Starting phenix.real_space_refine on Fri Mar 15 07:18:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpc_14117/03_2024/7qpc_14117_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpc_14117/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpc_14117/03_2024/7qpc_14117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpc_14117/03_2024/7qpc_14117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpc_14117/03_2024/7qpc_14117_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qpc_14117/03_2024/7qpc_14117_trim_updated.pdb" } 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 Residue "A TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.51, per 1000 atoms: 0.51 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 - 3.50 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: 8.93 Conformation dependent library (CDL) restraints added in 1.3 seconds 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... running ksdssp... Secondary structure from input PDB file: 34 helices and 0 sheets defined 75.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 4 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 36 through 59 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 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 69 through 92 removed outlier: 3.847A pdb=" N VAL A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 134 through 147 removed outlier: 4.087A pdb=" N LEU A 138 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLU A 139 " --> pdb=" O SER A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 163 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 219 Processing helix chain 'A' and resid 222 through 239 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 246 through 256 removed outlier: 3.844A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 282 through 307 removed outlier: 4.074A pdb=" N GLY A 296 " --> pdb=" O LYS A 292 " (cutoff:3.500A) Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 314 through 321 Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 340 through 352 Processing helix chain 'A' and resid 354 through 366 removed outlier: 3.768A pdb=" N ALA A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 29 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 36 through 59 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 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 69 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 102 through 108 Processing helix chain 'B' and resid 123 through 130 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 138 through 147 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) Processing helix chain 'B' and resid 149 through 163 Processing helix chain 'B' and resid 207 through 219 Processing helix chain 'B' and resid 222 through 239 Processing helix chain 'B' and resid 246 through 256 removed outlier: 3.869A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 273 Processing helix chain 'B' and resid 282 through 307 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) removed outlier: 3.998A pdb=" N GLY B 296 " --> pdb=" O LYS B 292 " (cutoff:3.500A) Proline residue: B 297 - end of helix Processing helix chain 'B' and resid 314 through 321 Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 340 through 366 removed outlier: 5.225A pdb=" N LEU B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) Proline residue: B 356 - end of helix removed outlier: 3.600A pdb=" N ASP B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) 314 hydrogen bonds defined for protein. 915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.77 Time building geometry restraints manager: 9.32 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: 99.85 - 106.68: 183 106.68 - 113.50: 13191 113.50 - 120.32: 3403 120.32 - 127.15: 2760 127.15 - 133.97: 73 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: 1432 2.26 - 2.84: 24792 2.84 - 3.43: 28940 3.43 - 4.01: 39719 4.01 - 4.60: 61321 Nonbonded interactions: 156204 Sorted by model distance: nonbonded pdb=" OE2 GLU B 158 " pdb=" HH TYR B 336 " model vdw 1.671 1.850 nonbonded pdb=" O LEU A 138 " pdb=" H VAL A 142 " model vdw 1.677 1.850 nonbonded pdb=" H SER A 35 " pdb=" OE1 GLN A 38 " model vdw 1.695 1.850 nonbonded pdb="HD22 ASN B 62 " pdb=" OE1 GLU B 139 " model vdw 1.713 1.850 nonbonded pdb=" O SER A 50 " pdb=" H LEU A 54 " model vdw 1.728 1.850 ... (remaining 156199 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.460 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: 2.500 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 38.770 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 45.280 ------------------------------------------------------------------------------- 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= 0.263 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 fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3861 time to fit residues: 54.2079 Evaluate side-chains 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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: 0.9990 chunk 50 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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: 0.7766 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5352 Z= 0.254 Angle : 0.540 4.725 7252 Z= 0.278 Chirality : 0.036 0.121 862 Planarity : 0.004 0.043 858 Dihedral : 10.761 107.433 784 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.36 % Allowed : 5.42 % Favored : 94.22 % 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: 1.42 (0.35), residues: 646 helix: 1.55 (0.24), residues: 516 sheet: None (None), residues: 0 loop : -1.49 (0.52), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.002 0.001 HIS B 9 PHE 0.010 0.001 PHE B 45 TYR 0.009 0.001 TYR A 362 ARG 0.002 0.000 ARG A 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 fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 ASN cc_start: 0.7184 (m110) cc_final: 0.6902 (m110) outliers start: 2 outliers final: 2 residues processed: 104 average time/residue: 0.4112 time to fit residues: 54.6025 Evaluate side-chains 101 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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: 1.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7767 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5352 Z= 0.205 Angle : 0.511 4.323 7252 Z= 0.261 Chirality : 0.035 0.117 862 Planarity : 0.004 0.041 858 Dihedral : 10.606 98.639 784 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.36 % Allowed : 7.22 % Favored : 92.42 % 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 (0.35), residues: 646 helix: 1.56 (0.24), residues: 514 sheet: None (None), residues: 0 loop : -1.32 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.002 0.001 HIS B 9 PHE 0.008 0.001 PHE A 314 TYR 0.008 0.001 TYR A 362 ARG 0.003 0.000 ARG B 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 107 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 106 average time/residue: 0.4156 time to fit residues: 55.9159 Evaluate side-chains 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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: 1.9990 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7787 moved from start: 0.0998 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= 0.237 Angle : 0.516 4.405 7252 Z= 0.266 Chirality : 0.035 0.118 862 Planarity : 0.004 0.040 858 Dihedral : 10.479 93.206 784 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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: 1.35 (0.34), residues: 646 helix: 1.48 (0.24), residues: 512 sheet: None (None), residues: 0 loop : -1.34 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.002 0.001 HIS B 9 PHE 0.008 0.001 PHE A 330 TYR 0.007 0.001 TYR A 362 ARG 0.003 0.000 ARG A 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 106 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8465 (mm) cc_final: 0.8128 (mm) outliers start: 2 outliers final: 2 residues processed: 105 average time/residue: 0.4155 time to fit residues: 56.1625 Evaluate side-chains 100 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE 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: 0.9990 chunk 25 optimal weight: 0.9990 chunk 52 optimal weight: 0.0070 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- 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: 0.7783 moved from start: 0.1093 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= 0.201 Angle : 0.509 4.341 7252 Z= 0.261 Chirality : 0.035 0.116 862 Planarity : 0.004 0.039 858 Dihedral : 10.389 89.741 784 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.54 % Allowed : 10.11 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.34), residues: 646 helix: 1.49 (0.24), residues: 512 sheet: None (None), residues: 0 loop : -1.30 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 233 HIS 0.001 0.000 HIS B 9 PHE 0.009 0.001 PHE B 330 TYR 0.006 0.001 TYR A 362 ARG 0.003 0.000 ARG A 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 109 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8426 (mm) cc_final: 0.8095 (mm) outliers start: 3 outliers final: 2 residues processed: 107 average time/residue: 0.4023 time to fit residues: 55.1396 Evaluate side-chains 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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: 0.7800 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5352 Z= 0.245 Angle : 0.525 4.618 7252 Z= 0.271 Chirality : 0.036 0.116 862 Planarity : 0.004 0.041 858 Dihedral : 10.430 89.037 784 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.54 % Allowed : 11.73 % Favored : 87.73 % 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: 1.25 (0.34), residues: 646 helix: 1.41 (0.24), residues: 512 sheet: None (None), residues: 0 loop : -1.35 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 233 HIS 0.002 0.000 HIS B 9 PHE 0.009 0.001 PHE A 330 TYR 0.006 0.001 TYR A 362 ARG 0.004 0.000 ARG A 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 103 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8514 (mm) cc_final: 0.8159 (mm) REVERT: B 284 MET cc_start: 0.7256 (mmm) cc_final: 0.7054 (mmm) outliers start: 3 outliers final: 2 residues processed: 101 average time/residue: 0.3853 time to fit residues: 50.0210 Evaluate side-chains 101 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE 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: 0.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.7789 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5352 Z= 0.195 Angle : 0.515 4.492 7252 Z= 0.265 Chirality : 0.035 0.116 862 Planarity : 0.004 0.040 858 Dihedral : 10.287 87.280 784 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.54 % Allowed : 12.09 % 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: 1.32 (0.35), residues: 646 helix: 1.45 (0.24), residues: 512 sheet: None (None), residues: 0 loop : -1.30 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 233 HIS 0.001 0.000 HIS B 237 PHE 0.009 0.001 PHE B 330 TYR 0.005 0.001 TYR A 362 ARG 0.005 0.000 ARG B 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 107 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8468 (mm) cc_final: 0.8105 (mm) REVERT: B 284 MET cc_start: 0.7194 (mmm) cc_final: 0.6987 (mmm) outliers start: 3 outliers final: 2 residues processed: 106 average time/residue: 0.4094 time to fit residues: 55.1137 Evaluate side-chains 103 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE 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: 0.9990 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.7799 moved from start: 0.1302 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= 0.226 Angle : 0.524 4.511 7252 Z= 0.270 Chirality : 0.035 0.116 862 Planarity : 0.004 0.040 858 Dihedral : 10.229 85.613 784 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.18 % Allowed : 12.27 % 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: 1.25 (0.35), residues: 646 helix: 1.40 (0.24), residues: 512 sheet: None (None), residues: 0 loop : -1.33 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 233 HIS 0.001 0.000 HIS B 237 PHE 0.009 0.001 PHE B 330 TYR 0.006 0.001 TYR A 362 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 103 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8532 (mm) cc_final: 0.8188 (mm) outliers start: 1 outliers final: 1 residues processed: 103 average time/residue: 0.4172 time to fit residues: 55.2644 Evaluate side-chains 100 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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: 0.7980 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 chunk 60 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7787 moved from start: 0.1307 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 : 0.514 4.818 7252 Z= 0.262 Chirality : 0.035 0.116 862 Planarity : 0.004 0.039 858 Dihedral : 10.047 84.300 784 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.18 % Allowed : 12.64 % Favored : 87.18 % 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: 1.35 (0.35), residues: 646 helix: 1.48 (0.24), residues: 512 sheet: None (None), residues: 0 loop : -1.31 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 233 HIS 0.001 0.000 HIS B 237 PHE 0.010 0.001 PHE B 330 TYR 0.005 0.001 TYR A 361 ARG 0.006 0.000 ARG B 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 99 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8500 (mm) cc_final: 0.8135 (mm) REVERT: B 262 MET cc_start: 0.7741 (ttt) cc_final: 0.7464 (ttt) outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.4196 time to fit residues: 52.5689 Evaluate side-chains 98 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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: 0.7980 chunk 63 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7792 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5352 Z= 0.194 Angle : 0.521 4.943 7252 Z= 0.266 Chirality : 0.035 0.115 862 Planarity : 0.004 0.039 858 Dihedral : 9.983 83.306 784 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.18 % Allowed : 12.82 % 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: 1.35 (0.35), residues: 646 helix: 1.48 (0.24), residues: 512 sheet: None (None), residues: 0 loop : -1.33 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 233 HIS 0.001 0.000 HIS B 237 PHE 0.009 0.001 PHE B 330 TYR 0.005 0.001 TYR A 361 ARG 0.006 0.000 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 98 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8481 (mm) cc_final: 0.8132 (mm) REVERT: B 262 MET cc_start: 0.7576 (ttt) cc_final: 0.7276 (ttt) outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.4031 time to fit residues: 50.7129 Evaluate side-chains 96 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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: 0.4980 chunk 14 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3292 r_free = 0.3292 target = 0.120674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.103689 restraints weight = 18840.061| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.53 r_work: 0.2970 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5352 Z= 0.219 Angle : 0.528 5.039 7252 Z= 0.270 Chirality : 0.035 0.117 862 Planarity : 0.004 0.039 858 Dihedral : 10.012 82.663 784 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.18 % Allowed : 13.00 % Favored : 86.82 % 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: 1.29 (0.35), residues: 646 helix: 1.44 (0.24), residues: 512 sheet: None (None), residues: 0 loop : -1.33 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.001 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3174.45 seconds wall clock time: 56 minutes 19.73 seconds (3379.73 seconds total)