Starting phenix.real_space_refine on Thu Jul 24 00:38:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qia_13985/07_2025/7qia_13985.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qia_13985/07_2025/7qia_13985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qia_13985/07_2025/7qia_13985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qia_13985/07_2025/7qia_13985.map" model { file = "/net/cci-nas-00/data/ceres_data/7qia_13985/07_2025/7qia_13985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qia_13985/07_2025/7qia_13985.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 3148 2.51 5 N 809 2.21 5 O 858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4843 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2991 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 12, 'TRANS': 388} Chain: "C" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "B" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 3.30, per 1000 atoms: 0.68 Number of scatterers: 4843 At special positions: 0 Unit cell: (88.536, 106.764, 75.516, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 858 8.00 N 809 7.00 C 3148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 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: 1.28 Conformation dependent library (CDL) restraints added in 636.7 milliseconds 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 55.9% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.929A pdb=" N VAL A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 removed outlier: 4.281A pdb=" N THR A 73 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 removed outlier: 4.123A pdb=" N ILE A 79 " --> pdb=" O TRP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 111 through 143 Processing helix chain 'A' and resid 151 through 165 Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.976A pdb=" N VAL A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 192 removed outlier: 4.321A pdb=" N THR A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 211 through 226 Processing helix chain 'A' and resid 227 through 242 removed outlier: 4.203A pdb=" N MET A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 247 through 277 removed outlier: 4.036A pdb=" N GLN A 251 " --> pdb=" O ASP A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.540A pdb=" N ALA A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 301 through 333 removed outlier: 3.555A pdb=" N PHE A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Proline residue: A 322 - end of helix removed outlier: 4.067A pdb=" N PHE A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 365 removed outlier: 3.550A pdb=" N LYS A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 398 removed outlier: 4.650A pdb=" N GLN A 379 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 384 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 386 " --> pdb=" O ASN A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Processing helix chain 'A' and resid 409 through 437 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.857A pdb=" N HIS B 31 " --> pdb=" O THR B 28 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 62 through 65 removed outlier: 4.023A pdb=" N LYS B 65 " --> pdb=" O ASP B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.836A pdb=" N TYR B 112 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 8 removed outlier: 3.717A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 68 " --> pdb=" O GLN C 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.591A pdb=" N LEU B 18 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 60 removed outlier: 5.075A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 786 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: 1.23 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1530 1.34 - 1.46: 1003 1.46 - 1.58: 2361 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 4942 Sorted by residual: bond pdb=" CB ASP A 247 " pdb=" CG ASP A 247 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.06e-01 bond pdb=" CA GLU B 44 " pdb=" CB GLU B 44 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.51e-02 4.39e+03 8.04e-01 bond pdb=" SD MET A 80 " pdb=" CE MET A 80 " ideal model delta sigma weight residual 1.791 1.769 0.022 2.50e-02 1.60e+03 7.98e-01 bond pdb=" CB THR A 61 " pdb=" CG2 THR A 61 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.52e-01 bond pdb=" CB GLU B 44 " pdb=" CG GLU B 44 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.49e-01 ... (remaining 4937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 6649 2.38 - 4.76: 61 4.76 - 7.13: 9 7.13 - 9.51: 1 9.51 - 11.89: 1 Bond angle restraints: 6721 Sorted by residual: angle pdb=" CA LEU C 103 " pdb=" CB LEU C 103 " pdb=" CG LEU C 103 " ideal model delta sigma weight residual 116.30 128.19 -11.89 3.50e+00 8.16e-02 1.15e+01 angle pdb=" C THR A 130 " pdb=" N PHE A 131 " pdb=" CA PHE A 131 " ideal model delta sigma weight residual 121.14 115.44 5.70 1.75e+00 3.27e-01 1.06e+01 angle pdb=" N ASP A 247 " pdb=" CA ASP A 247 " pdb=" C ASP A 247 " ideal model delta sigma weight residual 112.25 108.54 3.71 1.36e+00 5.41e-01 7.44e+00 angle pdb=" CA GLU B 44 " pdb=" CB GLU B 44 " pdb=" CG GLU B 44 " ideal model delta sigma weight residual 114.10 119.48 -5.38 2.00e+00 2.50e-01 7.24e+00 angle pdb=" CA LEU C 47 " pdb=" CB LEU C 47 " pdb=" CG LEU C 47 " ideal model delta sigma weight residual 116.30 124.49 -8.19 3.50e+00 8.16e-02 5.48e+00 ... (remaining 6716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 2578 16.06 - 32.11: 243 32.11 - 48.17: 59 48.17 - 64.23: 6 64.23 - 80.29: 3 Dihedral angle restraints: 2889 sinusoidal: 1068 harmonic: 1821 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 95 " pdb=" CB CYS C 95 " ideal model delta sinusoidal sigma weight residual 93.00 173.29 -80.29 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CA ASP B 80 " pdb=" C ASP B 80 " pdb=" N LEU B 81 " pdb=" CA LEU B 81 " ideal model delta harmonic sigma weight residual 180.00 160.69 19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA VAL C 28 " pdb=" C VAL C 28 " pdb=" N PHE C 29 " pdb=" CA PHE C 29 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 2886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 482 0.034 - 0.068: 224 0.068 - 0.101: 68 0.101 - 0.135: 19 0.135 - 0.169: 2 Chirality restraints: 795 Sorted by residual: chirality pdb=" CA PHE A 131 " pdb=" N PHE A 131 " pdb=" C PHE A 131 " pdb=" CB PHE A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CA PRO A 228 " pdb=" N PRO A 228 " pdb=" C PRO A 228 " pdb=" CB PRO A 228 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA ILE A 366 " pdb=" N ILE A 366 " pdb=" C ILE A 366 " pdb=" CB ILE A 366 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 792 not shown) Planarity restraints: 837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 247 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.90e+00 pdb=" CG ASP A 247 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASP A 247 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP A 247 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 247 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C ASP A 247 " -0.032 2.00e-02 2.50e+03 pdb=" O ASP A 247 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU A 248 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 312 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C ALA A 312 " -0.028 2.00e-02 2.50e+03 pdb=" O ALA A 312 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 313 " 0.010 2.00e-02 2.50e+03 ... (remaining 834 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1141 2.79 - 3.32: 4636 3.32 - 3.84: 8078 3.84 - 4.37: 9062 4.37 - 4.90: 16067 Nonbonded interactions: 38984 Sorted by model distance: nonbonded pdb=" O MET A 94 " pdb=" OG1 THR A 98 " model vdw 2.259 3.040 nonbonded pdb=" O GLU A 133 " pdb=" OG SER A 314 " model vdw 2.263 3.040 nonbonded pdb=" ND2 ASN A 126 " pdb=" OG1 THR A 325 " model vdw 2.280 3.120 nonbonded pdb=" O PHE A 71 " pdb=" OG SER A 202 " model vdw 2.303 3.040 nonbonded pdb=" O LYS A 100 " pdb=" NE2 GLN A 235 " model vdw 2.322 3.120 ... (remaining 38979 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.390 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 0.003 0.036 4944 Z= 0.130 Angle : 0.600 11.890 6725 Z= 0.310 Chirality : 0.043 0.169 795 Planarity : 0.005 0.040 837 Dihedral : 12.907 76.043 1717 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -1.03 (0.34), residues: 633 helix: 0.40 (0.31), residues: 308 sheet: -1.43 (0.64), residues: 84 loop : -1.77 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 53 HIS 0.001 0.000 HIS B 31 PHE 0.020 0.001 PHE A 131 TYR 0.016 0.001 TYR A 185 ARG 0.002 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.17893 ( 272) hydrogen bonds : angle 7.21635 ( 786) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.79026 ( 4) covalent geometry : bond 0.00283 ( 4942) covalent geometry : angle 0.59994 ( 6721) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.537 Fit side-chains REVERT: A 191 MET cc_start: 0.7990 (ttp) cc_final: 0.7788 (ttp) REVERT: A 247 ASP cc_start: 0.7922 (t0) cc_final: 0.7675 (t0) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1553 time to fit residues: 11.4642 Evaluate side-chains 49 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 6.9990 chunk 47 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.0020 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 0.0980 chunk 57 optimal weight: 3.9990 overall best weight: 0.3386 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.158411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.127334 restraints weight = 4953.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.128482 restraints weight = 4244.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.129274 restraints weight = 3768.361| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4944 Z= 0.127 Angle : 0.580 10.029 6725 Z= 0.301 Chirality : 0.043 0.173 795 Planarity : 0.004 0.036 837 Dihedral : 4.196 18.902 686 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.00 % Allowed : 6.37 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.35), residues: 633 helix: 1.10 (0.30), residues: 316 sheet: -1.65 (0.58), residues: 97 loop : -1.96 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 53 HIS 0.001 0.000 HIS A 207 PHE 0.038 0.001 PHE A 131 TYR 0.012 0.001 TYR A 185 ARG 0.002 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 272) hydrogen bonds : angle 4.76747 ( 786) SS BOND : bond 0.00307 ( 2) SS BOND : angle 1.16347 ( 4) covalent geometry : bond 0.00278 ( 4942) covalent geometry : angle 0.57918 ( 6721) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.7988 (ttp) cc_final: 0.7788 (ttp) REVERT: A 247 ASP cc_start: 0.8318 (t0) cc_final: 0.7987 (t0) REVERT: A 372 MET cc_start: 0.8524 (tpt) cc_final: 0.8058 (tpp) REVERT: A 375 MET cc_start: 0.8322 (mtm) cc_final: 0.7990 (mtp) REVERT: B 39 GLN cc_start: 0.8241 (tt0) cc_final: 0.8010 (tt0) outliers start: 5 outliers final: 4 residues processed: 57 average time/residue: 0.1683 time to fit residues: 12.8133 Evaluate side-chains 57 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 61 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.152591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.120569 restraints weight = 5015.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.121759 restraints weight = 4283.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.122254 restraints weight = 3856.096| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4944 Z= 0.156 Angle : 0.572 7.356 6725 Z= 0.301 Chirality : 0.043 0.182 795 Planarity : 0.004 0.036 837 Dihedral : 4.212 20.301 686 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.39 % Allowed : 12.35 % Favored : 86.25 % 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: -0.37 (0.35), residues: 633 helix: 1.30 (0.30), residues: 316 sheet: -1.43 (0.66), residues: 77 loop : -1.98 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 267 HIS 0.001 0.000 HIS A 207 PHE 0.034 0.002 PHE A 131 TYR 0.010 0.001 TYR A 185 ARG 0.002 0.000 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 272) hydrogen bonds : angle 4.46637 ( 786) SS BOND : bond 0.00499 ( 2) SS BOND : angle 0.78126 ( 4) covalent geometry : bond 0.00371 ( 4942) covalent geometry : angle 0.57208 ( 6721) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.513 Fit side-chains REVERT: A 80 MET cc_start: 0.7781 (ttm) cc_final: 0.7537 (ttm) REVERT: A 247 ASP cc_start: 0.8422 (t0) cc_final: 0.8091 (t0) outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.1903 time to fit residues: 13.3789 Evaluate side-chains 54 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 52 optimal weight: 0.0370 chunk 14 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.153085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.121548 restraints weight = 5072.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.122761 restraints weight = 4372.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.122939 restraints weight = 3907.328| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4944 Z= 0.135 Angle : 0.546 5.928 6725 Z= 0.287 Chirality : 0.042 0.175 795 Planarity : 0.004 0.036 837 Dihedral : 4.190 19.803 686 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.59 % Allowed : 14.74 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.35), residues: 633 helix: 1.38 (0.30), residues: 316 sheet: -1.03 (0.70), residues: 69 loop : -2.07 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 229 HIS 0.001 0.000 HIS A 207 PHE 0.036 0.002 PHE C 50 TYR 0.008 0.001 TYR A 185 ARG 0.005 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 272) hydrogen bonds : angle 4.33905 ( 786) SS BOND : bond 0.00383 ( 2) SS BOND : angle 0.66578 ( 4) covalent geometry : bond 0.00315 ( 4942) covalent geometry : angle 0.54562 ( 6721) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.498 Fit side-chains REVERT: A 247 ASP cc_start: 0.8375 (t0) cc_final: 0.8006 (t0) outliers start: 13 outliers final: 7 residues processed: 54 average time/residue: 0.1577 time to fit residues: 11.5554 Evaluate side-chains 53 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 4 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 57 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.152192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.120555 restraints weight = 5129.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.121879 restraints weight = 4363.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.122273 restraints weight = 3897.288| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4944 Z= 0.145 Angle : 0.556 5.488 6725 Z= 0.291 Chirality : 0.043 0.178 795 Planarity : 0.004 0.037 837 Dihedral : 4.198 20.281 686 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.39 % Allowed : 16.14 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.34), residues: 633 helix: 1.29 (0.30), residues: 322 sheet: -1.03 (0.70), residues: 69 loop : -2.20 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 267 HIS 0.000 0.000 HIS A 207 PHE 0.035 0.002 PHE A 131 TYR 0.008 0.001 TYR A 168 ARG 0.001 0.000 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 272) hydrogen bonds : angle 4.30844 ( 786) SS BOND : bond 0.00411 ( 2) SS BOND : angle 0.70511 ( 4) covalent geometry : bond 0.00345 ( 4942) covalent geometry : angle 0.55609 ( 6721) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.494 Fit side-chains REVERT: A 80 MET cc_start: 0.7685 (ttm) cc_final: 0.7366 (ttm) REVERT: A 247 ASP cc_start: 0.8397 (t0) cc_final: 0.7912 (t0) outliers start: 12 outliers final: 8 residues processed: 57 average time/residue: 0.1517 time to fit residues: 11.8686 Evaluate side-chains 55 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 0.0030 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.151708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.118971 restraints weight = 5071.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.120332 restraints weight = 4353.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.120893 restraints weight = 3966.137| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4944 Z= 0.152 Angle : 0.562 5.666 6725 Z= 0.296 Chirality : 0.043 0.180 795 Planarity : 0.004 0.037 837 Dihedral : 4.218 20.583 686 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.19 % Allowed : 16.73 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.35), residues: 633 helix: 1.45 (0.30), residues: 316 sheet: -1.05 (0.70), residues: 69 loop : -2.12 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 229 HIS 0.001 0.000 HIS A 207 PHE 0.033 0.001 PHE A 131 TYR 0.011 0.001 TYR C 37 ARG 0.001 0.000 ARG A 292 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 272) hydrogen bonds : angle 4.27100 ( 786) SS BOND : bond 0.00427 ( 2) SS BOND : angle 0.65992 ( 4) covalent geometry : bond 0.00362 ( 4942) covalent geometry : angle 0.56204 ( 6721) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.492 Fit side-chains REVERT: A 80 MET cc_start: 0.7757 (ttm) cc_final: 0.7425 (ttm) REVERT: A 247 ASP cc_start: 0.8413 (t0) cc_final: 0.7935 (t0) REVERT: A 327 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7557 (m-10) outliers start: 11 outliers final: 8 residues processed: 57 average time/residue: 0.1534 time to fit residues: 12.1174 Evaluate side-chains 58 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.151184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.119573 restraints weight = 5047.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.120858 restraints weight = 4451.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.121152 restraints weight = 3980.612| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4944 Z= 0.149 Angle : 0.557 5.729 6725 Z= 0.294 Chirality : 0.043 0.179 795 Planarity : 0.004 0.037 837 Dihedral : 4.232 20.511 686 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.59 % Allowed : 18.13 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.34), residues: 633 helix: 1.47 (0.30), residues: 316 sheet: -1.04 (0.71), residues: 69 loop : -2.13 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 229 HIS 0.000 0.000 HIS A 207 PHE 0.033 0.001 PHE A 131 TYR 0.009 0.001 TYR C 37 ARG 0.001 0.000 ARG A 292 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 272) hydrogen bonds : angle 4.26795 ( 786) SS BOND : bond 0.00411 ( 2) SS BOND : angle 0.60794 ( 4) covalent geometry : bond 0.00354 ( 4942) covalent geometry : angle 0.55655 ( 6721) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.547 Fit side-chains REVERT: A 80 MET cc_start: 0.7859 (ttm) cc_final: 0.7622 (ttm) REVERT: A 247 ASP cc_start: 0.8405 (t0) cc_final: 0.7894 (t0) REVERT: A 327 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7513 (m-10) outliers start: 13 outliers final: 10 residues processed: 58 average time/residue: 0.1574 time to fit residues: 12.4165 Evaluate side-chains 60 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 0.0970 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.152364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.120365 restraints weight = 5041.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.120899 restraints weight = 4369.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.121295 restraints weight = 3838.944| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4944 Z= 0.135 Angle : 0.548 5.336 6725 Z= 0.288 Chirality : 0.042 0.176 795 Planarity : 0.004 0.037 837 Dihedral : 4.200 19.304 686 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.79 % Allowed : 18.33 % Favored : 78.88 % 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: -0.32 (0.34), residues: 633 helix: 1.44 (0.30), residues: 319 sheet: -1.01 (0.71), residues: 69 loop : -2.30 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 229 HIS 0.000 0.000 HIS A 207 PHE 0.039 0.002 PHE C 50 TYR 0.007 0.001 TYR A 168 ARG 0.001 0.000 ARG A 413 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 272) hydrogen bonds : angle 4.21719 ( 786) SS BOND : bond 0.00351 ( 2) SS BOND : angle 0.56826 ( 4) covalent geometry : bond 0.00314 ( 4942) covalent geometry : angle 0.54772 ( 6721) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.521 Fit side-chains REVERT: A 80 MET cc_start: 0.7845 (ttm) cc_final: 0.7609 (ttm) REVERT: A 247 ASP cc_start: 0.8425 (t0) cc_final: 0.7908 (t0) REVERT: A 327 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7546 (m-10) REVERT: C 47 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7909 (tt) outliers start: 14 outliers final: 10 residues processed: 61 average time/residue: 0.1506 time to fit residues: 12.6075 Evaluate side-chains 62 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 14 optimal weight: 0.0570 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.151191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.119352 restraints weight = 5000.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.120815 restraints weight = 4317.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.120975 restraints weight = 3839.711| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4944 Z= 0.145 Angle : 0.581 7.022 6725 Z= 0.300 Chirality : 0.043 0.178 795 Planarity : 0.004 0.038 837 Dihedral : 4.214 19.798 686 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.39 % Allowed : 18.73 % Favored : 78.88 % 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: -0.21 (0.34), residues: 633 helix: 1.56 (0.30), residues: 313 sheet: -0.98 (0.71), residues: 69 loop : -2.19 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 229 HIS 0.000 0.000 HIS A 207 PHE 0.038 0.002 PHE C 50 TYR 0.009 0.001 TYR C 37 ARG 0.001 0.000 ARG A 292 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 272) hydrogen bonds : angle 4.25338 ( 786) SS BOND : bond 0.00400 ( 2) SS BOND : angle 0.58326 ( 4) covalent geometry : bond 0.00342 ( 4942) covalent geometry : angle 0.58086 ( 6721) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.508 Fit side-chains REVERT: A 80 MET cc_start: 0.7766 (ttm) cc_final: 0.7515 (ttm) REVERT: A 247 ASP cc_start: 0.8393 (t0) cc_final: 0.7860 (t0) REVERT: A 327 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7581 (m-10) REVERT: C 47 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7960 (tt) outliers start: 12 outliers final: 9 residues processed: 63 average time/residue: 0.1737 time to fit residues: 14.7854 Evaluate side-chains 63 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 0.0020 chunk 62 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.150918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.118915 restraints weight = 5067.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.120350 restraints weight = 4376.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.120625 restraints weight = 3874.559| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4944 Z= 0.149 Angle : 0.621 16.330 6725 Z= 0.310 Chirality : 0.043 0.179 795 Planarity : 0.004 0.037 837 Dihedral : 4.235 19.633 686 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.59 % Allowed : 18.73 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.34), residues: 633 helix: 1.58 (0.30), residues: 312 sheet: -1.36 (0.67), residues: 77 loop : -2.16 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 229 HIS 0.000 0.000 HIS A 207 PHE 0.032 0.001 PHE A 131 TYR 0.008 0.001 TYR C 37 ARG 0.001 0.000 ARG A 292 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 272) hydrogen bonds : angle 4.27274 ( 786) SS BOND : bond 0.00423 ( 2) SS BOND : angle 0.59777 ( 4) covalent geometry : bond 0.00352 ( 4942) covalent geometry : angle 0.62087 ( 6721) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.498 Fit side-chains REVERT: A 80 MET cc_start: 0.7768 (ttm) cc_final: 0.7509 (ttm) REVERT: A 247 ASP cc_start: 0.8387 (t0) cc_final: 0.7865 (t0) REVERT: A 327 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7596 (m-10) REVERT: A 371 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8101 (mt) REVERT: C 47 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7917 (tt) outliers start: 13 outliers final: 9 residues processed: 62 average time/residue: 0.1527 time to fit residues: 13.0286 Evaluate side-chains 65 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.0010 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.152517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.120306 restraints weight = 5032.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.121862 restraints weight = 4402.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.122438 restraints weight = 3932.036| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4944 Z= 0.133 Angle : 0.596 14.885 6725 Z= 0.301 Chirality : 0.043 0.175 795 Planarity : 0.004 0.037 837 Dihedral : 4.213 19.357 686 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.79 % Allowed : 18.13 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.34), residues: 633 helix: 1.48 (0.30), residues: 319 sheet: -0.97 (0.71), residues: 69 loop : -2.34 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 229 HIS 0.000 0.000 HIS A 207 PHE 0.033 0.001 PHE A 131 TYR 0.006 0.001 TYR A 168 ARG 0.001 0.000 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 272) hydrogen bonds : angle 4.22990 ( 786) SS BOND : bond 0.00324 ( 2) SS BOND : angle 0.52011 ( 4) covalent geometry : bond 0.00304 ( 4942) covalent geometry : angle 0.59589 ( 6721) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2184.39 seconds wall clock time: 39 minutes 30.36 seconds (2370.36 seconds total)