Starting phenix.real_space_refine on Sun Dec 29 19:48:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qpc_14117/12_2024/7qpc_14117_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qpc_14117/12_2024/7qpc_14117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qpc_14117/12_2024/7qpc_14117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qpc_14117/12_2024/7qpc_14117.map" model { file = "/net/cci-nas-00/data/ceres_data/7qpc_14117/12_2024/7qpc_14117_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qpc_14117/12_2024/7qpc_14117_trim.cif" } resolution = 3.44 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= 0.040 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 34 5.16 5 C 3524 2.51 5 N 804 2.21 5 O 926 1.98 5 H 5540 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10830 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5246 Classifications: {'peptide': 327} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "B" Number of atoms: 5246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5246 Classifications: {'peptide': 327} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'DLP': 1, 'E7O': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'DLP': 1, 'E7O': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 96 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 90 Classifications: {'water': 30} Link IDs: {None: 29} Time building chain proxies: 5.82, per 1000 atoms: 0.54 Number of scatterers: 10830 At special positions: 0 Unit cell: (91.874, 90.58, 68.582, 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 34 16.00 P 2 15.00 O 926 8.00 N 804 7.00 C 3524 6.00 H 5540 1.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 724.9 milliseconds 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1216 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 85.3% 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 3 through 29 Proline residue: A 16 - end of helix removed outlier: 3.924A pdb=" N MET A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY A 24 " --> pdb=" O SER A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 60 removed outlier: 4.693A pdb=" N ILE A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 63 through 67 Processing helix chain 'A' and resid 68 through 93 removed outlier: 3.592A pdb=" N ILE A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 122 through 148 removed outlier: 6.931A pdb=" N ASP A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N GLU A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLN A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 removed outlier: 3.544A pdb=" N LEU A 154 " --> pdb=" O TYR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 220 removed outlier: 3.677A pdb=" N ILE A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 240 removed outlier: 3.738A pdb=" N TYR A 225 " --> pdb=" O ASN A 221 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.844A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 274 removed outlier: 3.595A pdb=" N GLN A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 294 through 308 Processing helix chain 'A' and resid 313 through 322 Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.502A pdb=" N ILE A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 366 removed outlier: 3.593A pdb=" N THR A 357 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 30 Proline residue: B 16 - end of helix removed outlier: 3.934A pdb=" N MET B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 60 removed outlier: 4.956A pdb=" N ILE B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Proline residue: B 52 - end of helix Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 68 through 91 removed outlier: 3.879A pdb=" N VAL B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 Processing helix chain 'B' and resid 122 through 164 removed outlier: 6.877A pdb=" N ASP B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N GLU B 133 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA B 135 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN B 140 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TRP B 149 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TYR B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 152 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 220 removed outlier: 3.709A pdb=" N ILE B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 240 removed outlier: 3.579A pdb=" N TYR B 225 " --> pdb=" O ASN B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 257 removed outlier: 3.869A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 274 removed outlier: 3.505A pdb=" N GLN B 274 " --> pdb=" O PHE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.602A pdb=" N ILE B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 288 " --> pdb=" O MET B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 308 Processing helix chain 'B' and resid 313 through 322 Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 339 through 353 Processing helix chain 'B' and resid 353 through 366 removed outlier: 3.600A pdb=" N ASP B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.15 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5534 1.03 - 1.23: 12 1.23 - 1.42: 2108 1.42 - 1.62: 3176 1.62 - 1.81: 62 Bond restraints: 10892 Sorted by residual: bond pdb=" C12 E7O A 401 " pdb=" N11 E7O A 401 " ideal model delta sigma weight residual 1.347 1.459 -0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C12 E7O B 401 " pdb=" N11 E7O B 401 " ideal model delta sigma weight residual 1.347 1.458 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C10 E7O B 401 " pdb=" N11 E7O B 401 " ideal model delta sigma weight residual 1.399 1.461 -0.062 2.00e-02 2.50e+03 9.58e+00 bond pdb=" C10 E7O A 401 " pdb=" N11 E7O A 401 " ideal model delta sigma weight residual 1.399 1.459 -0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" O4P DLP A 402 " pdb=" P DLP A 402 " ideal model delta sigma weight residual 1.649 1.596 0.053 2.00e-02 2.50e+03 7.13e+00 ... (remaining 10887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 19399 2.13 - 4.27: 190 4.27 - 6.40: 18 6.40 - 8.53: 1 8.53 - 10.66: 2 Bond angle restraints: 19610 Sorted by residual: angle pdb=" N LEU A 313 " pdb=" CA LEU A 313 " pdb=" C LEU A 313 " ideal model delta sigma weight residual 114.04 109.16 4.88 1.24e+00 6.50e-01 1.55e+01 angle pdb=" N ILE A 137 " pdb=" CA ILE A 137 " pdb=" C ILE A 137 " ideal model delta sigma weight residual 111.81 108.61 3.20 8.60e-01 1.35e+00 1.39e+01 angle pdb=" O3P DLP A 402 " pdb=" P DLP A 402 " pdb=" O4P DLP A 402 " ideal model delta sigma weight residual 93.58 104.24 -10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" O3P DLP B 402 " pdb=" P DLP B 402 " pdb=" O4P DLP B 402 " ideal model delta sigma weight residual 93.58 104.24 -10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" C VAL B 328 " pdb=" CA VAL B 328 " pdb=" CB VAL B 328 " ideal model delta sigma weight residual 114.35 111.05 3.30 1.06e+00 8.90e-01 9.72e+00 ... (remaining 19605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.78: 4619 20.78 - 41.56: 315 41.56 - 62.35: 104 62.35 - 83.13: 4 83.13 - 103.91: 2 Dihedral angle restraints: 5044 sinusoidal: 2776 harmonic: 2268 Sorted by residual: dihedral pdb=" CA THR B 108 " pdb=" C THR B 108 " pdb=" N GLY B 109 " pdb=" CA GLY B 109 " ideal model delta harmonic sigma weight residual 180.00 157.52 22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" N DLP B 402 " pdb=" C4 DLP B 402 " pdb=" C5 DLP B 402 " pdb=" O4P DLP B 402 " ideal model delta sinusoidal sigma weight residual -71.05 -174.96 103.91 1 3.00e+01 1.11e-03 1.32e+01 dihedral pdb=" N DLP A 402 " pdb=" C4 DLP A 402 " pdb=" C5 DLP A 402 " pdb=" O4P DLP A 402 " ideal model delta sinusoidal sigma weight residual -71.05 -174.81 103.76 1 3.00e+01 1.11e-03 1.32e+01 ... (remaining 5041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 690 0.041 - 0.083: 141 0.083 - 0.124: 29 0.124 - 0.165: 0 0.165 - 0.207: 2 Chirality restraints: 862 Sorted by residual: chirality pdb=" C2 DLP A 402 " pdb=" C1 DLP A 402 " pdb=" C3 DLP A 402 " pdb=" O2 DLP A 402 " both_signs ideal model delta sigma weight residual False -2.35 -2.56 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C2 DLP B 402 " pdb=" C1 DLP B 402 " pdb=" C3 DLP B 402 " pdb=" O2 DLP B 402 " both_signs ideal model delta sigma weight residual False -2.35 -2.56 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE A 2 " pdb=" N ILE A 2 " pdb=" C ILE A 2 " pdb=" CB ILE A 2 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.16e-01 ... (remaining 859 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 355 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO B 356 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 356 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 356 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 46 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C VAL A 46 " 0.023 2.00e-02 2.50e+03 pdb=" O VAL A 46 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA A 47 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 291 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C LEU B 291 " 0.023 2.00e-02 2.50e+03 pdb=" O LEU B 291 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS B 292 " -0.008 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 1390 2.26 - 2.84: 24759 2.84 - 3.43: 28901 3.43 - 4.01: 39628 4.01 - 4.60: 61268 Nonbonded interactions: 155946 Sorted by model distance: nonbonded pdb=" OE2 GLU B 158 " pdb=" HH TYR B 336 " model vdw 1.671 2.450 nonbonded pdb=" H SER A 35 " pdb=" OE1 GLN A 38 " model vdw 1.695 2.450 nonbonded pdb="HD22 ASN B 62 " pdb=" OE1 GLU B 139 " model vdw 1.713 2.450 nonbonded pdb=" O SER A 50 " pdb=" H LEU A 54 " model vdw 1.728 2.450 nonbonded pdb=" H ASN B 117 " pdb=" O PRO B 324 " model vdw 1.729 2.450 ... (remaining 155941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 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: 0.170 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.480 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 5352 Z= 0.296 Angle : 0.624 10.663 7252 Z= 0.303 Chirality : 0.036 0.207 862 Planarity : 0.003 0.035 858 Dihedral : 15.004 103.909 1948 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.61 (0.35), residues: 646 helix: 1.58 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -1.06 (0.54), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 233 HIS 0.001 0.000 HIS A 94 PHE 0.007 0.001 PHE B 330 TYR 0.005 0.001 TYR B 305 ARG 0.007 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.4166 time to fit residues: 58.5432 Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5352 Z= 0.229 Angle : 0.547 4.795 7252 Z= 0.285 Chirality : 0.036 0.125 862 Planarity : 0.004 0.039 858 Dihedral : 10.781 107.829 784 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.36 % Allowed : 5.78 % Favored : 93.86 % 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 (0.34), residues: 646 helix: 1.55 (0.24), residues: 520 sheet: None (None), residues: 0 loop : -1.42 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 93 HIS 0.006 0.001 HIS B 339 PHE 0.010 0.001 PHE A 314 TYR 0.009 0.001 TYR A 362 ARG 0.001 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 104 average time/residue: 0.3813 time to fit residues: 52.0970 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 57 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5352 Z= 0.184 Angle : 0.517 4.665 7252 Z= 0.266 Chirality : 0.035 0.126 862 Planarity : 0.004 0.040 858 Dihedral : 10.600 100.731 784 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.54 % Allowed : 6.68 % Favored : 92.78 % 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: 1.52 (0.34), residues: 646 helix: 1.61 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -1.55 (0.53), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.003 0.001 HIS B 339 PHE 0.010 0.001 PHE A 314 TYR 0.008 0.001 TYR A 362 ARG 0.002 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 ASN cc_start: 0.6976 (m110) cc_final: 0.6295 (m110) outliers start: 3 outliers final: 2 residues processed: 102 average time/residue: 0.3798 time to fit residues: 51.0780 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 0.0010 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5352 Z= 0.182 Angle : 0.517 4.601 7252 Z= 0.266 Chirality : 0.035 0.133 862 Planarity : 0.004 0.042 858 Dihedral : 10.349 94.922 784 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.36 % Allowed : 8.66 % Favored : 90.97 % 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: 1.50 (0.34), residues: 646 helix: 1.60 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.55 (0.53), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.003 0.001 HIS B 339 PHE 0.010 0.001 PHE B 330 TYR 0.007 0.001 TYR A 362 ARG 0.003 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 0.3866 time to fit residues: 53.6371 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5352 Z= 0.235 Angle : 0.537 4.690 7252 Z= 0.277 Chirality : 0.036 0.150 862 Planarity : 0.004 0.043 858 Dihedral : 10.308 89.754 784 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.36 % Allowed : 10.11 % Favored : 89.53 % 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: 1.38 (0.34), residues: 646 helix: 1.51 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.57 (0.53), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.002 0.001 HIS B 339 PHE 0.010 0.001 PHE B 330 TYR 0.007 0.001 TYR A 362 ARG 0.004 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8479 (mm) cc_final: 0.8115 (mm) REVERT: B 139 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6623 (tt0) outliers start: 2 outliers final: 1 residues processed: 105 average time/residue: 0.3657 time to fit residues: 50.2565 Evaluate side-chains 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 139 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 0.0040 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5352 Z= 0.181 Angle : 0.518 4.411 7252 Z= 0.266 Chirality : 0.035 0.151 862 Planarity : 0.004 0.042 858 Dihedral : 10.098 88.197 784 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.36 % Allowed : 12.09 % Favored : 87.55 % 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: 1.47 (0.34), residues: 646 helix: 1.61 (0.24), residues: 518 sheet: None (None), residues: 0 loop : -1.67 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.002 0.001 HIS B 339 PHE 0.010 0.001 PHE B 330 TYR 0.006 0.001 TYR A 362 ARG 0.005 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 284 MET cc_start: 0.7279 (mmm) cc_final: 0.7064 (mmm) outliers start: 2 outliers final: 1 residues processed: 102 average time/residue: 0.3717 time to fit residues: 49.7657 Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.0770 chunk 28 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 18 optimal weight: 0.0020 overall best weight: 0.3546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5352 Z= 0.151 Angle : 0.510 4.624 7252 Z= 0.261 Chirality : 0.035 0.140 862 Planarity : 0.004 0.042 858 Dihedral : 9.799 86.527 784 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.18 % Allowed : 12.45 % Favored : 87.36 % 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: 1.58 (0.34), residues: 646 helix: 1.70 (0.24), residues: 518 sheet: None (None), residues: 0 loop : -1.68 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.002 0.000 HIS B 339 PHE 0.010 0.001 PHE B 330 TYR 0.005 0.001 TYR A 361 ARG 0.005 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 284 MET cc_start: 0.7384 (mmm) cc_final: 0.7179 (mmm) outliers start: 1 outliers final: 1 residues processed: 101 average time/residue: 0.3753 time to fit residues: 50.3767 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 0.0170 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5352 Z= 0.183 Angle : 0.516 4.482 7252 Z= 0.264 Chirality : 0.035 0.128 862 Planarity : 0.004 0.042 858 Dihedral : 9.733 85.493 784 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.36 % Allowed : 12.64 % Favored : 87.00 % 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: 1.56 (0.34), residues: 646 helix: 1.69 (0.24), residues: 518 sheet: None (None), residues: 0 loop : -1.69 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.002 0.000 HIS B 237 PHE 0.009 0.001 PHE B 330 TYR 0.005 0.001 TYR A 361 ARG 0.006 0.001 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8460 (mm) cc_final: 0.8092 (mm) REVERT: B 284 MET cc_start: 0.7401 (mmm) cc_final: 0.7198 (mmm) outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.4027 time to fit residues: 52.8203 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 28 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5352 Z= 0.203 Angle : 0.534 4.519 7252 Z= 0.274 Chirality : 0.036 0.126 862 Planarity : 0.004 0.040 858 Dihedral : 9.744 84.644 784 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.18 % Allowed : 13.18 % Favored : 86.64 % 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: 1.49 (0.34), residues: 646 helix: 1.64 (0.24), residues: 518 sheet: None (None), residues: 0 loop : -1.71 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.002 0.000 HIS B 237 PHE 0.009 0.001 PHE B 330 TYR 0.008 0.001 TYR B 361 ARG 0.006 0.001 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8517 (mm) cc_final: 0.8154 (mm) REVERT: B 284 MET cc_start: 0.7421 (mmm) cc_final: 0.7219 (mmm) outliers start: 1 outliers final: 1 residues processed: 97 average time/residue: 0.3363 time to fit residues: 43.8039 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5352 Z= 0.182 Angle : 0.526 4.576 7252 Z= 0.269 Chirality : 0.035 0.126 862 Planarity : 0.004 0.040 858 Dihedral : 9.631 83.386 784 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.36 % Allowed : 13.18 % Favored : 86.46 % 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: 1.52 (0.34), residues: 646 helix: 1.66 (0.24), residues: 518 sheet: None (None), residues: 0 loop : -1.68 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 93 HIS 0.002 0.000 HIS B 237 PHE 0.009 0.001 PHE B 330 TYR 0.005 0.001 TYR A 361 ARG 0.006 0.001 ARG B 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8481 (mm) cc_final: 0.8119 (mm) outliers start: 2 outliers final: 1 residues processed: 98 average time/residue: 0.3622 time to fit residues: 46.7540 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 0.0370 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.122857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.105179 restraints weight = 18746.097| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.60 r_work: 0.2988 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5352 Z= 0.179 Angle : 0.527 5.072 7252 Z= 0.268 Chirality : 0.035 0.126 862 Planarity : 0.004 0.039 858 Dihedral : 9.554 82.426 784 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.18 % Allowed : 13.72 % Favored : 86.10 % 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: 1.56 (0.34), residues: 646 helix: 1.66 (0.24), residues: 520 sheet: None (None), residues: 0 loop : -1.59 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.002 0.000 HIS B 237 PHE 0.009 0.001 PHE B 330 TYR 0.008 0.001 TYR B 361 ARG 0.005 0.000 ARG A 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3081.07 seconds wall clock time: 55 minutes 55.34 seconds (3355.34 seconds total)