fit residues: 43.4542 Evaluate side-chains 167 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 153 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 205 SER Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 1097 GLU Chi-restraints excluded: chain D residue 434 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.0270 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 79 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 213 ASN K 5 GLN K 77 ASN ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7846 Z= 0.309 Angle : 0.661 8.670 10657 Z= 0.338 Chirality : 0.044 0.200 1194 Planarity : 0.005 0.059 1340 Dihedral : 4.819 21.207 1068 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.77 % Allowed : 12.64 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.16 (0.27), residues: 974 helix: 0.81 (0.31), residues: 281 sheet: 0.55 (0.33), residues: 250 loop : -1.08 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 332 HIS 0.005 0.001 HIS D 328 PHE 0.022 0.002 PHE D 358 TYR 0.028 0.002 TYR D 237 ARG 0.003 0.000 ARG D 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 131 LYS cc_start: 0.8447 (ptmm) cc_final: 0.8192 (ptmm) REVERT: H 191 SER cc_start: 0.8241 (p) cc_final: 0.7859 (m) REVERT: K 70 VAL cc_start: 0.8536 (t) cc_final: 0.8203 (p) REVERT: L 5 MET cc_start: 0.8634 (mmt) cc_final: 0.8269 (mmt) REVERT: L 51 SER cc_start: 0.8307 (t) cc_final: 0.7931 (p) REVERT: L 62 ARG cc_start: 0.7943 (ptt-90) cc_final: 0.7707 (ptt90) REVERT: L 66 SER cc_start: 0.8344 (m) cc_final: 0.8072 (p) REVERT: D 250 ILE cc_start: 0.8243 (mt) cc_final: 0.7964 (mt) REVERT: D 1091 GLU cc_start: 0.7364 (tm-30) cc_final: 0.6948 (tm-30) REVERT: D 1100 LYS cc_start: 0.8070 (mmtp) cc_final: 0.7631 (mmmt) REVERT: D 1110 TYR cc_start: 0.7846 (t80) cc_final: 0.7541 (t80) REVERT: D 424 TYR cc_start: 0.8685 (t80) cc_final: 0.8475 (t80) REVERT: D 438 GLU cc_start: 0.6749 (mm-30) cc_final: 0.6158 (mm-30) REVERT: D 484 LEU cc_start: 0.6840 (mm) cc_final: 0.6461 (mt) outliers start: 23 outliers final: 16 residues processed: 186 average time/residue: 0.1876 time to fit residues: 47.9668 Evaluate side-chains 179 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 205 SER Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 1097 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 434 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 0.0570 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS D1016 ASN ** D1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1085 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7846 Z= 0.311 Angle : 0.637 9.242 10657 Z= 0.327 Chirality : 0.044 0.170 1194 Planarity : 0.005 0.058 1340 Dihedral : 4.801 23.823 1068 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.95 % Favored : 93.94 % Rotamer: Outliers : 2.53 % Allowed : 15.88 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.17 (0.27), residues: 974 helix: 0.82 (0.31), residues: 288 sheet: 0.60 (0.33), residues: 244 loop : -1.15 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 332 HIS 0.004 0.001 HIS L 191 PHE 0.019 0.002 PHE D 337 TYR 0.027 0.002 TYR D 237 ARG 0.003 0.000 ARG K 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 10 SER cc_start: 0.8305 (m) cc_final: 0.7920 (t) REVERT: H 131 LYS cc_start: 0.8455 (ptmm) cc_final: 0.8189 (ptmm) REVERT: H 165 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7904 (p) REVERT: H 191 SER cc_start: 0.8298 (OUTLIER) cc_final: 0.7889 (m) REVERT: H 194 SER cc_start: 0.8465 (t) cc_final: 0.8076 (p) REVERT: L 51 SER cc_start: 0.8302 (t) cc_final: 0.7991 (p) REVERT: L 66 SER cc_start: 0.8358 (m) cc_final: 0.8093 (p) REVERT: L 182 THR cc_start: 0.7842 (p) cc_final: 0.7619 (t) REVERT: L 183 LEU cc_start: 0.8175 (mt) cc_final: 0.7879 (mp) REVERT: D 250 ILE cc_start: 0.8234 (mt) cc_final: 0.7959 (mt) REVERT: D 1088 LYS cc_start: 0.8216 (mtmm) cc_final: 0.7985 (mttm) REVERT: D 1091 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7055 (tm-30) REVERT: D 1100 LYS cc_start: 0.8109 (mmtp) cc_final: 0.7666 (mmmt) REVERT: D 484 LEU cc_start: 0.6860 (mm) cc_final: 0.6458 (mt) outliers start: 21 outliers final: 13 residues processed: 176 average time/residue: 0.1822 time to fit residues: 43.9972 Evaluate side-chains 175 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 160 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 1097 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 434 CYS Chi-restraints excluded: chain D residue 473 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1016 ASN ** D1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1085 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7846 Z= 0.340 Angle : 0.651 7.659 10657 Z= 0.335 Chirality : 0.045 0.177 1194 Planarity : 0.005 0.058 1340 Dihedral : 4.872 24.106 1068 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.63 % Rotamer: Outliers : 3.37 % Allowed : 17.45 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.19 (0.27), residues: 974 helix: 0.88 (0.30), residues: 289 sheet: 0.49 (0.33), residues: 251 loop : -1.19 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 332 HIS 0.008 0.001 HIS L 191 PHE 0.027 0.002 PHE H 136 TYR 0.028 0.002 TYR D 237 ARG 0.002 0.000 ARG D1115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: H 10 SER cc_start: 0.8274 (m) cc_final: 0.7889 (t) REVERT: H 131 LYS cc_start: 0.8510 (ptmm) cc_final: 0.8270 (ptmm) REVERT: H 191 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.7905 (m) REVERT: H 194 SER cc_start: 0.8539 (t) cc_final: 0.8149 (p) REVERT: H 216 PRO cc_start: 0.8293 (Cg_exo) cc_final: 0.8073 (Cg_endo) REVERT: H 224 LYS cc_start: 0.6621 (OUTLIER) cc_final: 0.6334 (mmtt) REVERT: L 18 ASP cc_start: 0.8038 (t0) cc_final: 0.7744 (t0) REVERT: L 66 SER cc_start: 0.8371 (m) cc_final: 0.8156 (p) REVERT: L 182 THR cc_start: 0.7891 (p) cc_final: 0.7681 (t) REVERT: L 190 LYS cc_start: 0.7675 (ptmm) cc_final: 0.7425 (ptmm) REVERT: D 250 ILE cc_start: 0.8235 (mt) cc_final: 0.7907 (mt) REVERT: D 390 ILE cc_start: 0.8230 (tt) cc_final: 0.7985 (tt) REVERT: D 1088 LYS cc_start: 0.8264 (mtmm) cc_final: 0.8002 (mttm) REVERT: D 1091 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7030 (tm-30) REVERT: D 484 LEU cc_start: 0.6866 (mm) cc_final: 0.6461 (mt) outliers start: 28 outliers final: 22 residues processed: 186 average time/residue: 0.1896 time to fit residues: 47.7847 Evaluate side-chains 185 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 224 LYS Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 205 SER Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 1038 MET Chi-restraints excluded: chain D residue 1049 THR Chi-restraints excluded: chain D residue 1097 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 434 CYS Chi-restraints excluded: chain D residue 473 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 91 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 1 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1085 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7846 Z= 0.259 Angle : 0.622 7.964 10657 Z= 0.317 Chirality : 0.043 0.173 1194 Planarity : 0.004 0.057 1340 Dihedral : 4.753 21.757 1068 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.65 % Favored : 94.25 % Rotamer: Outliers : 3.49 % Allowed : 19.13 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.08 (0.28), residues: 974 helix: 1.04 (0.30), residues: 289 sheet: 0.54 (0.33), residues: 245 loop : -1.13 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 332 HIS 0.004 0.001 HIS L 191 PHE 0.024 0.002 PHE H 136 TYR 0.021 0.002 TYR D 237 ARG 0.002 0.000 ARG K 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: H 10 SER cc_start: 0.8260 (m) cc_final: 0.7891 (t) REVERT: H 131 LYS cc_start: 0.8449 (ptmm) cc_final: 0.8210 (ptmm) REVERT: H 165 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.7971 (p) REVERT: H 191 SER cc_start: 0.8296 (OUTLIER) cc_final: 0.7884 (m) REVERT: H 194 SER cc_start: 0.8558 (t) cc_final: 0.8150 (p) REVERT: L 18 ASP cc_start: 0.8044 (t0) cc_final: 0.7757 (t0) REVERT: L 66 SER cc_start: 0.8375 (m) cc_final: 0.8157 (p) REVERT: L 147 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7865 (pttp) REVERT: L 182 THR cc_start: 0.7871 (p) cc_final: 0.7660 (t) REVERT: D 250 ILE cc_start: 0.8228 (mt) cc_final: 0.7755 (mt) REVERT: D 318 GLU cc_start: 0.7246 (mp0) cc_final: 0.7042 (mp0) REVERT: D 390 ILE cc_start: 0.8208 (tt) cc_final: 0.7982 (tt) REVERT: D 1088 LYS cc_start: 0.8209 (mtmm) cc_final: 0.7961 (mttm) REVERT: D 1091 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7021 (tm-30) REVERT: D 1100 LYS cc_start: 0.8133 (mmtp) cc_final: 0.7697 (mmmt) REVERT: D 484 LEU cc_start: 0.6874 (mm) cc_final: 0.6492 (mt) outliers start: 29 outliers final: 20 residues processed: 178 average time/residue: 0.1949 time to fit residues: 46.8526 Evaluate side-chains 179 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain K residue 1 GLN Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 1038 MET Chi-restraints excluded: chain D residue 1097 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 434 CYS Chi-restraints excluded: chain D residue 473 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 69 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 0.0040 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1085 ASN D1108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7846 Z= 0.231 Angle : 0.619 8.748 10657 Z= 0.314 Chirality : 0.043 0.182 1194 Planarity : 0.004 0.055 1340 Dihedral : 4.686 21.695 1068 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.35 % Rotamer: Outliers : 2.89 % Allowed : 21.42 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.02 (0.28), residues: 974 helix: 1.14 (0.31), residues: 289 sheet: 0.42 (0.33), residues: 245 loop : -1.03 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 332 HIS 0.002 0.001 HIS H 214 PHE 0.023 0.002 PHE H 136 TYR 0.020 0.001 TYR D 237 ARG 0.002 0.000 ARG L 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: H 10 SER cc_start: 0.8239 (m) cc_final: 0.7880 (t) REVERT: H 131 LYS cc_start: 0.8438 (ptmm) cc_final: 0.8174 (ptmm) REVERT: H 165 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.7961 (p) REVERT: H 191 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.7856 (m) REVERT: H 194 SER cc_start: 0.8492 (t) cc_final: 0.8085 (p) REVERT: H 224 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.6268 (mmtt) REVERT: L 18 ASP cc_start: 0.8043 (t0) cc_final: 0.7765 (t0) REVERT: L 66 SER cc_start: 0.8357 (m) cc_final: 0.8145 (p) REVERT: L 147 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7835 (pttp) REVERT: L 182 THR cc_start: 0.7854 (p) cc_final: 0.7651 (t) REVERT: D 250 ILE cc_start: 0.8221 (mt) cc_final: 0.7949 (mt) REVERT: D 318 GLU cc_start: 0.7252 (mp0) cc_final: 0.7026 (mp0) REVERT: D 390 ILE cc_start: 0.8236 (tt) cc_final: 0.8016 (tt) REVERT: D 1088 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7979 (mttm) REVERT: D 1091 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7043 (tm-30) REVERT: D 1100 LYS cc_start: 0.8120 (mmtp) cc_final: 0.7688 (mmmt) REVERT: D 484 LEU cc_start: 0.6897 (mm) cc_final: 0.6522 (mt) outliers start: 24 outliers final: 18 residues processed: 170 average time/residue: 0.2062 time to fit residues: 46.6481 Evaluate side-chains 177 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 224 LYS Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 1038 MET Chi-restraints excluded: chain D residue 1097 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 434 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 0.0170 chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1085 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7846 Z= 0.261 Angle : 0.632 10.189 10657 Z= 0.320 Chirality : 0.043 0.192 1194 Planarity : 0.004 0.055 1340 Dihedral : 4.690 20.025 1068 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.95 % Favored : 93.94 % Rotamer: Outliers : 2.89 % Allowed : 21.42 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.00 (0.28), residues: 974 helix: 1.18 (0.31), residues: 289 sheet: 0.44 (0.34), residues: 240 loop : -1.03 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 332 HIS 0.002 0.001 HIS H 178 PHE 0.022 0.002 PHE H 136 TYR 0.022 0.002 TYR D 237 ARG 0.003 0.000 ARG K 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: H 10 SER cc_start: 0.8245 (m) cc_final: 0.7897 (t) REVERT: H 131 LYS cc_start: 0.8442 (ptmm) cc_final: 0.8182 (ptmm) REVERT: H 165 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8037 (p) REVERT: H 191 SER cc_start: 0.8289 (OUTLIER) cc_final: 0.7855 (m) REVERT: H 194 SER cc_start: 0.8450 (t) cc_final: 0.8053 (p) REVERT: H 224 LYS cc_start: 0.6751 (OUTLIER) cc_final: 0.6413 (mmtt) REVERT: K 46 GLU cc_start: 0.6643 (mp0) cc_final: 0.5926 (mp0) REVERT: L 18 ASP cc_start: 0.8047 (t0) cc_final: 0.7788 (t0) REVERT: L 66 SER cc_start: 0.8360 (m) cc_final: 0.8150 (p) REVERT: L 147 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7836 (pttp) REVERT: L 209 LYS cc_start: 0.8531 (mmtp) cc_final: 0.8324 (mmmm) REVERT: L 213 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7530 (ttt-90) REVERT: D 250 ILE cc_start: 0.8212 (mt) cc_final: 0.7961 (mt) REVERT: D 318 GLU cc_start: 0.7262 (mp0) cc_final: 0.7037 (mp0) REVERT: D 390 ILE cc_start: 0.8170 (tt) cc_final: 0.7967 (tt) REVERT: D 1088 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7979 (mttm) REVERT: D 1091 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7052 (tm-30) REVERT: D 1100 LYS cc_start: 0.8105 (mmtp) cc_final: 0.7681 (mmmt) REVERT: D 484 LEU cc_start: 0.6904 (mm) cc_final: 0.6521 (mt) outliers start: 24 outliers final: 20 residues processed: 177 average time/residue: 0.2173 time to fit residues: 51.2517 Evaluate side-chains 179 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 224 LYS Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 1014 THR Chi-restraints excluded: chain D residue 1097 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 434 CYS Chi-restraints excluded: chain D residue 473 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1085 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7846 Z= 0.258 Angle : 0.639 10.727 10657 Z= 0.324 Chirality : 0.043 0.178 1194 Planarity : 0.004 0.054 1340 Dihedral : 4.689 19.721 1068 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.95 % Favored : 93.94 % Rotamer: Outliers : 2.89 % Allowed : 22.02 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.01 (0.28), residues: 974 helix: 1.21 (0.31), residues: 289 sheet: 0.43 (0.35), residues: 240 loop : -1.04 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 332 HIS 0.002 0.001 HIS L 191 PHE 0.023 0.002 PHE H 136 TYR 0.021 0.002 TYR D 237 ARG 0.003 0.000 ARG K 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: H 10 SER cc_start: 0.8240 (m) cc_final: 0.7896 (t) REVERT: H 131 LYS cc_start: 0.8437 (ptmm) cc_final: 0.8173 (ptmm) REVERT: H 165 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8003 (p) REVERT: H 191 SER cc_start: 0.8283 (OUTLIER) cc_final: 0.7855 (m) REVERT: H 194 SER cc_start: 0.8445 (t) cc_final: 0.8058 (p) REVERT: H 198 VAL cc_start: 0.8569 (t) cc_final: 0.8330 (m) REVERT: H 224 LYS cc_start: 0.6786 (OUTLIER) cc_final: 0.6418 (mmtt) REVERT: K 46 GLU cc_start: 0.6622 (mp0) cc_final: 0.5958 (mp0) REVERT: L 18 ASP cc_start: 0.8033 (t0) cc_final: 0.7798 (t0) REVERT: L 66 SER cc_start: 0.8359 (m) cc_final: 0.8158 (p) REVERT: L 147 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7838 (pttp) REVERT: L 209 LYS cc_start: 0.8512 (mmtp) cc_final: 0.8299 (mmmm) REVERT: L 213 ARG cc_start: 0.8029 (ttp80) cc_final: 0.7543 (ttt-90) REVERT: D 171 GLN cc_start: 0.7484 (mp10) cc_final: 0.7262 (mp10) REVERT: D 250 ILE cc_start: 0.8218 (mt) cc_final: 0.7956 (mt) REVERT: D 318 GLU cc_start: 0.7241 (mp0) cc_final: 0.7022 (mp0) REVERT: D 390 ILE cc_start: 0.8193 (tt) cc_final: 0.7986 (tt) REVERT: D 1067 ARG cc_start: 0.7535 (ptp-170) cc_final: 0.7085 (mtp85) REVERT: D 1088 LYS cc_start: 0.8255 (mtmm) cc_final: 0.7995 (mttm) REVERT: D 1091 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7028 (tm-30) REVERT: D 1100 LYS cc_start: 0.8062 (mmtp) cc_final: 0.7642 (mmmt) REVERT: D 484 LEU cc_start: 0.7009 (mm) cc_final: 0.6637 (mt) outliers start: 24 outliers final: 18 residues processed: 172 average time/residue: 0.2180 time to fit residues: 49.4952 Evaluate side-chains 178 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 224 LYS Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 1097 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 434 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.0370 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 97 optimal weight: 0.0970 chunk 89 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 7846 Z= 0.217 Angle : 0.642 11.708 10657 Z= 0.324 Chirality : 0.043 0.177 1194 Planarity : 0.004 0.054 1340 Dihedral : 4.593 19.417 1068 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.53 % Allowed : 23.23 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.11 (0.28), residues: 974 helix: 1.29 (0.31), residues: 289 sheet: 0.63 (0.35), residues: 230 loop : -1.03 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 332 HIS 0.002 0.001 HIS L 191 PHE 0.027 0.002 PHE H 35 TYR 0.018 0.001 TYR D 237 ARG 0.002 0.000 ARG D1115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: H 10 SER cc_start: 0.8225 (m) cc_final: 0.7882 (t) REVERT: H 86 MET cc_start: 0.7467 (mmt) cc_final: 0.7111 (mmt) REVERT: H 131 LYS cc_start: 0.8406 (ptmm) cc_final: 0.8116 (ptmm) REVERT: H 165 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.7973 (p) REVERT: H 191 SER cc_start: 0.8264 (OUTLIER) cc_final: 0.7830 (m) REVERT: H 194 SER cc_start: 0.8428 (t) cc_final: 0.8034 (p) REVERT: H 198 VAL cc_start: 0.8540 (t) cc_final: 0.8287 (m) REVERT: H 224 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.6398 (mmtt) REVERT: K 46 GLU cc_start: 0.6576 (mp0) cc_final: 0.5912 (mp0) REVERT: L 18 ASP cc_start: 0.8022 (t0) cc_final: 0.7794 (t0) REVERT: L 147 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7798 (pttp) REVERT: L 209 LYS cc_start: 0.8500 (mmtp) cc_final: 0.8276 (mmmm) REVERT: D 171 GLN cc_start: 0.7452 (mp10) cc_final: 0.7237 (mp10) REVERT: D 250 ILE cc_start: 0.8204 (mt) cc_final: 0.7940 (mt) REVERT: D 390 ILE cc_start: 0.8168 (tt) cc_final: 0.7960 (tt) REVERT: D 1013 GLU cc_start: 0.6576 (tp30) cc_final: 0.6180 (tp30) REVERT: D 1088 LYS cc_start: 0.8251 (mtmm) cc_final: 0.8010 (mttm) REVERT: D 1091 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7008 (tm-30) REVERT: D 1100 LYS cc_start: 0.8038 (mmtp) cc_final: 0.7623 (mmmt) REVERT: D 484 LEU cc_start: 0.6978 (mm) cc_final: 0.6615 (mt) outliers start: 21 outliers final: 17 residues processed: 168 average time/residue: 0.2208 time to fit residues: 48.9466 Evaluate side-chains 174 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 224 LYS Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 1097 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 434 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 79 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 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 = 0.3979 r_free = 0.3979 target = 0.153673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.131408 restraints weight = 11593.363| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.71 r_work: 0.3543 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 7846 Z= 0.260 Angle : 0.651 11.889 10657 Z= 0.330 Chirality : 0.044 0.174 1194 Planarity : 0.004 0.054 1340 Dihedral : 4.668 20.208 1068 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.65 % Allowed : 22.86 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.08 (0.28), residues: 974 helix: 1.33 (0.31), residues: 289 sheet: 0.57 (0.35), residues: 230 loop : -1.07 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 332 HIS 0.002 0.001 HIS H 38 PHE 0.028 0.002 PHE D 337 TYR 0.021 0.002 TYR D 237 ARG 0.002 0.000 ARG K 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1957.48 seconds wall clock time: 35 minutes 30.61 seconds (2130.61 seconds total)