Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:53:46 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qia_13985/11_2022/7qia_13985.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qia_13985/11_2022/7qia_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_13985/11_2022/7qia_13985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qia_13985/11_2022/7qia_13985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qia_13985/11_2022/7qia_13985.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qia_13985/11_2022/7qia_13985.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/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: 3.21, 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 - 3.50 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: 1.86 Conformation dependent library (CDL) restraints added in 746.3 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: 0.31 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: 1.29 Time building geometry restraints manager: 2.02 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 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. 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: 0.210 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: 1.690 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.040 Process input model: 17.320 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 % 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 *********************** 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 : 0.523 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1436 time to fit residues: 10.6393 Evaluate side-chains 49 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.582 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7215 ------------------------------------------------------------------------------- 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: 0.5980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 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: 0.9984 ------------------------------------------------------------------------------- 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: 0.8058 moved from start: 0.0978 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= 0.285 Angle : 0.619 10.616 6721 Z= 0.320 Chirality : 0.044 0.184 795 Planarity : 0.005 0.038 837 Dihedral : 4.330 20.547 686 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.34), residues: 633 helix: 0.99 (0.29), residues: 315 sheet: -1.62 (0.63), residues: 84 loop : -2.03 (0.39), residues: 234 *********************** 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 55 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.547 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 0.1613 time to fit residues: 11.5403 Evaluate side-chains 51 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.539 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0490 time to fit residues: 1.1004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8073 moved from start: 0.1235 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= 0.256 Angle : 0.584 7.748 6721 Z= 0.304 Chirality : 0.043 0.179 795 Planarity : 0.005 0.038 837 Dihedral : 4.332 20.878 686 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 1.20 % 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: -0.46 (0.34), residues: 633 helix: 1.23 (0.30), residues: 312 sheet: -1.01 (0.70), residues: 69 loop : -2.14 (0.36), residues: 252 *********************** 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 fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.514 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 0.1926 time to fit residues: 14.0707 Evaluate side-chains 53 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.444 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0488 time to fit residues: 0.9786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 57 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8057 moved from start: 0.1350 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= 0.216 Angle : 0.547 5.950 6721 Z= 0.288 Chirality : 0.043 0.175 795 Planarity : 0.004 0.038 837 Dihedral : 4.266 20.723 686 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer Outliers : 1.20 % 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: -0.43 (0.34), residues: 633 helix: 1.32 (0.30), residues: 311 sheet: -1.03 (0.71), residues: 69 loop : -2.18 (0.36), residues: 253 *********************** 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 57 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.548 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.1489 time to fit residues: 11.0229 Evaluate side-chains 53 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.520 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0468 time to fit residues: 0.9979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 0.0670 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- 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: 0.8122 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 4942 Z= 0.320 Angle : 0.603 5.849 6721 Z= 0.317 Chirality : 0.045 0.185 795 Planarity : 0.005 0.040 837 Dihedral : 4.415 22.326 686 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer Outliers : 1.99 % 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: -0.61 (0.34), residues: 633 helix: 1.19 (0.30), residues: 311 sheet: -1.57 (0.66), residues: 77 loop : -2.15 (0.37), residues: 245 *********************** 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 59 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.520 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 57 average time/residue: 0.1423 time to fit residues: 11.2533 Evaluate side-chains 51 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.525 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0492 time to fit residues: 1.0075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8087 moved from start: 0.1653 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= 0.254 Angle : 0.569 5.480 6721 Z= 0.301 Chirality : 0.043 0.179 795 Planarity : 0.004 0.040 837 Dihedral : 4.364 21.406 686 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer Outliers : 0.80 % 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: -0.55 (0.34), residues: 633 helix: 1.22 (0.29), residues: 311 sheet: -1.07 (0.69), residues: 69 loop : -2.24 (0.36), residues: 253 *********************** 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 58 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.545 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 57 average time/residue: 0.1491 time to fit residues: 11.7214 Evaluate side-chains 55 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.459 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0467 time to fit residues: 0.9395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 44 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.8106 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 4942 Z= 0.274 Angle : 0.579 5.551 6721 Z= 0.306 Chirality : 0.044 0.187 795 Planarity : 0.004 0.041 837 Dihedral : 4.386 21.824 686 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.34), residues: 633 helix: 1.25 (0.29), residues: 311 sheet: -1.09 (0.70), residues: 69 loop : -2.13 (0.37), residues: 253 *********************** 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: 9 poor density : 51 time to evaluate : 0.525 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 57 average time/residue: 0.1445 time to fit residues: 11.3455 Evaluate side-chains 56 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0528 time to fit residues: 1.3007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 53 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1732 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= 0.209 Angle : 0.603 13.113 6721 Z= 0.303 Chirality : 0.043 0.180 795 Planarity : 0.004 0.039 837 Dihedral : 4.323 20.879 686 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer Outliers : 0.80 % 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: -0.42 (0.34), residues: 633 helix: 1.42 (0.30), residues: 309 sheet: -1.72 (0.63), residues: 81 loop : -2.04 (0.38), residues: 243 *********************** 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 59 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.527 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 59 average time/residue: 0.1446 time to fit residues: 11.9541 Evaluate side-chains 55 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.506 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0458 time to fit residues: 0.7929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 17 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 41 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1766 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= 0.200 Angle : 0.593 12.136 6721 Z= 0.298 Chirality : 0.043 0.177 795 Planarity : 0.004 0.039 837 Dihedral : 4.288 20.598 686 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer Outliers : 0.40 % 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: 1.43 (0.29), residues: 312 sheet: -1.69 (0.63), residues: 81 loop : -2.06 (0.38), residues: 240 *********************** 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 54 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.512 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 53 average time/residue: 0.1492 time to fit residues: 10.9280 Evaluate side-chains 51 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.636 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 53 optimal weight: 0.0170 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 4942 Z= 0.218 Angle : 0.608 11.698 6721 Z= 0.307 Chirality : 0.043 0.178 795 Planarity : 0.004 0.040 837 Dihedral : 4.282 20.620 686 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer Outliers : 0.40 % 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: 1.46 (0.29), residues: 312 sheet: -1.63 (0.64), residues: 81 loop : -2.05 (0.38), residues: 240 ********************** 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 54 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.557 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 0.1531 time to fit residues: 11.3536 Evaluate side-chains 52 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0658 time to fit residues: 0.8633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 20 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.0870 chunk 33 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.151629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.119709 restraints weight = 4981.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.121177 restraints weight = 4298.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.121546 restraints weight = 3686.728| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1795 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= 0.225 Angle : 0.614 10.915 6721 Z= 0.311 Chirality : 0.043 0.177 795 Planarity : 0.004 0.040 837 Dihedral : 4.291 20.906 686 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.34), residues: 633 helix: 1.40 (0.29), residues: 312 sheet: -1.05 (0.71), residues: 69 loop : -2.10 (0.37), residues: 252 =============================================================================== Job complete usr+sys time: 1195.68 seconds wall clock time: 22 minutes 25.56 seconds (1345.56 seconds total)