Starting phenix.real_space_refine on Wed Jan 17 16:53:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qia_13985/01_2024/7qia_13985.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qia_13985/01_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qia_13985/01_2024/7qia_13985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qia_13985/01_2024/7qia_13985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qia_13985/01_2024/7qia_13985.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qia_13985/01_2024/7qia_13985.pdb" } 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 Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 73": "OD1" <-> "OD2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 107": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 943.7 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: 0.49 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: 1.19 Time building geometry restraints manager: 1.92 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: 99.31 - 106.25: 108 106.25 - 113.19: 2704 113.19 - 120.14: 1750 120.14 - 127.08: 2110 127.08 - 134.02: 49 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 2.440 nonbonded pdb=" O GLU A 133 " pdb=" OG SER A 314 " model vdw 2.263 2.440 nonbonded pdb=" ND2 ASN A 126 " pdb=" OG1 THR A 325 " model vdw 2.280 2.520 nonbonded pdb=" O PHE A 71 " pdb=" OG SER A 202 " model vdw 2.303 2.440 nonbonded pdb=" O LYS A 100 " pdb=" NE2 GLN A 235 " model vdw 2.322 2.520 ... (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 ========== 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: 0.250 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: 1.510 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.490 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.490 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.508 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: 0.1513 time to fit residues: 11.1559 Evaluate side-chains 49 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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: 5.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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: 0.7680 moved from start: 0.0852 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= 0.235 Angle : 0.592 10.555 6721 Z= 0.306 Chirality : 0.043 0.178 795 Planarity : 0.005 0.037 837 Dihedral : 4.253 19.783 686 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 1.00 % Allowed : 6.18 % Favored : 92.83 % 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: -0.64 (0.34), residues: 633 helix: 1.02 (0.29), residues: 316 sheet: -1.55 (0.63), residues: 84 loop : -2.02 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 36 HIS 0.001 0.000 HIS A 207 PHE 0.036 0.001 PHE A 131 TYR 0.012 0.001 TYR A 185 ARG 0.002 0.000 ARG B 52 *********************** 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 54 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 247 ASP cc_start: 0.8135 (t0) cc_final: 0.7892 (t0) outliers start: 5 outliers final: 4 residues processed: 52 average time/residue: 0.1663 time to fit residues: 11.5064 Evaluate side-chains 52 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 B residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 51 optimal weight: 0.0010 chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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: 0.7682 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4942 Z= 0.202 Angle : 0.548 7.513 6721 Z= 0.286 Chirality : 0.042 0.172 795 Planarity : 0.004 0.036 837 Dihedral : 4.216 19.775 686 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.20 % Allowed : 13.15 % Favored : 85.66 % 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: 1.26 (0.30), residues: 316 sheet: -1.09 (0.67), residues: 76 loop : -2.13 (0.37), residues: 241 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 0.035 0.002 PHE A 131 TYR 0.010 0.001 TYR A 185 ARG 0.001 0.000 ARG A 292 *********************** 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 54 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.461 Fit side-chains REVERT: A 80 MET cc_start: 0.7808 (ttm) cc_final: 0.7554 (mtp) REVERT: A 247 ASP cc_start: 0.8156 (t0) cc_final: 0.7828 (t0) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 0.1684 time to fit residues: 11.2439 Evaluate side-chains 51 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 B residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.0670 chunk 43 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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: 0.7679 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4942 Z= 0.187 Angle : 0.524 5.824 6721 Z= 0.275 Chirality : 0.042 0.171 795 Planarity : 0.004 0.036 837 Dihedral : 4.160 19.760 686 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.99 % Allowed : 15.14 % Favored : 82.87 % 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: -0.35 (0.34), residues: 633 helix: 1.36 (0.30), residues: 315 sheet: -1.19 (0.67), residues: 76 loop : -2.12 (0.37), residues: 242 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 0.033 0.001 PHE A 131 TYR 0.008 0.001 TYR A 168 ARG 0.003 0.000 ARG B 19 *********************** 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 61 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.498 Fit side-chains REVERT: A 247 ASP cc_start: 0.8143 (t0) cc_final: 0.7720 (t0) outliers start: 10 outliers final: 6 residues processed: 58 average time/residue: 0.1437 time to fit residues: 11.6025 Evaluate side-chains 54 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7725 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4942 Z= 0.244 Angle : 0.559 5.429 6721 Z= 0.293 Chirality : 0.043 0.178 795 Planarity : 0.004 0.037 837 Dihedral : 4.239 20.705 686 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 1.99 % Allowed : 16.33 % Favored : 81.67 % 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: -0.35 (0.34), residues: 633 helix: 1.40 (0.30), residues: 312 sheet: -0.94 (0.71), residues: 69 loop : -2.21 (0.36), residues: 252 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 0.031 0.001 PHE A 131 TYR 0.008 0.001 TYR A 168 ARG 0.002 0.000 ARG B 99 *********************** 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 58 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.517 Fit side-chains REVERT: A 80 MET cc_start: 0.7648 (ttm) cc_final: 0.7382 (ttm) REVERT: A 247 ASP cc_start: 0.8175 (t0) cc_final: 0.7713 (t0) outliers start: 10 outliers final: 8 residues processed: 54 average time/residue: 0.1461 time to fit residues: 10.9194 Evaluate side-chains 55 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 31 ILE 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: 0.9980 chunk 12 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4942 Z= 0.229 Angle : 0.545 5.403 6721 Z= 0.287 Chirality : 0.043 0.174 795 Planarity : 0.004 0.036 837 Dihedral : 4.229 20.689 686 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.59 % Allowed : 16.73 % Favored : 80.68 % 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: 1.41 (0.30), residues: 315 sheet: -0.95 (0.71), residues: 69 loop : -2.20 (0.36), residues: 249 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 0.033 0.001 PHE A 131 TYR 0.008 0.001 TYR A 168 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 62 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.473 Fit side-chains REVERT: A 80 MET cc_start: 0.7668 (ttm) cc_final: 0.7406 (ttm) REVERT: A 247 ASP cc_start: 0.8178 (t0) cc_final: 0.7701 (t0) REVERT: A 327 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7614 (m-10) outliers start: 13 outliers final: 9 residues processed: 58 average time/residue: 0.1450 time to fit residues: 11.5782 Evaluate side-chains 58 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 C residue 21 SER Chi-restraints excluded: chain C residue 31 ILE 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: 0.8980 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 36 optimal weight: 0.0470 chunk 18 optimal weight: 0.1980 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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: 0.7679 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4942 Z= 0.176 Angle : 0.521 5.332 6721 Z= 0.275 Chirality : 0.042 0.170 795 Planarity : 0.004 0.036 837 Dihedral : 4.167 19.751 686 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.19 % Allowed : 17.73 % Favored : 80.08 % 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: 1.50 (0.30), residues: 315 sheet: -1.15 (0.66), residues: 77 loop : -2.28 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 229 HIS 0.000 0.000 HIS A 207 PHE 0.037 0.001 PHE C 50 TYR 0.008 0.001 TYR A 168 ARG 0.001 0.000 ARG B 120 *********************** 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 60 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.489 Fit side-chains REVERT: A 247 ASP cc_start: 0.8108 (t0) cc_final: 0.7615 (t0) REVERT: A 327 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7683 (m-10) outliers start: 11 outliers final: 8 residues processed: 57 average time/residue: 0.1419 time to fit residues: 11.0970 Evaluate side-chains 58 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 364 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 31 ILE 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: 2.9990 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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: 0.7818 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 4942 Z= 0.399 Angle : 0.668 8.872 6721 Z= 0.345 Chirality : 0.047 0.193 795 Planarity : 0.005 0.041 837 Dihedral : 4.457 23.159 686 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.39 % Allowed : 16.33 % Favored : 80.28 % 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: -0.51 (0.34), residues: 633 helix: 1.30 (0.30), residues: 308 sheet: -1.48 (0.66), residues: 77 loop : -2.13 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 229 HIS 0.001 0.001 HIS A 207 PHE 0.042 0.002 PHE C 50 TYR 0.010 0.001 TYR C 37 ARG 0.004 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 69 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 0.508 Fit side-chains REVERT: A 185 TYR cc_start: 0.8178 (OUTLIER) cc_final: 0.5276 (t80) REVERT: A 247 ASP cc_start: 0.8185 (t0) cc_final: 0.7684 (t0) REVERT: A 327 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7480 (m-10) outliers start: 17 outliers final: 13 residues processed: 65 average time/residue: 0.1555 time to fit residues: 13.5159 Evaluate side-chains 66 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 185 TYR 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 31 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 78 VAL 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: 0.5980 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.7777 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 : 0.004 0.047 4942 Z= 0.278 Angle : 0.613 8.293 6721 Z= 0.319 Chirality : 0.044 0.183 795 Planarity : 0.005 0.038 837 Dihedral : 4.484 21.796 686 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.59 % Allowed : 17.13 % Favored : 80.28 % 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: -0.50 (0.34), residues: 633 helix: 1.34 (0.30), residues: 310 sheet: -1.68 (0.63), residues: 81 loop : -2.10 (0.37), 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 0.042 0.002 PHE C 50 TYR 0.008 0.001 TYR A 168 ARG 0.006 0.000 ARG B 19 *********************** 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 65 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.481 Fit side-chains REVERT: A 247 ASP cc_start: 0.8175 (t0) cc_final: 0.7665 (t0) REVERT: A 327 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7521 (m-10) REVERT: B 83 MET cc_start: 0.6164 (mmp) cc_final: 0.5768 (mmp) outliers start: 13 outliers final: 11 residues processed: 61 average time/residue: 0.1473 time to fit residues: 12.2898 Evaluate side-chains 64 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 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 31 ILE Chi-restraints excluded: chain C residue 78 VAL 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 57 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7733 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4942 Z= 0.217 Angle : 0.594 9.580 6721 Z= 0.305 Chirality : 0.043 0.175 795 Planarity : 0.004 0.037 837 Dihedral : 4.364 20.085 686 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 1.99 % Allowed : 17.93 % Favored : 80.08 % 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: -0.41 (0.34), residues: 633 helix: 1.43 (0.30), residues: 312 sheet: -1.65 (0.63), residues: 81 loop : -2.11 (0.38), residues: 240 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 0.032 0.001 PHE A 131 TYR 0.006 0.001 TYR A 168 ARG 0.005 0.000 ARG B 19 ********************** 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 62 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.478 Fit side-chains REVERT: A 247 ASP cc_start: 0.8167 (t0) cc_final: 0.7649 (t0) REVERT: A 327 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7648 (m-10) REVERT: C 109 TRP cc_start: 0.8783 (m100) cc_final: 0.8572 (m100) REVERT: B 83 MET cc_start: 0.6391 (mmp) cc_final: 0.5945 (mmp) outliers start: 10 outliers final: 8 residues processed: 58 average time/residue: 0.1518 time to fit residues: 12.1267 Evaluate side-chains 61 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 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: 0.0670 chunk 20 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 43 optimal weight: 0.1980 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.151715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.119591 restraints weight = 4992.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.120660 restraints weight = 4722.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.121344 restraints weight = 4012.110| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1805 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= 0.186 Angle : 0.572 8.328 6721 Z= 0.295 Chirality : 0.042 0.173 795 Planarity : 0.004 0.038 837 Dihedral : 4.272 19.514 686 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.19 % Allowed : 17.33 % Favored : 80.48 % 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 (0.35), residues: 633 helix: 1.58 (0.30), residues: 312 sheet: -1.57 (0.64), residues: 81 loop : -2.08 (0.38), residues: 240 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 0.006 0.001 TYR A 168 ARG 0.006 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1292.95 seconds wall clock time: 24 minutes 4.73 seconds (1444.73 seconds total)