Starting phenix.real_space_refine on Mon Nov 13 17:48:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3n_25665/11_2023/7t3n_25665_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3n_25665/11_2023/7t3n_25665.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3n_25665/11_2023/7t3n_25665_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3n_25665/11_2023/7t3n_25665_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3n_25665/11_2023/7t3n_25665_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3n_25665/11_2023/7t3n_25665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3n_25665/11_2023/7t3n_25665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3n_25665/11_2023/7t3n_25665_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3n_25665/11_2023/7t3n_25665_updated.pdb" } resolution = 3.0 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= 1.000 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 25 5.16 5 C 2318 2.51 5 N 564 2.21 5 O 605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A ASP 507": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 3512 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3512 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3507 Unusual residues: {'I7Y': 1} Classifications: {'peptide': 453, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 19, 'TRANS': 433, None: 1} Not linked: pdbres="C5B A 601 " pdbres="I7Y A 602 " Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 7, 'P1L:plan-1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 Conformer: "B" Number of residues, atoms: 454, 3507 Unusual residues: {'I7Y': 1} Classifications: {'peptide': 453, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 19, 'TRANS': 433, None: 1} Not linked: pdbres="C5B A 601 " pdbres="I7Y A 602 " Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 7, 'P1L:plan-1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 bond proxies already assigned to first conformer: 3605 Time building chain proxies: 4.41, per 1000 atoms: 1.26 Number of scatterers: 3512 At special positions: 0 Unit cell: (75.985, 72.645, 76.82, 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 25 16.00 O 605 8.00 N 564 7.00 C 2318 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: 1.77 Conformation dependent library (CDL) restraints added in 1.3 seconds 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 816 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 0 sheets defined 71.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 69 through 98 removed outlier: 3.745A pdb=" N ALA A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS A 89 " --> pdb=" O PHE A 85 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A 90 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU A 91 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 93 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 135 removed outlier: 4.653A pdb=" N PHE A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 151 through 173 removed outlier: 4.048A pdb=" N LEU A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.836A pdb=" N VAL A 183 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 205 removed outlier: 3.582A pdb=" N GLY A 200 " --> pdb=" O PRO A 196 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 233 removed outlier: 3.623A pdb=" N ARG A 211 " --> pdb=" O PRO A 208 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N SER A 212 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG A 213 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 214 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR A 216 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS A 220 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 221 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY A 225 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 226 " --> pdb=" O TYR A 223 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 229 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N MET A 230 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 241 through 263 removed outlier: 4.468A pdb=" N VAL A 245 " --> pdb=" O GLY A 241 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N PHE A 246 " --> pdb=" O TRP A 242 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 262 " --> pdb=" O MET A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 310 through 331 removed outlier: 4.289A pdb=" N ILE A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A 325 " --> pdb=" O CYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 340 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 354 through 375 Proline residue: A 364 - end of helix Processing helix chain 'A' and resid 381 through 404 removed outlier: 3.526A pdb=" N ARG A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 428 removed outlier: 3.804A pdb=" N GLY A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALA A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 437 removed outlier: 3.697A pdb=" N ILE A 437 " --> pdb=" O HIS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 467 removed outlier: 3.579A pdb=" N LEU A 455 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Proline residue: A 461 - end of helix Processing helix chain 'A' and resid 474 through 496 removed outlier: 3.780A pdb=" N TYR A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' 182 hydrogen bonds defined for protein. 516 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: 0.92 Time building geometry restraints manager: 1.80 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: 1049 1.34 - 1.46: 744 1.46 - 1.57: 1774 1.57 - 1.69: 6 1.69 - 1.81: 44 Bond restraints: 3617 Sorted by residual: bond pdb=" C07 I7Y A 602 " pdb=" C15 I7Y A 602 " ideal model delta sigma weight residual 1.782 1.591 0.191 2.00e-02 2.50e+03 9.08e+01 bond pdb=" C07 I7Y A 602 " pdb=" C08 I7Y A 602 " ideal model delta sigma weight residual 1.323 1.509 -0.186 2.00e-02 2.50e+03 8.60e+01 bond pdb=" C13 I7Y A 602 " pdb=" C14 I7Y A 602 " ideal model delta sigma weight residual 1.582 1.726 -0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" CG1 I7Y A 602 " pdb=" O20 I7Y A 602 " ideal model delta sigma weight residual 1.338 1.475 -0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" C02 I7Y A 602 " pdb=" C10 I7Y A 602 " ideal model delta sigma weight residual 1.327 1.456 -0.129 2.00e-02 2.50e+03 4.13e+01 ... (remaining 3612 not shown) Histogram of bond angle deviations from ideal: 100.24 - 107.01: 130 107.01 - 113.77: 2046 113.77 - 120.54: 1512 120.54 - 127.31: 1199 127.31 - 134.08: 49 Bond angle restraints: 4936 Sorted by residual: angle pdb=" C11 I7Y A 602 " pdb=" C13 I7Y A 602 " pdb=" C16 I7Y A 602 " ideal model delta sigma weight residual 111.25 125.71 -14.46 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C11 I7Y A 602 " pdb=" C13 I7Y A 602 " pdb=" C14 I7Y A 602 " ideal model delta sigma weight residual 123.33 114.97 8.36 3.00e+00 1.11e-01 7.77e+00 angle pdb=" OG1 THR A 138 " pdb=" CB THR A 138 " pdb=" CG2 THR A 138 " ideal model delta sigma weight residual 109.30 104.54 4.76 2.00e+00 2.50e-01 5.66e+00 angle pdb=" C LEU A 262 " pdb=" N VAL A 263 " pdb=" CA VAL A 263 " ideal model delta sigma weight residual 121.97 117.92 4.05 1.80e+00 3.09e-01 5.06e+00 angle pdb=" C14 I7Y A 602 " pdb=" C13 I7Y A 602 " pdb=" C16 I7Y A 602 " ideal model delta sigma weight residual 125.42 118.81 6.61 3.00e+00 1.11e-01 4.85e+00 ... (remaining 4931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.23: 1994 29.23 - 58.45: 53 58.45 - 87.67: 9 87.67 - 116.90: 5 116.90 - 146.12: 2 Dihedral angle restraints: 2063 sinusoidal: 774 harmonic: 1289 Sorted by residual: dihedral pdb=" C1C I7Y A 602 " pdb=" C48 I7Y A 602 " pdb=" O1C I7Y A 602 " pdb=" C23 I7Y A 602 " ideal model delta sinusoidal sigma weight residual 128.87 -85.01 -146.12 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" CA LEU A 232 " pdb=" C LEU A 232 " pdb=" N ALA A 233 " pdb=" CA ALA A 233 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" C11 I7Y A 602 " pdb=" C18 I7Y A 602 " pdb=" C19 I7Y A 602 " pdb=" C17 I7Y A 602 " ideal model delta sinusoidal sigma weight residual 53.13 -65.15 118.28 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 2060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 348 0.040 - 0.080: 162 0.080 - 0.120: 47 0.120 - 0.160: 5 0.160 - 0.200: 2 Chirality restraints: 564 Sorted by residual: chirality pdb=" C02 I7Y A 602 " pdb=" C03 I7Y A 602 " pdb=" C06 I7Y A 602 " pdb=" C10 I7Y A 602 " both_signs ideal model delta sigma weight residual False 2.06 2.26 -0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CA C5B A 601 " pdb=" C C5B A 601 " pdb=" CB1 C5B A 601 " pdb=" CB2 C5B A 601 " both_signs ideal model delta sigma weight residual False -2.96 -2.79 -0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" C11 I7Y A 602 " pdb=" C08 I7Y A 602 " pdb=" C13 I7Y A 602 " pdb=" C19 I7Y A 602 " both_signs ideal model delta sigma weight residual False 2.95 2.81 0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 561 not shown) Planarity restraints: 599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 I7Y A 602 " -0.067 2.00e-02 2.50e+03 2.05e-01 5.23e+02 pdb=" C13 I7Y A 602 " -0.002 2.00e-02 2.50e+03 pdb=" C14 I7Y A 602 " -0.340 2.00e-02 2.50e+03 pdb=" C15 I7Y A 602 " 0.257 2.00e-02 2.50e+03 pdb=" C16 I7Y A 602 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 230 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO A 231 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 310 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.23e+00 pdb=" N PRO A 311 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 311 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 311 " -0.025 5.00e-02 4.00e+02 ... (remaining 596 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 53 2.69 - 3.24: 3572 3.24 - 3.79: 5407 3.79 - 4.35: 7523 4.35 - 4.90: 12492 Nonbonded interactions: 29047 Sorted by model distance: nonbonded pdb=" OG1 THR A 162 " pdb=" OE1 GLN A 187 " model vdw 2.131 2.440 nonbonded pdb=" OH TYR A 327 " pdb=" OZ1 C5B A 601 " model vdw 2.241 2.440 nonbonded pdb=" O SER A 332 " pdb=" OG SER A 332 " model vdw 2.244 2.440 nonbonded pdb=" O PHE A 307 " pdb=" OH TYR A 313 " model vdw 2.348 2.440 nonbonded pdb=" N ARG A 213 " pdb=" OD2 ASP A 371 " model vdw 2.359 2.520 ... (remaining 29042 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=0.00 max=1.00 mean=0.99 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: 3.600 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: 0.000 Extract box with map and model: 13.070 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.790 Find NCS groups from input model: 0.100 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:13.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.009 0.191 3617 Z= 0.604 Angle : 0.729 14.458 4936 Z= 0.362 Chirality : 0.048 0.200 564 Planarity : 0.010 0.205 599 Dihedral : 16.244 146.124 1247 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -3.24 (0.34), residues: 448 helix: -1.57 (0.26), residues: 320 sheet: None (None), residues: 0 loop : -3.35 (0.44), residues: 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.381 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 1.2794 time to fit residues: 88.2537 Evaluate side-chains 51 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 191 GLN A 407 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3617 Z= 0.242 Angle : 0.661 6.994 4936 Z= 0.320 Chirality : 0.044 0.172 564 Planarity : 0.005 0.055 599 Dihedral : 12.981 128.718 546 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.16 % Allowed : 10.76 % Favored : 88.08 % 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: -1.75 (0.38), residues: 448 helix: -0.47 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -2.66 (0.46), residues: 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.355 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 60 average time/residue: 1.1943 time to fit residues: 73.9464 Evaluate side-chains 49 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.5317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 0.0970 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 191 GLN A 368 GLN A 407 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3617 Z= 0.181 Angle : 0.624 7.242 4936 Z= 0.301 Chirality : 0.043 0.199 564 Planarity : 0.005 0.052 599 Dihedral : 9.903 117.013 546 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.03 % Allowed : 12.50 % Favored : 85.47 % 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: -1.16 (0.40), residues: 448 helix: -0.15 (0.30), residues: 328 sheet: None (None), residues: 0 loop : -2.28 (0.51), residues: 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.393 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 61 average time/residue: 1.1601 time to fit residues: 73.1473 Evaluate side-chains 56 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.422 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.5275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 43 optimal weight: 0.0270 chunk 21 optimal weight: 0.4980 chunk 38 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 191 GLN A 407 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3617 Z= 0.170 Angle : 0.598 7.274 4936 Z= 0.292 Chirality : 0.041 0.147 564 Planarity : 0.005 0.048 599 Dihedral : 9.455 100.986 546 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.03 % Allowed : 14.24 % Favored : 83.72 % 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: -0.70 (0.40), residues: 448 helix: 0.21 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -2.09 (0.51), residues: 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.377 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 1.1887 time to fit residues: 73.6747 Evaluate side-chains 58 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.437 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0439 time to fit residues: 0.6011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.0980 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3617 Z= 0.223 Angle : 0.626 7.183 4936 Z= 0.309 Chirality : 0.043 0.143 564 Planarity : 0.005 0.047 599 Dihedral : 8.961 88.986 546 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.33 % Allowed : 15.12 % Favored : 82.56 % 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: -0.64 (0.40), residues: 448 helix: 0.26 (0.30), residues: 323 sheet: None (None), residues: 0 loop : -2.10 (0.50), residues: 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.391 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. outliers start: 8 outliers final: 5 residues processed: 61 average time/residue: 1.2226 time to fit residues: 76.8722 Evaluate side-chains 60 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0377 time to fit residues: 0.5933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 0.0030 chunk 24 optimal weight: 0.0030 chunk 31 optimal weight: 2.9990 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3617 Z= 0.184 Angle : 0.611 7.556 4936 Z= 0.303 Chirality : 0.041 0.145 564 Planarity : 0.005 0.045 599 Dihedral : 8.483 89.942 546 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.03 % Allowed : 15.99 % Favored : 81.98 % 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: -0.42 (0.40), residues: 448 helix: 0.40 (0.30), residues: 323 sheet: None (None), residues: 0 loop : -1.97 (0.51), residues: 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.397 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 1.2200 time to fit residues: 75.5165 Evaluate side-chains 59 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0353 time to fit residues: 0.5472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.0030 chunk 36 optimal weight: 0.5980 chunk 43 optimal weight: 0.0270 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 overall best weight: 0.3448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 368 GLN A 407 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3617 Z= 0.171 Angle : 0.602 8.642 4936 Z= 0.298 Chirality : 0.041 0.144 564 Planarity : 0.005 0.048 599 Dihedral : 8.335 89.615 546 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.45 % Allowed : 16.28 % Favored : 82.27 % 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: -0.24 (0.41), residues: 448 helix: 0.55 (0.31), residues: 323 sheet: None (None), residues: 0 loop : -1.92 (0.50), residues: 125 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.386 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. outliers start: 5 outliers final: 5 residues processed: 58 average time/residue: 1.2629 time to fit residues: 75.5055 Evaluate side-chains 59 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.378 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0368 time to fit residues: 0.5783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.0670 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.0070 chunk 24 optimal weight: 0.0870 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3617 Z= 0.168 Angle : 0.598 8.289 4936 Z= 0.297 Chirality : 0.041 0.143 564 Planarity : 0.005 0.052 599 Dihedral : 8.231 89.458 546 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.74 % Allowed : 15.99 % Favored : 82.27 % 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 (0.41), residues: 448 helix: 0.57 (0.30), residues: 324 sheet: None (None), residues: 0 loop : -1.87 (0.51), residues: 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.406 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. outliers start: 6 outliers final: 3 residues processed: 61 average time/residue: 1.2481 time to fit residues: 78.6075 Evaluate side-chains 57 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.406 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.5213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 368 GLN A 407 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3617 Z= 0.230 Angle : 0.636 8.438 4936 Z= 0.317 Chirality : 0.043 0.140 564 Planarity : 0.005 0.057 599 Dihedral : 8.480 90.243 546 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.16 % Allowed : 16.28 % Favored : 82.56 % 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: -0.27 (0.40), residues: 448 helix: 0.51 (0.30), residues: 323 sheet: None (None), residues: 0 loop : -1.90 (0.50), residues: 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.400 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. outliers start: 4 outliers final: 4 residues processed: 57 average time/residue: 1.3209 time to fit residues: 77.6395 Evaluate side-chains 56 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0466 time to fit residues: 0.6139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3617 Z= 0.208 Angle : 0.628 8.323 4936 Z= 0.313 Chirality : 0.043 0.142 564 Planarity : 0.005 0.061 599 Dihedral : 8.428 89.964 546 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.87 % Allowed : 16.86 % Favored : 82.27 % 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 (0.41), residues: 448 helix: 0.56 (0.30), residues: 323 sheet: None (None), residues: 0 loop : -1.81 (0.51), residues: 125 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.392 Fit side-chains TARDY: cannot create tardy model for: "PHE A 65 " (corrupted residue). Skipping it. outliers start: 3 outliers final: 3 residues processed: 56 average time/residue: 1.3637 time to fit residues: 78.8529 Evaluate side-chains 55 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.598 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.7482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 0.0570 chunk 31 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 0.0270 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.146695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121129 restraints weight = 9321.427| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.02 r_work: 0.3276 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3617 Z= 0.179 Angle : 0.611 8.228 4936 Z= 0.306 Chirality : 0.042 0.143 564 Planarity : 0.005 0.062 599 Dihedral : 8.294 89.639 546 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.87 % Allowed : 17.15 % Favored : 81.98 % 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 (0.41), residues: 448 helix: 0.65 (0.31), residues: 323 sheet: None (None), residues: 0 loop : -1.75 (0.51), residues: 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1978.60 seconds wall clock time: 35 minutes 51.86 seconds (2151.86 seconds total)