Starting phenix.real_space_refine on Fri Dec 27 12:39:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qia_13985/12_2024/7qia_13985.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qia_13985/12_2024/7qia_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_13985/12_2024/7qia_13985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qia_13985/12_2024/7qia_13985.map" model { file = "/net/cci-nas-00/data/ceres_data/7qia_13985/12_2024/7qia_13985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qia_13985/12_2024/7qia_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-5532/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: 3.22, per 1000 atoms: 0.66 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: 1.24 Conformation dependent library (CDL) restraints added in 627.1 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: 0.47 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: 1.25 Time building geometry restraints manager: 1.45 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: 0.000 Normalize map: mean=0, sd=1: 0.290 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.140 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.600 ------------------------------------------------------------------------------- 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 4942 Z= 0.181 Angle : 0.600 11.890 6721 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 *********************** 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 : 0.458 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: 0.1442 time to fit residues: 10.7736 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 : 0.493 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 4942 Z= 0.177 Angle : 0.579 10.029 6721 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 *********************** 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 : 0.509 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.7957 (ttp) cc_final: 0.7752 (ttp) REVERT: A 247 ASP cc_start: 0.8101 (t0) cc_final: 0.7776 (t0) REVERT: A 372 MET cc_start: 0.8522 (tpt) cc_final: 0.8099 (tpp) REVERT: A 375 MET cc_start: 0.8271 (mtm) cc_final: 0.7965 (mtp) outliers start: 5 outliers final: 4 residues processed: 57 average time/residue: 0.1668 time to fit residues: 12.5834 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 : 0.493 ------------------------------------------------------------------------------- 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 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 51 optimal weight: 0.0170 chunk 56 optimal weight: 0.0670 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4942 Z= 0.161 Angle : 0.528 6.592 6721 Z= 0.278 Chirality : 0.042 0.170 795 Planarity : 0.004 0.035 837 Dihedral : 4.097 18.751 686 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.80 % Allowed : 11.16 % Favored : 88.05 % 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: 1.37 (0.30), residues: 316 sheet: -1.01 (0.66), residues: 76 loop : -2.04 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 53 HIS 0.001 0.000 HIS A 207 PHE 0.035 0.001 PHE A 131 TYR 0.011 0.001 TYR A 185 ARG 0.002 0.000 ARG B 99 *********************** 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 57 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 80 MET cc_start: 0.7715 (ttm) cc_final: 0.7427 (ttm) REVERT: A 247 ASP cc_start: 0.8120 (t0) cc_final: 0.7789 (t0) REVERT: A 375 MET cc_start: 0.8282 (mtm) cc_final: 0.8046 (mtp) outliers start: 4 outliers final: 4 residues processed: 54 average time/residue: 0.2066 time to fit residues: 14.3386 Evaluate side-chains 54 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.0070 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 16 optimal weight: 0.0040 overall best weight: 0.4210 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4942 Z= 0.168 Angle : 0.513 5.599 6721 Z= 0.271 Chirality : 0.042 0.172 795 Planarity : 0.004 0.035 837 Dihedral : 4.025 19.016 686 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.99 % Allowed : 14.14 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.34), residues: 633 helix: 1.47 (0.30), residues: 316 sheet: -0.95 (0.70), residues: 69 loop : -2.03 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 267 HIS 0.001 0.000 HIS A 207 PHE 0.033 0.001 PHE A 131 TYR 0.009 0.001 TYR A 185 ARG 0.002 0.000 ARG B 103 *********************** 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 59 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.508 Fit side-chains REVERT: A 247 ASP cc_start: 0.8110 (t0) cc_final: 0.7701 (t0) outliers start: 10 outliers final: 6 residues processed: 55 average time/residue: 0.1500 time to fit residues: 11.2067 Evaluate side-chains 55 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET 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 50 optimal weight: 0.0070 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 0.0670 chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 4942 Z= 0.373 Angle : 0.648 7.169 6721 Z= 0.339 Chirality : 0.046 0.193 795 Planarity : 0.005 0.039 837 Dihedral : 4.381 22.366 686 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 1.79 % Allowed : 16.93 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.34), residues: 633 helix: 1.31 (0.30), residues: 312 sheet: -1.37 (0.66), residues: 77 loop : -1.94 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 267 HIS 0.001 0.000 HIS A 207 PHE 0.034 0.002 PHE A 131 TYR 0.009 0.001 TYR C 37 ARG 0.003 0.000 ARG A 413 *********************** 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 60 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.512 Fit side-chains REVERT: A 80 MET cc_start: 0.7775 (ttm) cc_final: 0.7488 (ttm) REVERT: A 247 ASP cc_start: 0.8217 (t0) cc_final: 0.7757 (t0) outliers start: 9 outliers final: 7 residues processed: 57 average time/residue: 0.1677 time to fit residues: 12.6611 Evaluate side-chains 54 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 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 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 54 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4942 Z= 0.229 Angle : 0.569 5.780 6721 Z= 0.300 Chirality : 0.043 0.181 795 Planarity : 0.004 0.037 837 Dihedral : 4.300 20.759 686 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 1.99 % Allowed : 18.13 % Favored : 79.88 % 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: -0.34 (0.34), residues: 633 helix: 1.37 (0.30), residues: 313 sheet: -0.97 (0.70), residues: 69 loop : -2.14 (0.36), residues: 251 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 0.040 0.002 PHE C 50 TYR 0.010 0.001 TYR C 37 ARG 0.002 0.000 ARG B 99 *********************** 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 60 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.523 Fit side-chains REVERT: A 80 MET cc_start: 0.7827 (ttm) cc_final: 0.7569 (ttm) REVERT: A 247 ASP cc_start: 0.8163 (t0) cc_final: 0.7681 (t0) REVERT: A 327 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7638 (m-10) outliers start: 10 outliers final: 7 residues processed: 54 average time/residue: 0.1506 time to fit residues: 11.1062 Evaluate side-chains 57 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 B residue 51 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4942 Z= 0.247 Angle : 0.582 6.616 6721 Z= 0.305 Chirality : 0.044 0.181 795 Planarity : 0.004 0.038 837 Dihedral : 4.295 20.561 686 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.19 % Allowed : 18.53 % 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: -0.41 (0.34), residues: 633 helix: 1.33 (0.30), residues: 315 sheet: -1.43 (0.66), residues: 77 loop : -2.09 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.001 0.000 HIS A 207 PHE 0.035 0.002 PHE C 50 TYR 0.010 0.001 TYR C 37 ARG 0.002 0.000 ARG B 99 *********************** 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 62 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.507 Fit side-chains REVERT: A 80 MET cc_start: 0.7867 (ttm) cc_final: 0.7648 (ttm) REVERT: A 247 ASP cc_start: 0.8194 (t0) cc_final: 0.7723 (t0) REVERT: A 327 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7570 (m-10) outliers start: 11 outliers final: 10 residues processed: 58 average time/residue: 0.1506 time to fit residues: 11.9135 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 : 0.504 ------------------------------------------------------------------------------- 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 11 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.0670 chunk 53 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4942 Z= 0.228 Angle : 0.610 15.005 6721 Z= 0.308 Chirality : 0.043 0.178 795 Planarity : 0.004 0.037 837 Dihedral : 4.272 20.230 686 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.39 % Allowed : 18.92 % 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: -0.49 (0.34), residues: 633 helix: 1.27 (0.30), residues: 320 sheet: -1.43 (0.66), residues: 77 loop : -2.23 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.001 0.000 HIS A 207 PHE 0.033 0.001 PHE A 131 TYR 0.009 0.001 TYR C 37 ARG 0.002 0.000 ARG B 99 *********************** 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 63 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.659 Fit side-chains REVERT: A 80 MET cc_start: 0.7852 (ttm) cc_final: 0.7627 (ttm) REVERT: A 247 ASP cc_start: 0.8137 (t0) cc_final: 0.7634 (t0) REVERT: A 327 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7656 (m-10) outliers start: 12 outliers final: 10 residues processed: 58 average time/residue: 0.1475 time to fit residues: 11.8988 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 : 0.518 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4942 Z= 0.356 Angle : 0.677 13.742 6721 Z= 0.345 Chirality : 0.046 0.189 795 Planarity : 0.005 0.039 837 Dihedral : 4.466 22.691 686 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.39 % Allowed : 19.32 % Favored : 78.29 % 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: -0.50 (0.34), residues: 633 helix: 1.29 (0.30), residues: 310 sheet: -1.70 (0.64), residues: 81 loop : -2.01 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 229 HIS 0.001 0.000 HIS A 207 PHE 0.031 0.002 PHE A 131 TYR 0.008 0.001 TYR C 37 ARG 0.003 0.000 ARG B 99 *********************** 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 63 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.530 Fit side-chains REVERT: A 80 MET cc_start: 0.7808 (ttm) cc_final: 0.7399 (ttm) REVERT: A 247 ASP cc_start: 0.8157 (t0) cc_final: 0.7671 (t0) REVERT: A 327 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7546 (m-10) outliers start: 12 outliers final: 10 residues processed: 60 average time/residue: 0.1754 time to fit residues: 14.5528 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 : 0.485 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 15 optimal weight: 0.0770 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4942 Z= 0.203 Angle : 0.605 13.487 6721 Z= 0.308 Chirality : 0.043 0.175 795 Planarity : 0.004 0.038 837 Dihedral : 4.342 20.151 686 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.99 % Allowed : 19.72 % Favored : 78.29 % 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: -0.41 (0.34), residues: 633 helix: 1.28 (0.30), residues: 320 sheet: -1.11 (0.70), residues: 69 loop : -2.20 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.001 0.000 HIS A 207 PHE 0.040 0.002 PHE C 50 TYR 0.006 0.001 TYR A 168 ARG 0.002 0.000 ARG B 99 ********************** 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 64 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.550 Fit side-chains REVERT: A 80 MET cc_start: 0.7743 (ttm) cc_final: 0.7511 (ttm) REVERT: A 247 ASP cc_start: 0.8148 (t0) cc_final: 0.7627 (t0) REVERT: A 327 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7673 (m-10) outliers start: 10 outliers final: 9 residues processed: 60 average time/residue: 0.1598 time to fit residues: 13.0916 Evaluate side-chains 63 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.150989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.119989 restraints weight = 5022.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.120670 restraints weight = 4419.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.121372 restraints weight = 4117.292| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4942 Z= 0.219 Angle : 0.602 13.076 6721 Z= 0.307 Chirality : 0.043 0.175 795 Planarity : 0.004 0.039 837 Dihedral : 4.295 20.546 686 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.59 % Allowed : 19.32 % Favored : 78.09 % 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: -0.39 (0.34), residues: 633 helix: 1.34 (0.30), residues: 319 sheet: -1.11 (0.70), residues: 69 loop : -2.24 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.001 0.000 HIS A 207 PHE 0.040 0.002 PHE C 50 TYR 0.006 0.001 TYR A 168 ARG 0.002 0.000 ARG B 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1244.12 seconds wall clock time: 23 minutes 18.97 seconds (1398.97 seconds total)