Starting phenix.real_space_refine on Tue Jun 10 11:52:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qp9_14115/06_2025/7qp9_14115_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qp9_14115/06_2025/7qp9_14115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qp9_14115/06_2025/7qp9_14115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qp9_14115/06_2025/7qp9_14115.map" model { file = "/net/cci-nas-00/data/ceres_data/7qp9_14115/06_2025/7qp9_14115_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qp9_14115/06_2025/7qp9_14115_trim.cif" } resolution = 2.89 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 34 5.16 5 C 3576 2.51 5 N 804 2.21 5 O 1001 1.98 5 H 5668 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11087 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5245 Classifications: {'peptide': 327} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "B" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5245 Classifications: {'peptide': 327} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'DLP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'DLP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 198 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "B" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 183 Classifications: {'water': 61} Link IDs: {None: 60} Time building chain proxies: 6.39, per 1000 atoms: 0.58 Number of scatterers: 11087 At special positions: 0 Unit cell: (89.933, 88.639, 64.053, 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 4 15.00 O 1001 8.00 N 804 7.00 C 3576 6.00 H 5668 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: 3.02 Conformation dependent library (CDL) restraints added in 733.1 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: 34 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 5 through 30 Proline residue: A 16 - end of helix Processing helix chain 'A' and resid 35 through 49 Processing helix chain 'A' and resid 49 through 61 Processing helix chain 'A' and resid 63 through 67 removed outlier: 3.805A pdb=" N MET A 67 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 91 Processing helix chain 'A' and resid 101 through 114 Processing helix chain 'A' and resid 121 through 130 removed outlier: 4.457A pdb=" N ILE A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 164 removed outlier: 4.010A pdb=" N ALA A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TYR A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 219 Processing helix chain 'A' and resid 221 through 241 removed outlier: 3.670A pdb=" N TYR A 225 " --> pdb=" O ASN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.675A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 273 removed outlier: 3.761A pdb=" N SER A 273 " --> pdb=" O LEU A 269 " (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 310 through 321 removed outlier: 3.842A pdb=" N ALA A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.563A pdb=" N ILE A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 353 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU A 355 " --> pdb=" O MET A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'B' and resid 5 through 30 Proline residue: B 16 - end of helix Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 49 through 61 removed outlier: 3.535A pdb=" N GLU B 61 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 93 removed outlier: 3.760A pdb=" N PHE B 92 " --> pdb=" O MET B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.658A pdb=" N GLY B 97 " --> pdb=" O HIS B 94 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY B 98 " --> pdb=" O PRO B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 98' Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 121 through 130 removed outlier: 4.427A pdb=" N ILE B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 164 removed outlier: 3.987A pdb=" N ALA B 135 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TYR B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N THR B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 164 " --> pdb=" O ASN B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 219 Processing helix chain 'B' and resid 221 through 241 removed outlier: 3.709A pdb=" N TYR B 225 " --> pdb=" O ASN B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 257 removed outlier: 3.672A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 273 removed outlier: 3.756A pdb=" N SER B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 294 through 308 Processing helix chain 'B' and resid 310 through 321 removed outlier: 3.518A pdb=" N PHE B 314 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 339 through 367 removed outlier: 3.528A pdb=" N ILE B 343 " --> pdb=" O HIS B 339 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 353 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) Proline residue: B 356 - end of helix 391 hydrogen bonds defined for protein. 1170 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: 3.82 Time building geometry restraints manager: 3.56 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: 5662 1.03 - 1.23: 15 1.23 - 1.42: 2081 1.42 - 1.61: 3258 1.61 - 1.81: 62 Bond restraints: 11078 Sorted by residual: bond pdb=" O4P DLP B 501 " pdb=" P DLP B 501 " ideal model delta sigma weight residual 1.649 1.595 0.054 2.00e-02 2.50e+03 7.39e+00 bond pdb=" O4P DLP A 502 " pdb=" P DLP A 502 " ideal model delta sigma weight residual 1.649 1.595 0.054 2.00e-02 2.50e+03 7.25e+00 bond pdb=" O4P DLP A 501 " pdb=" P DLP A 501 " ideal model delta sigma weight residual 1.649 1.596 0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" O4P DLP B 502 " pdb=" P DLP B 502 " ideal model delta sigma weight residual 1.649 1.596 0.053 2.00e-02 2.50e+03 7.05e+00 bond pdb=" C4 DLP A 502 " pdb=" O4P DLP A 502 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 4.08e+00 ... (remaining 11073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 19493 2.32 - 4.64: 220 4.64 - 6.96: 10 6.96 - 9.28: 0 9.28 - 11.60: 4 Bond angle restraints: 19727 Sorted by residual: angle pdb=" O3P DLP B 502 " pdb=" P DLP B 502 " pdb=" O4P DLP B 502 " ideal model delta sigma weight residual 93.58 105.18 -11.60 3.00e+00 1.11e-01 1.50e+01 angle pdb=" O3P DLP A 502 " pdb=" P DLP A 502 " pdb=" O4P DLP A 502 " ideal model delta sigma weight residual 93.58 105.17 -11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" O3P DLP B 501 " pdb=" P DLP B 501 " pdb=" O4P DLP B 501 " ideal model delta sigma weight residual 93.58 103.98 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" O3P DLP A 501 " pdb=" P DLP A 501 " pdb=" O4P DLP A 501 " ideal model delta sigma weight residual 93.58 103.90 -10.32 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C1 DLP B 501 " pdb=" C2 DLP B 501 " pdb=" O2 DLP B 501 " ideal model delta sigma weight residual 111.29 105.02 6.27 3.00e+00 1.11e-01 4.37e+00 ... (remaining 19722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 4754 23.43 - 46.85: 268 46.85 - 70.28: 72 70.28 - 93.70: 16 93.70 - 117.13: 2 Dihedral angle restraints: 5112 sinusoidal: 2846 harmonic: 2266 Sorted by residual: dihedral pdb=" CA SER B 113 " pdb=" C SER B 113 " pdb=" N VAL B 114 " pdb=" CA VAL B 114 " ideal model delta harmonic sigma weight residual 180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA SER A 113 " pdb=" C SER A 113 " pdb=" N VAL A 114 " pdb=" CA VAL A 114 " ideal model delta harmonic sigma weight residual 180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" N DLP B 501 " pdb=" C4 DLP B 501 " pdb=" C5 DLP B 501 " pdb=" O4P DLP B 501 " ideal model delta sinusoidal sigma weight residual 288.95 171.82 117.13 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 5109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 744 0.056 - 0.111: 113 0.111 - 0.167: 3 0.167 - 0.223: 2 0.223 - 0.278: 2 Chirality restraints: 864 Sorted by residual: chirality pdb=" C2 DLP A 501 " pdb=" C1 DLP A 501 " pdb=" C3 DLP A 501 " pdb=" O2 DLP A 501 " both_signs ideal model delta sigma weight residual False -2.35 -2.63 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C2 DLP B 501 " pdb=" C1 DLP B 501 " pdb=" C3 DLP B 501 " pdb=" O2 DLP B 501 " both_signs ideal model delta sigma weight residual False -2.35 -2.63 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C2 DLP B 502 " pdb=" C1 DLP B 502 " pdb=" C3 DLP B 502 " pdb=" O2 DLP B 502 " both_signs ideal model delta sigma weight residual False -2.35 -2.57 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 861 not shown) Planarity restraints: 1482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 145 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C GLN A 145 " -0.024 2.00e-02 2.50e+03 pdb=" O GLN A 145 " 0.009 2.00e-02 2.50e+03 pdb=" N SER A 146 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 145 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.81e+00 pdb=" C GLN B 145 " 0.023 2.00e-02 2.50e+03 pdb=" O GLN B 145 " -0.009 2.00e-02 2.50e+03 pdb=" N SER B 146 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 15 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO B 16 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 16 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 16 " 0.016 5.00e-02 4.00e+02 ... (remaining 1479 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 929 2.22 - 2.82: 24185 2.82 - 3.41: 31632 3.41 - 4.01: 43690 4.01 - 4.60: 67762 Nonbonded interactions: 168198 Sorted by model distance: nonbonded pdb=" HD1 HIS A 237 " pdb=" O TRP A 242 " model vdw 1.629 2.450 nonbonded pdb=" OE1 GLN A 57 " pdb=" HG SER A 256 " model vdw 1.638 2.450 nonbonded pdb=" HD1 HIS B 237 " pdb=" O TRP B 242 " model vdw 1.645 2.450 nonbonded pdb=" O ALA A 354 " pdb=" H THR A 358 " model vdw 1.688 2.450 nonbonded pdb=" O SER B 74 " pdb=" HG SER B 303 " model vdw 1.703 2.450 ... (remaining 168193 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: 0.03 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.770 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: 0.210 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 27.710 Find NCS groups from input model: 0.290 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:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 0.054 5410 Z= 0.191 Angle : 0.627 11.603 7308 Z= 0.274 Chirality : 0.039 0.278 864 Planarity : 0.003 0.028 862 Dihedral : 15.528 117.129 2018 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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: 2.00 (0.35), residues: 646 helix: 1.94 (0.24), residues: 526 sheet: None (None), residues: 0 loop : -1.49 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 233 HIS 0.001 0.000 HIS A 237 PHE 0.016 0.001 PHE B 330 TYR 0.005 0.001 TYR A 130 ARG 0.001 0.000 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.12800 ( 391) hydrogen bonds : angle 6.27755 ( 1170) covalent geometry : bond 0.00407 ( 5410) covalent geometry : angle 0.62725 ( 7308) *********************** 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 71 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.921 Fit side-chains REVERT: A 277 ILE cc_start: 0.8899 (tt) cc_final: 0.8654 (tp) REVERT: B 249 ASP cc_start: 0.8063 (t0) cc_final: 0.7807 (t0) REVERT: B 277 ILE cc_start: 0.8903 (tt) cc_final: 0.8662 (tp) outliers start: 0 outliers final: 1 residues processed: 71 average time/residue: 2.1776 time to fit residues: 163.3388 Evaluate side-chains 61 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.0980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.142717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.118406 restraints weight = 17007.381| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.46 r_work: 0.3032 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5410 Z= 0.135 Angle : 0.505 4.221 7308 Z= 0.259 Chirality : 0.036 0.127 864 Planarity : 0.004 0.030 862 Dihedral : 15.292 120.500 856 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.36 % Allowed : 6.86 % 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: 1.97 (0.34), residues: 646 helix: 1.90 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.53 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 233 HIS 0.005 0.001 HIS A 237 PHE 0.017 0.001 PHE B 330 TYR 0.005 0.001 TYR A 8 ARG 0.001 0.000 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 391) hydrogen bonds : angle 4.95487 ( 1170) covalent geometry : bond 0.00311 ( 5410) covalent geometry : angle 0.50512 ( 7308) *********************** 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 63 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.893 Fit side-chains REVERT: A 228 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7564 (tt) REVERT: A 277 ILE cc_start: 0.8761 (tt) cc_final: 0.8468 (tp) REVERT: B 249 ASP cc_start: 0.8150 (t0) cc_final: 0.7839 (t0) REVERT: B 277 ILE cc_start: 0.8771 (tt) cc_final: 0.8481 (tp) outliers start: 2 outliers final: 0 residues processed: 63 average time/residue: 2.1754 time to fit residues: 145.2860 Evaluate side-chains 61 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.132693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.105098 restraints weight = 17203.241| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.75 r_work: 0.3095 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5410 Z= 0.174 Angle : 0.527 4.345 7308 Z= 0.270 Chirality : 0.037 0.125 864 Planarity : 0.004 0.037 862 Dihedral : 14.734 124.078 854 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.72 % Allowed : 7.40 % Favored : 91.88 % 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: 1.77 (0.34), residues: 646 helix: 1.74 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.36 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.004 0.001 HIS A 237 PHE 0.018 0.002 PHE B 330 TYR 0.007 0.001 TYR B 361 ARG 0.001 0.000 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 391) hydrogen bonds : angle 4.83623 ( 1170) covalent geometry : bond 0.00429 ( 5410) covalent geometry : angle 0.52704 ( 7308) *********************** 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 67 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.903 Fit side-chains REVERT: A 228 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7799 (tt) REVERT: A 277 ILE cc_start: 0.8846 (tt) cc_final: 0.8575 (tp) REVERT: B 91 ARG cc_start: 0.7049 (ttt90) cc_final: 0.6693 (mtp85) REVERT: B 249 ASP cc_start: 0.8388 (t0) cc_final: 0.8044 (t0) REVERT: B 277 ILE cc_start: 0.8823 (tt) cc_final: 0.8554 (tp) outliers start: 4 outliers final: 1 residues processed: 65 average time/residue: 2.1405 time to fit residues: 147.3107 Evaluate side-chains 62 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.132266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.105183 restraints weight = 17214.298| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.70 r_work: 0.3117 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5410 Z= 0.177 Angle : 0.519 4.349 7308 Z= 0.269 Chirality : 0.037 0.128 864 Planarity : 0.005 0.040 862 Dihedral : 14.770 126.973 854 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.72 % Allowed : 7.58 % Favored : 91.70 % 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: 1.62 (0.34), residues: 646 helix: 1.65 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.49 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 233 HIS 0.004 0.001 HIS A 237 PHE 0.019 0.002 PHE A 330 TYR 0.007 0.001 TYR B 361 ARG 0.001 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 391) hydrogen bonds : angle 4.74675 ( 1170) covalent geometry : bond 0.00431 ( 5410) covalent geometry : angle 0.51879 ( 7308) *********************** 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 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.891 Fit side-chains REVERT: A 277 ILE cc_start: 0.8837 (tt) cc_final: 0.8569 (tp) REVERT: B 91 ARG cc_start: 0.7078 (ttt90) cc_final: 0.6695 (mtp85) REVERT: B 249 ASP cc_start: 0.8397 (t0) cc_final: 0.8089 (t0) REVERT: B 277 ILE cc_start: 0.8843 (tt) cc_final: 0.8570 (tp) outliers start: 4 outliers final: 3 residues processed: 63 average time/residue: 2.1639 time to fit residues: 144.2377 Evaluate side-chains 64 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 228 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 55 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.134135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.106738 restraints weight = 16959.815| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.75 r_work: 0.3101 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5410 Z= 0.131 Angle : 0.489 4.282 7308 Z= 0.253 Chirality : 0.036 0.125 864 Planarity : 0.004 0.039 862 Dihedral : 14.603 125.473 854 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.54 % Allowed : 7.94 % Favored : 91.52 % 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: 1.77 (0.34), residues: 646 helix: 1.78 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.54 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.002 0.001 HIS A 237 PHE 0.017 0.001 PHE B 330 TYR 0.005 0.001 TYR B 361 ARG 0.000 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 391) hydrogen bonds : angle 4.60738 ( 1170) covalent geometry : bond 0.00314 ( 5410) covalent geometry : angle 0.48926 ( 7308) *********************** 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 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.922 Fit side-chains REVERT: A 91 ARG cc_start: 0.7102 (ttt90) cc_final: 0.6869 (mtp85) REVERT: A 277 ILE cc_start: 0.8809 (tt) cc_final: 0.8549 (tp) REVERT: B 91 ARG cc_start: 0.7051 (ttt90) cc_final: 0.6650 (mtp85) REVERT: B 249 ASP cc_start: 0.8352 (t0) cc_final: 0.8052 (t0) REVERT: B 277 ILE cc_start: 0.8795 (tt) cc_final: 0.8526 (tp) outliers start: 3 outliers final: 3 residues processed: 64 average time/residue: 2.2972 time to fit residues: 155.0129 Evaluate side-chains 64 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 228 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 53 optimal weight: 0.9980 chunk 62 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.134737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.107257 restraints weight = 17122.967| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.76 r_work: 0.3183 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5410 Z= 0.149 Angle : 0.501 4.324 7308 Z= 0.259 Chirality : 0.037 0.125 864 Planarity : 0.005 0.040 862 Dihedral : 14.635 125.245 854 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.72 % Allowed : 8.12 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.34), residues: 646 helix: 1.77 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.64 (0.58), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 233 HIS 0.002 0.001 HIS A 237 PHE 0.018 0.002 PHE A 330 TYR 0.006 0.001 TYR B 361 ARG 0.001 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 391) hydrogen bonds : angle 4.59919 ( 1170) covalent geometry : bond 0.00366 ( 5410) covalent geometry : angle 0.50081 ( 7308) *********************** 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 66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.853 Fit side-chains REVERT: A 91 ARG cc_start: 0.7044 (ttt90) cc_final: 0.6793 (mtp85) REVERT: A 277 ILE cc_start: 0.8823 (tt) cc_final: 0.8571 (tp) REVERT: B 91 ARG cc_start: 0.7054 (ttt90) cc_final: 0.6702 (mtp85) REVERT: B 228 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7797 (tt) REVERT: B 249 ASP cc_start: 0.8324 (t0) cc_final: 0.8017 (t0) REVERT: B 277 ILE cc_start: 0.8786 (tt) cc_final: 0.8525 (tp) outliers start: 4 outliers final: 2 residues processed: 65 average time/residue: 2.2600 time to fit residues: 155.2386 Evaluate side-chains 64 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 228 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 50 optimal weight: 0.0670 chunk 54 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.134369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.106807 restraints weight = 17222.140| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.76 r_work: 0.3217 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5410 Z= 0.124 Angle : 0.483 4.271 7308 Z= 0.249 Chirality : 0.036 0.125 864 Planarity : 0.004 0.040 862 Dihedral : 14.545 123.578 854 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.54 % Allowed : 8.30 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.34), residues: 646 helix: 1.80 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.64 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.002 0.001 HIS A 237 PHE 0.017 0.001 PHE B 330 TYR 0.005 0.001 TYR B 361 ARG 0.001 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 391) hydrogen bonds : angle 4.50991 ( 1170) covalent geometry : bond 0.00294 ( 5410) covalent geometry : angle 0.48280 ( 7308) *********************** 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 64 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.910 Fit side-chains REVERT: A 91 ARG cc_start: 0.7038 (ttt90) cc_final: 0.6779 (mtp85) REVERT: A 277 ILE cc_start: 0.8811 (tt) cc_final: 0.8562 (tp) REVERT: B 91 ARG cc_start: 0.7039 (ttt90) cc_final: 0.6678 (mtp85) REVERT: B 228 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7762 (tt) REVERT: B 249 ASP cc_start: 0.8298 (t0) cc_final: 0.8018 (t0) REVERT: B 277 ILE cc_start: 0.8772 (tt) cc_final: 0.8515 (tp) outliers start: 3 outliers final: 2 residues processed: 63 average time/residue: 2.3015 time to fit residues: 153.3196 Evaluate side-chains 62 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 228 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 52 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 0.0980 chunk 44 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.133644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.108151 restraints weight = 17001.342| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.57 r_work: 0.2997 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5410 Z= 0.112 Angle : 0.471 4.268 7308 Z= 0.242 Chirality : 0.036 0.125 864 Planarity : 0.004 0.039 862 Dihedral : 14.330 120.802 854 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.90 % Allowed : 8.12 % 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: 1.90 (0.34), residues: 646 helix: 1.89 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.64 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.002 0.001 HIS B 237 PHE 0.016 0.001 PHE B 330 TYR 0.005 0.001 TYR B 361 ARG 0.001 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 391) hydrogen bonds : angle 4.43331 ( 1170) covalent geometry : bond 0.00263 ( 5410) covalent geometry : angle 0.47128 ( 7308) *********************** 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 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.893 Fit side-chains REVERT: A 88 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7465 (mmm) REVERT: A 91 ARG cc_start: 0.7014 (ttt90) cc_final: 0.6749 (mtp85) REVERT: A 277 ILE cc_start: 0.8803 (tt) cc_final: 0.8548 (tp) REVERT: B 91 ARG cc_start: 0.6997 (ttt90) cc_final: 0.6631 (mtp85) REVERT: B 228 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7676 (tt) REVERT: B 249 ASP cc_start: 0.8209 (t0) cc_final: 0.7917 (t0) REVERT: B 277 ILE cc_start: 0.8776 (tt) cc_final: 0.8523 (tp) outliers start: 5 outliers final: 3 residues processed: 62 average time/residue: 2.4686 time to fit residues: 161.3888 Evaluate side-chains 64 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 228 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 60 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.133593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.108052 restraints weight = 17039.776| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.58 r_work: 0.2997 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5410 Z= 0.116 Angle : 0.472 4.243 7308 Z= 0.243 Chirality : 0.036 0.132 864 Planarity : 0.004 0.039 862 Dihedral : 14.124 118.376 854 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.72 % Allowed : 8.48 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.34), residues: 646 helix: 1.92 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.63 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.002 0.001 HIS A 237 PHE 0.017 0.001 PHE B 330 TYR 0.005 0.001 TYR B 361 ARG 0.001 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 391) hydrogen bonds : angle 4.39615 ( 1170) covalent geometry : bond 0.00275 ( 5410) covalent geometry : angle 0.47248 ( 7308) *********************** 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 66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.991 Fit side-chains REVERT: A 91 ARG cc_start: 0.7049 (ttt90) cc_final: 0.6778 (mtp85) REVERT: A 277 ILE cc_start: 0.8771 (tt) cc_final: 0.8524 (tp) REVERT: B 88 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7549 (mmm) REVERT: B 91 ARG cc_start: 0.7003 (ttt90) cc_final: 0.6632 (mtp85) REVERT: B 249 ASP cc_start: 0.8215 (t0) cc_final: 0.7933 (t0) REVERT: B 277 ILE cc_start: 0.8769 (tt) cc_final: 0.8519 (tp) REVERT: B 308 ARG cc_start: 0.7373 (mtp-110) cc_final: 0.6309 (mmm160) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 3.2200 time to fit residues: 219.4790 Evaluate side-chains 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 88 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.132505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.106750 restraints weight = 17073.127| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.58 r_work: 0.2980 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5410 Z= 0.145 Angle : 0.495 4.332 7308 Z= 0.255 Chirality : 0.037 0.132 864 Planarity : 0.005 0.039 862 Dihedral : 14.226 118.775 854 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.72 % Allowed : 8.66 % Favored : 90.61 % 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: 1.88 (0.34), residues: 646 helix: 1.89 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.64 (0.58), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.003 0.001 HIS A 237 PHE 0.019 0.002 PHE B 330 TYR 0.006 0.001 TYR B 361 ARG 0.001 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 391) hydrogen bonds : angle 4.46963 ( 1170) covalent geometry : bond 0.00355 ( 5410) covalent geometry : angle 0.49511 ( 7308) ********************** 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 66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.803 Fit side-chains REVERT: A 88 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7508 (mmm) REVERT: A 91 ARG cc_start: 0.7055 (ttt90) cc_final: 0.6608 (mtp85) REVERT: A 277 ILE cc_start: 0.8764 (tt) cc_final: 0.8518 (tp) REVERT: B 88 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7534 (mmm) REVERT: B 91 ARG cc_start: 0.6997 (ttt90) cc_final: 0.6622 (mtp85) REVERT: B 249 ASP cc_start: 0.8260 (t0) cc_final: 0.7974 (t0) REVERT: B 277 ILE cc_start: 0.8774 (tt) cc_final: 0.8528 (tp) REVERT: B 308 ARG cc_start: 0.7417 (mtp-110) cc_final: 0.6337 (mmm160) outliers start: 4 outliers final: 2 residues processed: 63 average time/residue: 2.6036 time to fit residues: 172.5957 Evaluate side-chains 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 88 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 18 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 23 optimal weight: 0.0570 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 60 optimal weight: 0.5980 chunk 1 optimal weight: 0.2980 overall best weight: 0.3098 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.134513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.108873 restraints weight = 16993.581| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.58 r_work: 0.3012 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5410 Z= 0.101 Angle : 0.465 4.356 7308 Z= 0.238 Chirality : 0.036 0.136 864 Planarity : 0.004 0.039 862 Dihedral : 13.857 115.161 854 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.72 % Allowed : 9.03 % Favored : 90.25 % 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: 2.05 (0.34), residues: 646 helix: 2.00 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.65 (0.58), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.002 0.000 HIS A 237 PHE 0.015 0.001 PHE B 330 TYR 0.004 0.001 TYR B 18 ARG 0.001 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 391) hydrogen bonds : angle 4.33664 ( 1170) covalent geometry : bond 0.00228 ( 5410) covalent geometry : angle 0.46482 ( 7308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7683.60 seconds wall clock time: 132 minutes 51.67 seconds (7971.67 seconds total)