Starting phenix.real_space_refine on Thu Mar 14 19:57:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pde_13335/03_2024/7pde_13335_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pde_13335/03_2024/7pde_13335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pde_13335/03_2024/7pde_13335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pde_13335/03_2024/7pde_13335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pde_13335/03_2024/7pde_13335_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pde_13335/03_2024/7pde_13335_updated.pdb" } resolution = 4.5 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 81 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 69 5.16 5 C 6144 2.51 5 N 1604 2.21 5 O 1732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 114": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 508": "OD1" <-> "OD2" Residue "A TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1083": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1127": "NH1" <-> "NH2" Residue "A ARG 1148": "NH1" <-> "NH2" Residue "A PHE 1162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1197": "NH1" <-> "NH2" Residue "A ARG 1206": "NH1" <-> "NH2" Residue "A TYR 1222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 343": "OD1" <-> "OD2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 381": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9553 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6711 Classifications: {'peptide': 846} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 825} Chain breaks: 6 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2842 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'peptide': 341, 'undetermined': 2} Link IDs: {'PTRANS': 13, 'TRANS': 327, None: 2} Not linked: pdbres="GLN B 390 " pdbres="GSP B 501 " Not linked: pdbres="GSP B 501 " pdbres=" MG B 502 " Chain breaks: 1 Time building chain proxies: 5.44, per 1000 atoms: 0.57 Number of scatterers: 9553 At special positions: 0 Unit cell: (166.05, 103.68, 115.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 69 16.00 P 3 15.00 Mg 1 11.99 O 1732 8.00 N 1604 7.00 C 6144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2246 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 5 sheets defined 56.8% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 100 through 136 removed outlier: 3.552A pdb=" N MET A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 147 through 164 removed outlier: 4.378A pdb=" N PHE A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 192 Processing helix chain 'A' and resid 220 through 237 Processing helix chain 'A' and resid 242 through 260 Processing helix chain 'A' and resid 279 through 336 removed outlier: 4.254A pdb=" N VAL A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 348 removed outlier: 3.582A pdb=" N LYS A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 403 through 406 No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'A' and resid 414 through 433 removed outlier: 3.850A pdb=" N GLU A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 479 Processing helix chain 'A' and resid 512 through 522 Processing helix chain 'A' and resid 533 through 538 removed outlier: 4.787A pdb=" N TYR A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 807 Processing helix chain 'A' and resid 818 through 842 Processing helix chain 'A' and resid 850 through 857 Processing helix chain 'A' and resid 863 through 883 Proline residue: A 876 - end of helix removed outlier: 4.777A pdb=" N HIS A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 911 removed outlier: 3.704A pdb=" N GLN A 908 " --> pdb=" O THR A 904 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TYR A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N CYS A 910 " --> pdb=" O VAL A 906 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN A 911 " --> pdb=" O VAL A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 936 Proline residue: A 931 - end of helix Processing helix chain 'A' and resid 978 through 1036 Processing helix chain 'A' and resid 1039 through 1047 Processing helix chain 'A' and resid 1066 through 1071 removed outlier: 4.275A pdb=" N SER A1069 " --> pdb=" O VAL A1066 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU A1070 " --> pdb=" O ASN A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1097 removed outlier: 3.847A pdb=" N LEU A1096 " --> pdb=" O ASP A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1104 removed outlier: 3.561A pdb=" N SER A1104 " --> pdb=" O ASP A1101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1101 through 1104' Processing helix chain 'A' and resid 1134 through 1155 removed outlier: 3.635A pdb=" N LEU A1139 " --> pdb=" O LEU A1136 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N MET A1147 " --> pdb=" O LYS A1144 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A1150 " --> pdb=" O MET A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1201 removed outlier: 3.706A pdb=" N THR A1201 " --> pdb=" O ARG A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1219 removed outlier: 3.503A pdb=" N VAL A1216 " --> pdb=" O GLU A1212 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 53 through 64 Processing helix chain 'B' and resid 90 through 111 removed outlier: 3.879A pdb=" N LYS B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 107 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 removed outlier: 4.369A pdb=" N PHE B 126 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.534A pdb=" N ARG B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER B 166 " --> pdb=" O CYS B 162 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASN B 167 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.509A pdb=" N ASP B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASP B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 265 through 278 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 308 through 311 No H-bonds generated for 'chain 'B' and resid 308 through 311' Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 332 through 350 removed outlier: 4.104A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 389 removed outlier: 4.389A pdb=" N LEU B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG B 389 " --> pdb=" O ARG B 385 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 508 through 510 removed outlier: 6.331A pdb=" N VAL A 495 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLU A 391 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N CYS A 497 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLN A 389 " --> pdb=" O CYS A 497 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A 394 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 439 " --> pdb=" O TYR A 446 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL A 448 " --> pdb=" O LYS A 437 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS A 437 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 529 through 531 Processing sheet with id= C, first strand: chain 'A' and resid 1052 through 1055 Processing sheet with id= D, first strand: chain 'A' and resid 1106 through 1111 removed outlier: 7.162A pdb=" N MET A1116 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR A1110 " --> pdb=" O THR A1114 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS A1170 " --> pdb=" O SER A1210 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY A1228 " --> pdb=" O THR A1240 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU A1242 " --> pdb=" O TYR A1226 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N TYR A1226 " --> pdb=" O LEU A1242 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 287 through 292 removed outlier: 5.964A pdb=" N ILE B 244 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N PHE B 290 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE B 246 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ASN B 292 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL B 248 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 247 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN B 218 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU B 43 " --> pdb=" O ASN B 218 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N HIS B 220 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU B 45 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE B 222 " --> pdb=" O LEU B 45 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1488 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: 3.00 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3055 1.34 - 1.46: 2250 1.46 - 1.58: 4343 1.58 - 1.69: 5 1.69 - 1.81: 106 Bond restraints: 9759 Sorted by residual: bond pdb=" C HIS A 239 " pdb=" N LEU A 240 " ideal model delta sigma weight residual 1.331 1.238 0.093 2.07e-02 2.33e+03 2.03e+01 bond pdb=" CA TYR A 909 " pdb=" C TYR A 909 " ideal model delta sigma weight residual 1.522 1.476 0.046 1.45e-02 4.76e+03 9.97e+00 bond pdb=" CA LEU B 43 " pdb=" CB LEU B 43 " ideal model delta sigma weight residual 1.526 1.503 0.024 1.53e-02 4.27e+03 2.39e+00 bond pdb=" CA GLY A1167 " pdb=" C GLY A1167 " ideal model delta sigma weight residual 1.520 1.509 0.011 7.30e-03 1.88e+04 2.29e+00 bond pdb=" CB PHE A1001 " pdb=" CG PHE A1001 " ideal model delta sigma weight residual 1.502 1.467 0.035 2.30e-02 1.89e+03 2.27e+00 ... (remaining 9754 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.79: 224 106.79 - 114.43: 5859 114.43 - 122.08: 5426 122.08 - 129.73: 1624 129.73 - 137.37: 71 Bond angle restraints: 13204 Sorted by residual: angle pdb=" N VAL A 337 " pdb=" CA VAL A 337 " pdb=" C VAL A 337 " ideal model delta sigma weight residual 113.71 109.46 4.25 9.50e-01 1.11e+00 2.00e+01 angle pdb=" N VAL B 134 " pdb=" CA VAL B 134 " pdb=" C VAL B 134 " ideal model delta sigma weight residual 111.91 107.99 3.92 8.90e-01 1.26e+00 1.94e+01 angle pdb=" C SER A1130 " pdb=" N HIS A1131 " pdb=" CA HIS A1131 " ideal model delta sigma weight residual 120.65 114.79 5.86 1.36e+00 5.41e-01 1.86e+01 angle pdb=" C THR A 196 " pdb=" N PRO A 197 " pdb=" CD PRO A 197 " ideal model delta sigma weight residual 125.00 137.37 -12.37 4.10e+00 5.95e-02 9.11e+00 angle pdb=" N VAL B 367 " pdb=" CA VAL B 367 " pdb=" C VAL B 367 " ideal model delta sigma weight residual 112.98 109.41 3.57 1.25e+00 6.40e-01 8.17e+00 ... (remaining 13199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 5132 17.52 - 35.03: 547 35.03 - 52.55: 99 52.55 - 70.07: 10 70.07 - 87.58: 12 Dihedral angle restraints: 5800 sinusoidal: 2329 harmonic: 3471 Sorted by residual: dihedral pdb=" CA VAL B 114 " pdb=" C VAL B 114 " pdb=" N PRO B 115 " pdb=" CA PRO B 115 " ideal model delta harmonic sigma weight residual 180.00 153.28 26.72 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA CYS A 910 " pdb=" C CYS A 910 " pdb=" N ASN A 911 " pdb=" CA ASN A 911 " ideal model delta harmonic sigma weight residual 180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA THR A 236 " pdb=" C THR A 236 " pdb=" N VAL A 237 " pdb=" CA VAL A 237 " ideal model delta harmonic sigma weight residual -180.00 -160.66 -19.34 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 5797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 880 0.033 - 0.067: 424 0.067 - 0.100: 146 0.100 - 0.133: 33 0.133 - 0.166: 5 Chirality restraints: 1488 Sorted by residual: chirality pdb=" CA ASP B 215 " pdb=" N ASP B 215 " pdb=" C ASP B 215 " pdb=" CB ASP B 215 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" C3' GSP B 501 " pdb=" C2' GSP B 501 " pdb=" C4' GSP B 501 " pdb=" O3' GSP B 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.63 0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA HIS B 64 " pdb=" N HIS B 64 " pdb=" C HIS B 64 " pdb=" CB HIS B 64 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.68e-01 ... (remaining 1485 not shown) Planarity restraints: 1660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1037 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO A1038 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A1038 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1038 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 993 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C LEU A 993 " -0.031 2.00e-02 2.50e+03 pdb=" O LEU A 993 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A 994 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 815 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A 816 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 816 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 816 " 0.020 5.00e-02 4.00e+02 ... (remaining 1657 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 161 2.47 - 3.08: 8090 3.08 - 3.69: 16578 3.69 - 4.29: 23449 4.29 - 4.90: 34661 Nonbonded interactions: 82939 Sorted by model distance: nonbonded pdb=" O2B GSP B 501 " pdb="MG MG B 502 " model vdw 1.869 2.170 nonbonded pdb=" O3G GSP B 501 " pdb="MG MG B 502 " model vdw 2.027 2.170 nonbonded pdb=" O ALA A 412 " pdb=" OG SER A1052 " model vdw 2.097 2.440 nonbonded pdb=" OG SER B 54 " pdb=" OG1 THR B 204 " model vdw 2.125 2.440 nonbonded pdb=" O ARG A 503 " pdb=" NZ LYS A1107 " model vdw 2.131 2.520 ... (remaining 82934 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 group one per residue 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 5.760 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 29.920 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.006 0.093 9759 Z= 0.367 Angle : 0.788 12.375 13204 Z= 0.459 Chirality : 0.043 0.166 1488 Planarity : 0.004 0.047 1660 Dihedral : 14.841 87.582 3554 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 29.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.19 % Allowed : 8.45 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.21), residues: 1169 helix: -2.14 (0.16), residues: 669 sheet: -2.59 (0.38), residues: 126 loop : -2.43 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 130 HIS 0.008 0.002 HIS A 319 PHE 0.023 0.002 PHE A 232 TYR 0.018 0.002 TYR A 445 ARG 0.007 0.001 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TRP cc_start: 0.8591 (m100) cc_final: 0.8330 (m100) REVERT: A 229 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8525 (mt-10) REVERT: A 288 HIS cc_start: 0.9197 (m90) cc_final: 0.8955 (m90) REVERT: A 338 MET cc_start: 0.9000 (mtp) cc_final: 0.8620 (ttm) REVERT: A 502 MET cc_start: 0.8407 (mmm) cc_final: 0.8129 (mmm) REVERT: A 840 ARG cc_start: 0.5571 (mtt-85) cc_final: 0.4866 (ttp80) REVERT: A 849 MET cc_start: 0.8664 (ttt) cc_final: 0.8104 (tpp) REVERT: A 991 LEU cc_start: 0.9797 (mm) cc_final: 0.9513 (tt) REVERT: A 1002 GLU cc_start: 0.9194 (tp30) cc_final: 0.8810 (mt-10) REVERT: A 1022 ILE cc_start: 0.8276 (tp) cc_final: 0.7770 (tp) REVERT: A 1146 MET cc_start: 0.9504 (ptm) cc_final: 0.9187 (ppp) REVERT: A 1147 MET cc_start: 0.9401 (tpp) cc_final: 0.9170 (tpp) REVERT: B 65 VAL cc_start: 0.8254 (t) cc_final: 0.7620 (t) outliers start: 2 outliers final: 0 residues processed: 154 average time/residue: 0.2288 time to fit residues: 49.0278 Evaluate side-chains 118 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.1980 chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 30 optimal weight: 0.1980 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1040 HIS A1075 ASN ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 GLN ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 98 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 271 ASN B 278 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9759 Z= 0.170 Angle : 0.643 11.773 13204 Z= 0.324 Chirality : 0.041 0.234 1488 Planarity : 0.004 0.045 1660 Dihedral : 5.127 50.538 1302 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.10 % Allowed : 3.75 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.23), residues: 1169 helix: -0.28 (0.18), residues: 698 sheet: -1.80 (0.39), residues: 135 loop : -1.83 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 281 HIS 0.011 0.001 HIS A 292 PHE 0.023 0.002 PHE A 121 TYR 0.021 0.001 TYR A 252 ARG 0.006 0.000 ARG A 999 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TRP cc_start: 0.8345 (m100) cc_final: 0.8066 (m100) REVERT: A 184 PHE cc_start: 0.9277 (m-10) cc_final: 0.9006 (m-80) REVERT: A 220 GLN cc_start: 0.8972 (mt0) cc_final: 0.8751 (mt0) REVERT: A 224 PHE cc_start: 0.9548 (t80) cc_final: 0.9196 (t80) REVERT: A 228 ILE cc_start: 0.9651 (mm) cc_final: 0.9221 (mm) REVERT: A 318 MET cc_start: 0.8956 (tmm) cc_final: 0.8618 (tmm) REVERT: A 338 MET cc_start: 0.9124 (mtp) cc_final: 0.8723 (ttm) REVERT: A 469 MET cc_start: 0.9574 (ptp) cc_final: 0.8558 (ptp) REVERT: A 502 MET cc_start: 0.8265 (mmm) cc_final: 0.7989 (mmm) REVERT: A 849 MET cc_start: 0.8505 (ttt) cc_final: 0.7905 (tpp) REVERT: A 896 MET cc_start: 0.9591 (mtm) cc_final: 0.9180 (mtt) REVERT: A 987 PHE cc_start: 0.8892 (t80) cc_final: 0.8648 (t80) REVERT: A 992 LEU cc_start: 0.9545 (mm) cc_final: 0.9274 (mm) REVERT: A 1083 TYR cc_start: 0.9263 (m-10) cc_final: 0.9044 (m-80) REVERT: A 1108 ILE cc_start: 0.9667 (mm) cc_final: 0.9236 (mt) REVERT: A 1116 MET cc_start: 0.9221 (ttm) cc_final: 0.8932 (ttm) REVERT: A 1220 MET cc_start: 0.9509 (mtm) cc_final: 0.9025 (mtp) REVERT: B 110 MET cc_start: 0.9339 (mtt) cc_final: 0.8917 (mmm) REVERT: B 289 LEU cc_start: 0.9256 (tt) cc_final: 0.9054 (tt) outliers start: 1 outliers final: 1 residues processed: 165 average time/residue: 0.1874 time to fit residues: 44.9948 Evaluate side-chains 128 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 HIS ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 GLN A1156 ASN A1193 ASN ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9759 Z= 0.270 Angle : 0.661 12.184 13204 Z= 0.340 Chirality : 0.041 0.186 1488 Planarity : 0.004 0.046 1660 Dihedral : 5.175 51.288 1302 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.10 % Allowed : 5.76 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.24), residues: 1169 helix: 0.05 (0.19), residues: 689 sheet: -1.52 (0.41), residues: 130 loop : -1.60 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 510 HIS 0.007 0.001 HIS A1170 PHE 0.018 0.002 PHE A 397 TYR 0.021 0.002 TYR A 445 ARG 0.008 0.001 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TRP cc_start: 0.8408 (m100) cc_final: 0.8154 (m100) REVERT: A 224 PHE cc_start: 0.9561 (t80) cc_final: 0.9162 (t80) REVERT: A 228 ILE cc_start: 0.9448 (mm) cc_final: 0.9207 (mm) REVERT: A 300 ILE cc_start: 0.9657 (pt) cc_final: 0.9456 (pt) REVERT: A 318 MET cc_start: 0.9076 (tmm) cc_final: 0.8818 (tmm) REVERT: A 469 MET cc_start: 0.9402 (ptp) cc_final: 0.9164 (ptm) REVERT: A 502 MET cc_start: 0.8419 (mmm) cc_final: 0.8154 (mmm) REVERT: A 849 MET cc_start: 0.8617 (ttt) cc_final: 0.8022 (tpp) REVERT: A 987 PHE cc_start: 0.8997 (t80) cc_final: 0.8515 (t80) REVERT: A 992 LEU cc_start: 0.9556 (mm) cc_final: 0.9329 (mm) REVERT: A 1146 MET cc_start: 0.9551 (mtp) cc_final: 0.9309 (ttm) REVERT: A 1184 LEU cc_start: 0.9587 (tt) cc_final: 0.8761 (mt) REVERT: A 1186 ASP cc_start: 0.9107 (t0) cc_final: 0.8824 (t0) REVERT: A 1220 MET cc_start: 0.9427 (mtm) cc_final: 0.9158 (mtm) REVERT: B 110 MET cc_start: 0.9327 (mtt) cc_final: 0.8871 (mmm) REVERT: B 289 LEU cc_start: 0.9251 (tt) cc_final: 0.9000 (tt) outliers start: 1 outliers final: 1 residues processed: 142 average time/residue: 0.1940 time to fit residues: 40.3401 Evaluate side-chains 118 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 51 optimal weight: 40.0000 chunk 72 optimal weight: 30.0000 chunk 107 optimal weight: 8.9990 chunk 114 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 102 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 overall best weight: 2.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 HIS ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9759 Z= 0.177 Angle : 0.605 11.867 13204 Z= 0.303 Chirality : 0.040 0.310 1488 Planarity : 0.003 0.045 1660 Dihedral : 4.876 46.603 1302 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.25), residues: 1169 helix: 0.38 (0.19), residues: 701 sheet: -1.40 (0.41), residues: 134 loop : -1.60 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 130 HIS 0.005 0.001 HIS A 319 PHE 0.032 0.002 PHE A 397 TYR 0.015 0.002 TYR A 446 ARG 0.006 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TRP cc_start: 0.8330 (m100) cc_final: 0.8106 (m100) REVERT: A 238 MET cc_start: 0.8441 (mmp) cc_final: 0.8003 (mmp) REVERT: A 240 LEU cc_start: 0.9423 (mp) cc_final: 0.8882 (tp) REVERT: A 338 MET cc_start: 0.9230 (mtp) cc_final: 0.8166 (ttm) REVERT: A 429 LEU cc_start: 0.9793 (mt) cc_final: 0.9499 (tp) REVERT: A 465 MET cc_start: 0.9006 (tpp) cc_final: 0.8372 (tpt) REVERT: A 502 MET cc_start: 0.8290 (mmm) cc_final: 0.8040 (mmm) REVERT: A 849 MET cc_start: 0.8574 (ttt) cc_final: 0.7988 (tpp) REVERT: A 992 LEU cc_start: 0.9546 (mm) cc_final: 0.9284 (mm) REVERT: A 1108 ILE cc_start: 0.9662 (mm) cc_final: 0.9201 (mt) REVERT: A 1116 MET cc_start: 0.9248 (ttm) cc_final: 0.8923 (ttm) REVERT: A 1146 MET cc_start: 0.9501 (mtp) cc_final: 0.9252 (ttm) REVERT: A 1183 LEU cc_start: 0.9631 (mt) cc_final: 0.9333 (mt) REVERT: A 1184 LEU cc_start: 0.9512 (tt) cc_final: 0.8610 (mt) REVERT: A 1220 MET cc_start: 0.9394 (mtm) cc_final: 0.9106 (mtp) REVERT: B 289 LEU cc_start: 0.9228 (tt) cc_final: 0.8934 (tt) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1736 time to fit residues: 38.6393 Evaluate side-chains 127 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 40.0000 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 0.0770 chunk 28 optimal weight: 9.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9759 Z= 0.250 Angle : 0.642 12.165 13204 Z= 0.329 Chirality : 0.040 0.189 1488 Planarity : 0.004 0.043 1660 Dihedral : 4.986 47.637 1302 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1169 helix: 0.39 (0.19), residues: 688 sheet: -1.39 (0.41), residues: 134 loop : -1.25 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 510 HIS 0.007 0.001 HIS B 220 PHE 0.024 0.002 PHE A 987 TYR 0.021 0.002 TYR A 445 ARG 0.004 0.001 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8859 (mtt180) cc_final: 0.8146 (mtp85) REVERT: A 130 TRP cc_start: 0.8371 (m100) cc_final: 0.8047 (m100) REVERT: A 300 ILE cc_start: 0.9652 (pt) cc_final: 0.9451 (pt) REVERT: A 397 PHE cc_start: 0.8842 (m-10) cc_final: 0.8620 (m-10) REVERT: A 441 LEU cc_start: 0.9065 (mp) cc_final: 0.8675 (tt) REVERT: A 502 MET cc_start: 0.8331 (mmm) cc_final: 0.8074 (mmm) REVERT: A 849 MET cc_start: 0.8630 (ttt) cc_final: 0.8013 (tpp) REVERT: A 925 THR cc_start: 0.9433 (m) cc_final: 0.8985 (m) REVERT: A 992 LEU cc_start: 0.9566 (mm) cc_final: 0.9327 (mm) REVERT: A 1001 PHE cc_start: 0.9181 (m-80) cc_final: 0.8867 (m-80) REVERT: A 1184 LEU cc_start: 0.9627 (tt) cc_final: 0.8812 (mt) REVERT: A 1186 ASP cc_start: 0.9225 (t0) cc_final: 0.8955 (t70) REVERT: B 289 LEU cc_start: 0.9300 (tt) cc_final: 0.9003 (tt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1997 time to fit residues: 42.6618 Evaluate side-chains 123 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 8.9990 chunk 102 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 66 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9759 Z= 0.164 Angle : 0.599 11.689 13204 Z= 0.303 Chirality : 0.040 0.157 1488 Planarity : 0.003 0.040 1660 Dihedral : 4.778 43.722 1302 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1169 helix: 0.71 (0.19), residues: 695 sheet: -0.99 (0.45), residues: 123 loop : -1.28 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 995 HIS 0.006 0.001 HIS B 220 PHE 0.054 0.002 PHE A 184 TYR 0.019 0.001 TYR A 445 ARG 0.006 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8870 (mtt180) cc_final: 0.8558 (mtp85) REVERT: A 130 TRP cc_start: 0.8349 (m100) cc_final: 0.8090 (m100) REVERT: A 184 PHE cc_start: 0.9538 (m-80) cc_final: 0.9293 (m-80) REVERT: A 224 PHE cc_start: 0.9551 (t80) cc_final: 0.9141 (t80) REVERT: A 228 ILE cc_start: 0.9387 (mm) cc_final: 0.9156 (mm) REVERT: A 441 LEU cc_start: 0.9076 (mp) cc_final: 0.8711 (tt) REVERT: A 502 MET cc_start: 0.8337 (mmm) cc_final: 0.8083 (mmm) REVERT: A 849 MET cc_start: 0.8524 (ttt) cc_final: 0.7921 (tpp) REVERT: A 992 LEU cc_start: 0.9565 (mm) cc_final: 0.9300 (mm) REVERT: A 1001 PHE cc_start: 0.9114 (m-80) cc_final: 0.8856 (m-80) REVERT: A 1108 ILE cc_start: 0.9682 (mm) cc_final: 0.9165 (mt) REVERT: A 1116 MET cc_start: 0.9239 (ttm) cc_final: 0.8864 (ttm) REVERT: A 1220 MET cc_start: 0.9401 (mtp) cc_final: 0.9118 (mtp) REVERT: B 255 MET cc_start: 0.9417 (mmm) cc_final: 0.9079 (mmm) REVERT: B 289 LEU cc_start: 0.9254 (tt) cc_final: 0.8941 (tt) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1963 time to fit residues: 44.6794 Evaluate side-chains 129 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 64 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9759 Z= 0.157 Angle : 0.607 11.910 13204 Z= 0.302 Chirality : 0.040 0.160 1488 Planarity : 0.003 0.040 1660 Dihedral : 4.651 41.154 1302 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1169 helix: 0.77 (0.20), residues: 697 sheet: -0.81 (0.49), residues: 107 loop : -1.37 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 995 HIS 0.006 0.001 HIS B 220 PHE 0.048 0.002 PHE A 184 TYR 0.037 0.001 TYR A 252 ARG 0.006 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8823 (mtt180) cc_final: 0.8178 (mtp85) REVERT: A 441 LEU cc_start: 0.9079 (mp) cc_final: 0.8677 (tt) REVERT: A 469 MET cc_start: 0.9291 (ppp) cc_final: 0.9037 (ppp) REVERT: A 502 MET cc_start: 0.8301 (mmm) cc_final: 0.8064 (mmm) REVERT: A 849 MET cc_start: 0.8511 (ttt) cc_final: 0.7918 (tpp) REVERT: A 987 PHE cc_start: 0.9087 (t80) cc_final: 0.8763 (t80) REVERT: A 992 LEU cc_start: 0.9587 (mm) cc_final: 0.9352 (mm) REVERT: A 1001 PHE cc_start: 0.9118 (m-80) cc_final: 0.8770 (m-80) REVERT: A 1073 GLU cc_start: 0.7610 (mp0) cc_final: 0.7380 (mp0) REVERT: A 1108 ILE cc_start: 0.9684 (mm) cc_final: 0.9482 (mp) REVERT: A 1220 MET cc_start: 0.9331 (mtp) cc_final: 0.9088 (mtp) REVERT: B 60 MET cc_start: 0.9001 (tpt) cc_final: 0.8668 (tpt) REVERT: B 110 MET cc_start: 0.9034 (mtt) cc_final: 0.8590 (mmm) REVERT: B 221 MET cc_start: 0.8488 (ptm) cc_final: 0.8195 (ttp) REVERT: B 255 MET cc_start: 0.9399 (mmm) cc_final: 0.8951 (mmm) REVERT: B 289 LEU cc_start: 0.9243 (tt) cc_final: 0.8922 (tt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1949 time to fit residues: 44.3921 Evaluate side-chains 127 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9759 Z= 0.223 Angle : 0.634 12.124 13204 Z= 0.321 Chirality : 0.040 0.151 1488 Planarity : 0.004 0.040 1660 Dihedral : 4.719 41.908 1302 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.25), residues: 1169 helix: 0.66 (0.19), residues: 698 sheet: -1.00 (0.47), residues: 111 loop : -1.26 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 995 HIS 0.007 0.001 HIS B 220 PHE 0.018 0.002 PHE A 125 TYR 0.023 0.002 TYR A 252 ARG 0.005 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8828 (mtt180) cc_final: 0.8168 (mtp85) REVERT: A 228 ILE cc_start: 0.9465 (mm) cc_final: 0.9162 (mm) REVERT: A 232 PHE cc_start: 0.8652 (m-10) cc_final: 0.8255 (m-80) REVERT: A 469 MET cc_start: 0.9361 (ppp) cc_final: 0.9110 (ppp) REVERT: A 502 MET cc_start: 0.8384 (mmm) cc_final: 0.8094 (mmm) REVERT: A 849 MET cc_start: 0.8560 (ttt) cc_final: 0.7965 (tpp) REVERT: A 987 PHE cc_start: 0.9104 (t80) cc_final: 0.8787 (t80) REVERT: A 1001 PHE cc_start: 0.9150 (m-80) cc_final: 0.8785 (m-80) REVERT: A 1108 ILE cc_start: 0.9694 (mm) cc_final: 0.9433 (mp) REVERT: A 1116 MET cc_start: 0.9262 (ttm) cc_final: 0.9021 (ttm) REVERT: A 1186 ASP cc_start: 0.9200 (t0) cc_final: 0.8986 (t70) REVERT: A 1220 MET cc_start: 0.9415 (mtp) cc_final: 0.9126 (mtp) REVERT: B 110 MET cc_start: 0.9048 (mtt) cc_final: 0.8609 (mmm) REVERT: B 255 MET cc_start: 0.9450 (mmm) cc_final: 0.9039 (mmm) REVERT: B 289 LEU cc_start: 0.9262 (tt) cc_final: 0.8938 (tt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2018 time to fit residues: 42.4603 Evaluate side-chains 119 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9759 Z= 0.251 Angle : 0.660 12.176 13204 Z= 0.335 Chirality : 0.041 0.154 1488 Planarity : 0.004 0.039 1660 Dihedral : 4.887 43.785 1302 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.25), residues: 1169 helix: 0.68 (0.19), residues: 689 sheet: -1.04 (0.46), residues: 113 loop : -1.22 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 995 HIS 0.006 0.001 HIS B 220 PHE 0.043 0.002 PHE A 184 TYR 0.024 0.002 TYR A 445 ARG 0.006 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TRP cc_start: 0.8483 (m100) cc_final: 0.7917 (m100) REVERT: A 184 PHE cc_start: 0.9604 (m-80) cc_final: 0.9371 (m-80) REVERT: A 224 PHE cc_start: 0.9649 (t80) cc_final: 0.9313 (t80) REVERT: A 228 ILE cc_start: 0.9498 (mm) cc_final: 0.9158 (mm) REVERT: A 232 PHE cc_start: 0.8790 (m-10) cc_final: 0.8317 (m-80) REVERT: A 238 MET cc_start: 0.8438 (mmp) cc_final: 0.8231 (mmp) REVERT: A 469 MET cc_start: 0.9384 (ppp) cc_final: 0.9129 (ppp) REVERT: A 502 MET cc_start: 0.8410 (mmm) cc_final: 0.8138 (mmm) REVERT: A 849 MET cc_start: 0.8604 (ttt) cc_final: 0.8007 (tpp) REVERT: A 987 PHE cc_start: 0.9118 (t80) cc_final: 0.8792 (t80) REVERT: A 1108 ILE cc_start: 0.9691 (mm) cc_final: 0.9299 (mt) REVERT: A 1116 MET cc_start: 0.9271 (ttm) cc_final: 0.8924 (ttm) REVERT: A 1220 MET cc_start: 0.9456 (mtp) cc_final: 0.9079 (mtp) REVERT: B 60 MET cc_start: 0.9203 (tpt) cc_final: 0.8969 (tpt) REVERT: B 110 MET cc_start: 0.9045 (mtt) cc_final: 0.8603 (mmm) REVERT: B 255 MET cc_start: 0.9473 (mmm) cc_final: 0.9059 (mmm) REVERT: B 289 LEU cc_start: 0.9239 (tt) cc_final: 0.8935 (tt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2022 time to fit residues: 41.0001 Evaluate side-chains 119 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 7.9990 chunk 53 optimal weight: 0.0020 chunk 77 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 93 optimal weight: 0.0570 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 30.0000 chunk 57 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 overall best weight: 0.9510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9759 Z= 0.161 Angle : 0.640 11.892 13204 Z= 0.315 Chirality : 0.041 0.196 1488 Planarity : 0.003 0.039 1660 Dihedral : 4.598 38.284 1302 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1169 helix: 0.75 (0.20), residues: 703 sheet: -0.93 (0.46), residues: 113 loop : -1.37 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 995 HIS 0.011 0.001 HIS A 297 PHE 0.044 0.002 PHE A 184 TYR 0.018 0.001 TYR A 445 ARG 0.004 0.000 ARG A 305 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TRP cc_start: 0.8453 (m100) cc_final: 0.7620 (m100) REVERT: A 184 PHE cc_start: 0.9555 (m-80) cc_final: 0.9289 (m-80) REVERT: A 228 ILE cc_start: 0.9534 (mm) cc_final: 0.9203 (mt) REVERT: A 232 PHE cc_start: 0.8728 (m-10) cc_final: 0.8308 (m-80) REVERT: A 288 HIS cc_start: 0.9317 (m90) cc_final: 0.8983 (m90) REVERT: A 469 MET cc_start: 0.9302 (ppp) cc_final: 0.9029 (ppp) REVERT: A 502 MET cc_start: 0.8330 (mmm) cc_final: 0.8074 (mmm) REVERT: A 849 MET cc_start: 0.8492 (ttt) cc_final: 0.7907 (tpp) REVERT: A 987 PHE cc_start: 0.9073 (t80) cc_final: 0.8782 (t80) REVERT: A 992 LEU cc_start: 0.9553 (mm) cc_final: 0.9301 (mm) REVERT: A 1025 MET cc_start: 0.8502 (mmp) cc_final: 0.7748 (tpp) REVERT: A 1220 MET cc_start: 0.9358 (mtp) cc_final: 0.9108 (mtp) REVERT: B 110 MET cc_start: 0.8957 (mtt) cc_final: 0.8545 (mmm) REVERT: B 255 MET cc_start: 0.9392 (mmm) cc_final: 0.8947 (mmm) REVERT: B 289 LEU cc_start: 0.9197 (tt) cc_final: 0.8875 (tt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1970 time to fit residues: 43.7933 Evaluate side-chains 120 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 93 optimal weight: 0.0470 chunk 39 optimal weight: 0.4980 chunk 96 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 5 optimal weight: 0.2980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 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 = 0.3396 r_free = 0.3396 target = 0.055439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.044798 restraints weight = 76620.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.046013 restraints weight = 50598.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.046882 restraints weight = 37458.043| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9759 Z= 0.152 Angle : 0.635 11.798 13204 Z= 0.307 Chirality : 0.041 0.154 1488 Planarity : 0.003 0.039 1660 Dihedral : 4.431 33.491 1302 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1169 helix: 0.84 (0.20), residues: 700 sheet: -0.94 (0.45), residues: 120 loop : -1.12 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 995 HIS 0.008 0.001 HIS A 297 PHE 0.048 0.002 PHE A 184 TYR 0.028 0.001 TYR A 252 ARG 0.005 0.000 ARG A 840 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1957.52 seconds wall clock time: 36 minutes 26.55 seconds (2186.55 seconds total)