Starting phenix.real_space_refine on Thu Nov 14 02:32:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swh_40814/11_2024/8swh_40814.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swh_40814/11_2024/8swh_40814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swh_40814/11_2024/8swh_40814.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swh_40814/11_2024/8swh_40814.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swh_40814/11_2024/8swh_40814.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swh_40814/11_2024/8swh_40814.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 14 5.16 5 C 2155 2.51 5 N 560 2.21 5 O 661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3390 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1509 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain breaks: 5 Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "L" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 847 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 8, 'TRANS': 101} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.05, per 1000 atoms: 1.49 Number of scatterers: 3390 At special positions: 0 Unit cell: (59.45, 89.175, 89.9, 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 14 16.00 O 661 8.00 N 560 7.00 C 2155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 149 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 399.1 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 11 sheets defined 4.3% alpha, 40.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 96 through 99 Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 70 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.692A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.191A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 206 through 207 Processing sheet with id=AA5, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.727A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.727A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AA9, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AB1, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.726A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.726A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 127 hydrogen bonds defined for protein. 294 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: 0.92 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 775 1.32 - 1.46: 1087 1.46 - 1.59: 1577 1.59 - 1.73: 12 1.73 - 1.86: 20 Bond restraints: 3471 Sorted by residual: bond pdb=" CB TYR A 266 " pdb=" CG TYR A 266 " ideal model delta sigma weight residual 1.512 1.661 -0.149 2.20e-02 2.07e+03 4.58e+01 bond pdb=" CD ARG A 102 " pdb=" NE ARG A 102 " ideal model delta sigma weight residual 1.458 1.378 0.080 1.40e-02 5.10e+03 3.30e+01 bond pdb=" CB ILE L 106 " pdb=" CG1 ILE L 106 " ideal model delta sigma weight residual 1.530 1.639 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" CG PHE A 192 " pdb=" CD1 PHE A 192 " ideal model delta sigma weight residual 1.384 1.493 -0.109 2.10e-02 2.27e+03 2.70e+01 bond pdb=" CG PHE A 186 " pdb=" CD2 PHE A 186 " ideal model delta sigma weight residual 1.384 1.490 -0.106 2.10e-02 2.27e+03 2.53e+01 ... (remaining 3466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 3983 2.47 - 4.94: 605 4.94 - 7.42: 110 7.42 - 9.89: 18 9.89 - 12.36: 2 Bond angle restraints: 4718 Sorted by residual: angle pdb=" C THR A 250 " pdb=" N PRO A 251 " pdb=" CA PRO A 251 " ideal model delta sigma weight residual 119.56 128.38 -8.82 1.02e+00 9.61e-01 7.48e+01 angle pdb=" N VAL L 13 " pdb=" CA VAL L 13 " pdb=" C VAL L 13 " ideal model delta sigma weight residual 108.12 120.48 -12.36 1.44e+00 4.82e-01 7.37e+01 angle pdb=" C ASP H 52 " pdb=" N PRO H 52A" pdb=" CA PRO H 52A" ideal model delta sigma weight residual 119.47 128.90 -9.43 1.16e+00 7.43e-01 6.61e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.40 -7.37 9.90e-01 1.02e+00 5.53e+01 angle pdb=" C LEU A 24 " pdb=" N PRO A 25 " pdb=" CA PRO A 25 " ideal model delta sigma weight residual 120.38 127.95 -7.57 1.03e+00 9.43e-01 5.40e+01 ... (remaining 4713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.00: 2018 21.00 - 41.99: 49 41.99 - 62.98: 8 62.98 - 83.97: 11 83.97 - 104.97: 6 Dihedral angle restraints: 2092 sinusoidal: 874 harmonic: 1218 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 144.41 -51.41 1 1.00e+01 1.00e-02 3.61e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 61.81 31.19 1 1.00e+01 1.00e-02 1.39e+01 dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.26 104.97 1 3.00e+01 1.11e-03 1.34e+01 ... (remaining 2089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 359 0.096 - 0.191: 119 0.191 - 0.287: 45 0.287 - 0.382: 10 0.382 - 0.478: 6 Chirality restraints: 539 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.29e+02 chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.34e+01 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.75 0.48 2.00e-01 2.50e+01 5.71e+00 ... (remaining 536 not shown) Planarity restraints: 595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 149 " 0.055 2.00e-02 2.50e+03 5.87e-02 4.31e+01 pdb=" CG ASN A 149 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 149 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 149 " -0.093 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 87 " 0.054 2.00e-02 2.50e+03 3.92e-02 3.08e+01 pdb=" CG TYR L 87 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR L 87 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR L 87 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR L 87 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR L 87 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR L 87 " -0.027 2.00e-02 2.50e+03 pdb=" OH TYR L 87 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 192 " 0.065 2.00e-02 2.50e+03 3.97e-02 2.76e+01 pdb=" CG PHE A 192 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE A 192 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE A 192 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE A 192 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A 192 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 192 " 0.037 2.00e-02 2.50e+03 ... (remaining 592 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1291 2.88 - 3.39: 3037 3.39 - 3.89: 5703 3.89 - 4.40: 6762 4.40 - 4.90: 10627 Nonbonded interactions: 27420 Sorted by model distance: nonbonded pdb=" O THR A 108 " pdb=" OG1 THR A 236 " model vdw 2.378 3.040 nonbonded pdb=" N GLN H 62 " pdb=" O GLN H 62 " model vdw 2.445 2.496 nonbonded pdb=" N ASP L 60 " pdb=" OD1 ASP L 60 " model vdw 2.454 3.120 nonbonded pdb=" N ASP A 253 " pdb=" OD1 ASP A 253 " model vdw 2.454 3.120 nonbonded pdb=" N THR H 99 " pdb=" O THR H 99 " model vdw 2.458 2.496 ... (remaining 27415 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 9.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.450 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 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 : 0.021 0.149 3471 Z= 1.384 Angle : 1.931 12.361 4718 Z= 1.293 Chirality : 0.119 0.478 539 Planarity : 0.010 0.044 592 Dihedral : 12.946 104.968 1300 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.27 % Allowed : 0.82 % Favored : 98.91 % 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: -0.15 (0.40), residues: 406 helix: None (None), residues: 0 sheet: 0.14 (0.38), residues: 164 loop : -0.20 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.013 TRP H 47 HIS 0.005 0.002 HIS A 146 PHE 0.065 0.009 PHE A 192 TYR 0.076 0.011 TYR L 87 ARG 0.008 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.7643 (t0) cc_final: 0.7294 (t0) REVERT: A 83 VAL cc_start: 0.8524 (t) cc_final: 0.8118 (m) REVERT: A 151 SER cc_start: 0.8094 (p) cc_final: 0.7643 (m) REVERT: A 153 MET cc_start: 0.8307 (mtt) cc_final: 0.8072 (mtt) REVERT: A 242 LEU cc_start: 0.7954 (mt) cc_final: 0.7715 (mp) REVERT: H 31 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7868 (mt-10) REVERT: L 32 TYR cc_start: 0.5490 (m-80) cc_final: 0.5233 (m-10) REVERT: L 71 PHE cc_start: 0.7407 (m-80) cc_final: 0.6922 (m-10) REVERT: L 85 LEU cc_start: 0.8763 (mt) cc_final: 0.8341 (mt) REVERT: L 87 TYR cc_start: 0.8386 (m-80) cc_final: 0.8109 (m-80) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.1842 time to fit residues: 42.5613 Evaluate side-chains 126 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 32 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 134 GLN A 148 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN L 17 GLN L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 3471 Z= 0.288 Angle : 0.838 5.760 4718 Z= 0.453 Chirality : 0.052 0.312 539 Planarity : 0.006 0.049 592 Dihedral : 9.355 61.328 559 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 6.01 % Allowed : 17.49 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.01 (0.39), residues: 406 helix: None (None), residues: 0 sheet: -0.37 (0.38), residues: 166 loop : -0.85 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 104 HIS 0.004 0.001 HIS A 146 PHE 0.022 0.003 PHE A 133 TYR 0.020 0.002 TYR H 27 ARG 0.010 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.7939 (t0) cc_final: 0.7537 (t0) REVERT: A 82 PRO cc_start: 0.8551 (Cg_endo) cc_final: 0.8264 (Cg_exo) REVERT: A 83 VAL cc_start: 0.8580 (t) cc_final: 0.8216 (m) REVERT: A 150 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8647 (tttp) REVERT: H 48 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7326 (mtp) REVERT: H 58 ILE cc_start: 0.8696 (mm) cc_final: 0.8157 (pt) REVERT: H 61 GLN cc_start: 0.8322 (tt0) cc_final: 0.7916 (pm20) REVERT: H 72 ASP cc_start: 0.8765 (t0) cc_final: 0.8437 (t70) REVERT: H 96 PHE cc_start: 0.7687 (m-10) cc_final: 0.6812 (m-80) REVERT: L 4 LEU cc_start: 0.7034 (mp) cc_final: 0.6574 (mp) REVERT: L 70 ASP cc_start: 0.8611 (t0) cc_final: 0.8325 (t0) REVERT: L 71 PHE cc_start: 0.7390 (m-80) cc_final: 0.7023 (m-10) REVERT: L 88 CYS cc_start: 0.5110 (p) cc_final: 0.4500 (p) outliers start: 22 outliers final: 11 residues processed: 156 average time/residue: 0.1777 time to fit residues: 32.6224 Evaluate side-chains 133 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3471 Z= 0.270 Angle : 0.765 5.794 4718 Z= 0.414 Chirality : 0.051 0.364 539 Planarity : 0.005 0.045 592 Dihedral : 6.603 27.627 559 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 7.65 % Allowed : 19.95 % Favored : 72.40 % 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: -1.30 (0.39), residues: 406 helix: None (None), residues: 0 sheet: -0.47 (0.39), residues: 168 loop : -1.14 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 104 HIS 0.005 0.001 HIS A 66 PHE 0.019 0.003 PHE A 65 TYR 0.025 0.002 TYR A 91 ARG 0.006 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.8391 (t) cc_final: 0.8127 (m) REVERT: A 128 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8632 (mm) REVERT: H 58 ILE cc_start: 0.8743 (mm) cc_final: 0.8308 (pt) REVERT: H 61 GLN cc_start: 0.8361 (tt0) cc_final: 0.7921 (pm20) REVERT: H 81 GLU cc_start: 0.8423 (pp20) cc_final: 0.8204 (pp20) REVERT: L 4 LEU cc_start: 0.7170 (mp) cc_final: 0.6730 (mp) REVERT: L 70 ASP cc_start: 0.8600 (t0) cc_final: 0.8355 (t0) REVERT: L 71 PHE cc_start: 0.7585 (m-80) cc_final: 0.7064 (m-10) REVERT: L 88 CYS cc_start: 0.4428 (p) cc_final: 0.3961 (p) outliers start: 28 outliers final: 21 residues processed: 152 average time/residue: 0.1684 time to fit residues: 30.5372 Evaluate side-chains 150 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3471 Z= 0.219 Angle : 0.724 8.416 4718 Z= 0.387 Chirality : 0.051 0.402 539 Planarity : 0.005 0.038 592 Dihedral : 5.690 22.423 559 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.68 % Favored : 95.07 % Rotamer: Outliers : 7.10 % Allowed : 21.58 % Favored : 71.31 % 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: -1.36 (0.40), residues: 406 helix: None (None), residues: 0 sheet: -0.57 (0.39), residues: 166 loop : -1.13 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 104 HIS 0.005 0.001 HIS A 207 PHE 0.017 0.002 PHE A 106 TYR 0.022 0.002 TYR H 90 ARG 0.006 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.5817 (OUTLIER) cc_final: 0.5433 (mp10) REVERT: A 83 VAL cc_start: 0.8332 (t) cc_final: 0.8095 (m) REVERT: A 128 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8631 (mm) REVERT: A 177 MET cc_start: 0.6009 (OUTLIER) cc_final: 0.5782 (mmp) REVERT: H 31 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8171 (mt-10) REVERT: H 61 GLN cc_start: 0.8345 (tt0) cc_final: 0.7925 (pm20) REVERT: H 81 GLU cc_start: 0.8546 (pp20) cc_final: 0.8228 (pp20) REVERT: H 90 TYR cc_start: 0.8565 (m-80) cc_final: 0.8297 (m-80) REVERT: L 4 LEU cc_start: 0.7127 (mp) cc_final: 0.6753 (mp) REVERT: L 34 SER cc_start: 0.7400 (p) cc_final: 0.7127 (p) REVERT: L 70 ASP cc_start: 0.8532 (t0) cc_final: 0.8289 (t0) REVERT: L 71 PHE cc_start: 0.7514 (m-80) cc_final: 0.7008 (m-10) REVERT: L 87 TYR cc_start: 0.8418 (m-80) cc_final: 0.8207 (m-10) REVERT: L 88 CYS cc_start: 0.4530 (p) cc_final: 0.4140 (p) REVERT: L 105 ASP cc_start: 0.7198 (t0) cc_final: 0.6757 (t70) outliers start: 26 outliers final: 15 residues processed: 148 average time/residue: 0.1566 time to fit residues: 28.0490 Evaluate side-chains 144 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 27 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.6614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3471 Z= 0.269 Angle : 0.742 9.210 4718 Z= 0.391 Chirality : 0.051 0.329 539 Planarity : 0.005 0.037 592 Dihedral : 5.665 18.665 559 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.67 % Favored : 94.09 % Rotamer: Outliers : 7.38 % Allowed : 22.68 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.39), residues: 406 helix: None (None), residues: 0 sheet: -0.67 (0.39), residues: 167 loop : -1.38 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 104 HIS 0.004 0.001 HIS A 245 PHE 0.024 0.003 PHE A 106 TYR 0.022 0.002 TYR A 91 ARG 0.006 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8666 (mm) REVERT: A 158 ARG cc_start: 0.7850 (mmt180) cc_final: 0.7021 (mmp-170) REVERT: H 43 LYS cc_start: 0.7805 (tmmt) cc_final: 0.7456 (tttm) REVERT: H 61 GLN cc_start: 0.8471 (tt0) cc_final: 0.7905 (pm20) REVERT: H 81 GLU cc_start: 0.8550 (pp20) cc_final: 0.8320 (pp20) REVERT: H 105 GLN cc_start: 0.8207 (pm20) cc_final: 0.7565 (pm20) REVERT: L 4 LEU cc_start: 0.7399 (mp) cc_final: 0.6929 (mp) REVERT: L 34 SER cc_start: 0.7452 (p) cc_final: 0.7148 (p) REVERT: L 70 ASP cc_start: 0.8559 (t0) cc_final: 0.8332 (t0) REVERT: L 71 PHE cc_start: 0.7555 (m-80) cc_final: 0.7043 (m-10) REVERT: L 87 TYR cc_start: 0.8445 (m-80) cc_final: 0.8152 (m-10) REVERT: L 88 CYS cc_start: 0.4561 (p) cc_final: 0.4170 (p) REVERT: L 105 ASP cc_start: 0.6929 (t0) cc_final: 0.6394 (t70) outliers start: 27 outliers final: 17 residues processed: 138 average time/residue: 0.1546 time to fit residues: 26.0163 Evaluate side-chains 136 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.0060 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3471 Z= 0.240 Angle : 0.793 17.184 4718 Z= 0.397 Chirality : 0.051 0.346 539 Planarity : 0.005 0.044 592 Dihedral : 5.431 17.692 559 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.17 % Favored : 94.58 % Rotamer: Outliers : 5.74 % Allowed : 25.41 % Favored : 68.85 % 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: -1.71 (0.40), residues: 406 helix: None (None), residues: 0 sheet: -0.60 (0.40), residues: 163 loop : -1.55 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 64 HIS 0.003 0.001 HIS A 245 PHE 0.019 0.003 PHE A 106 TYR 0.023 0.002 TYR A 170 ARG 0.006 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8596 (mm) REVERT: A 158 ARG cc_start: 0.7845 (mmt180) cc_final: 0.7157 (mmp-170) REVERT: H 1 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7397 (pp30) REVERT: H 31 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8054 (tt0) REVERT: H 39 GLN cc_start: 0.8558 (tt0) cc_final: 0.8335 (tt0) REVERT: H 43 LYS cc_start: 0.7868 (tmmt) cc_final: 0.7486 (tttm) REVERT: H 61 GLN cc_start: 0.8457 (tt0) cc_final: 0.7948 (pm20) REVERT: H 105 GLN cc_start: 0.8208 (pm20) cc_final: 0.7574 (pm20) REVERT: L 70 ASP cc_start: 0.8508 (t0) cc_final: 0.8296 (t0) REVERT: L 71 PHE cc_start: 0.7586 (m-80) cc_final: 0.7060 (m-10) REVERT: L 105 ASP cc_start: 0.6674 (t0) cc_final: 0.6118 (t70) outliers start: 21 outliers final: 16 residues processed: 138 average time/residue: 0.1648 time to fit residues: 27.2623 Evaluate side-chains 138 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 98 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.0470 chunk 11 optimal weight: 0.1980 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.7056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3471 Z= 0.231 Angle : 0.771 14.041 4718 Z= 0.390 Chirality : 0.051 0.264 539 Planarity : 0.005 0.067 592 Dihedral : 5.275 18.294 559 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.42 % Favored : 94.33 % Rotamer: Outliers : 5.19 % Allowed : 27.05 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.40), residues: 406 helix: None (None), residues: 0 sheet: -0.63 (0.41), residues: 163 loop : -1.59 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.003 0.001 HIS A 146 PHE 0.021 0.003 PHE A 106 TYR 0.013 0.001 TYR A 91 ARG 0.007 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8573 (mm) REVERT: A 158 ARG cc_start: 0.7863 (mmt180) cc_final: 0.6914 (mmp-170) REVERT: H 1 GLN cc_start: 0.8262 (tt0) cc_final: 0.7880 (pp30) REVERT: H 31 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8081 (tt0) REVERT: H 43 LYS cc_start: 0.7858 (tmmt) cc_final: 0.7622 (tttt) REVERT: H 61 GLN cc_start: 0.8425 (tt0) cc_final: 0.7921 (pm20) REVERT: H 105 GLN cc_start: 0.8187 (pm20) cc_final: 0.7887 (pm20) REVERT: L 71 PHE cc_start: 0.7553 (m-80) cc_final: 0.6990 (m-10) REVERT: L 105 ASP cc_start: 0.6511 (t0) cc_final: 0.5868 (t70) outliers start: 19 outliers final: 12 residues processed: 131 average time/residue: 0.1666 time to fit residues: 26.5594 Evaluate side-chains 129 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 27 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.0570 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.7213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3471 Z= 0.251 Angle : 0.779 11.462 4718 Z= 0.396 Chirality : 0.052 0.340 539 Planarity : 0.006 0.055 592 Dihedral : 5.255 18.325 559 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.40 % Favored : 93.35 % Rotamer: Outliers : 5.19 % Allowed : 27.05 % Favored : 67.76 % 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: -1.84 (0.40), residues: 406 helix: None (None), residues: 0 sheet: -0.71 (0.43), residues: 160 loop : -1.61 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 104 HIS 0.003 0.001 HIS A 245 PHE 0.022 0.003 PHE A 106 TYR 0.014 0.001 TYR A 91 ARG 0.007 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8546 (mm) REVERT: A 158 ARG cc_start: 0.7891 (mmt180) cc_final: 0.7233 (mmp-170) REVERT: H 31 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8083 (tt0) REVERT: H 43 LYS cc_start: 0.7884 (tmmt) cc_final: 0.7655 (tttt) REVERT: H 105 GLN cc_start: 0.8238 (pm20) cc_final: 0.7958 (pm20) REVERT: L 71 PHE cc_start: 0.7521 (m-80) cc_final: 0.6990 (m-10) REVERT: L 105 ASP cc_start: 0.6402 (t0) cc_final: 0.5762 (t70) outliers start: 19 outliers final: 13 residues processed: 131 average time/residue: 0.1425 time to fit residues: 23.0109 Evaluate side-chains 127 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 27 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.0040 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.7533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3471 Z= 0.249 Angle : 0.807 10.462 4718 Z= 0.414 Chirality : 0.051 0.266 539 Planarity : 0.006 0.056 592 Dihedral : 5.293 27.229 559 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.40 % Favored : 93.35 % Rotamer: Outliers : 4.37 % Allowed : 28.96 % Favored : 66.67 % 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: -1.78 (0.41), residues: 406 helix: None (None), residues: 0 sheet: -0.71 (0.41), residues: 167 loop : -1.56 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 104 HIS 0.001 0.000 HIS A 245 PHE 0.022 0.003 PHE A 106 TYR 0.015 0.001 TYR A 91 ARG 0.012 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8513 (mm) REVERT: A 158 ARG cc_start: 0.7870 (mmt180) cc_final: 0.7620 (mmp-170) REVERT: H 31 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7927 (tt0) REVERT: H 43 LYS cc_start: 0.7923 (tmmt) cc_final: 0.7689 (tttt) REVERT: H 51 PHE cc_start: 0.8049 (t80) cc_final: 0.7832 (t80) REVERT: H 61 GLN cc_start: 0.8494 (tt0) cc_final: 0.7989 (pm20) REVERT: H 81 GLU cc_start: 0.8643 (pp20) cc_final: 0.8339 (pp20) REVERT: H 105 GLN cc_start: 0.8214 (pm20) cc_final: 0.7617 (pm20) REVERT: L 71 PHE cc_start: 0.7476 (m-80) cc_final: 0.7006 (m-10) REVERT: L 105 ASP cc_start: 0.6075 (t0) cc_final: 0.5463 (t70) outliers start: 16 outliers final: 14 residues processed: 129 average time/residue: 0.1577 time to fit residues: 24.6715 Evaluate side-chains 128 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 27 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.0770 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.0770 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.7690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 3471 Z= 0.256 Angle : 0.788 10.170 4718 Z= 0.407 Chirality : 0.050 0.242 539 Planarity : 0.006 0.060 592 Dihedral : 5.342 27.138 559 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.13 % Favored : 91.63 % Rotamer: Outliers : 4.64 % Allowed : 29.78 % Favored : 65.57 % 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: -1.76 (0.41), residues: 406 helix: None (None), residues: 0 sheet: -0.57 (0.43), residues: 159 loop : -1.62 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 104 HIS 0.003 0.001 HIS A 245 PHE 0.026 0.003 PHE A 106 TYR 0.016 0.001 TYR A 170 ARG 0.010 0.001 ARG H 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7959 (tmmt) cc_final: 0.7717 (tttt) REVERT: H 51 PHE cc_start: 0.8071 (t80) cc_final: 0.7848 (t80) REVERT: H 100 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7874 (mmt) REVERT: H 105 GLN cc_start: 0.8271 (pm20) cc_final: 0.7652 (pm20) REVERT: L 34 SER cc_start: 0.7302 (p) cc_final: 0.7052 (p) REVERT: L 71 PHE cc_start: 0.7513 (m-80) cc_final: 0.7195 (m-10) REVERT: L 105 ASP cc_start: 0.5807 (t0) cc_final: 0.5226 (t70) outliers start: 17 outliers final: 14 residues processed: 123 average time/residue: 0.1536 time to fit residues: 23.0828 Evaluate side-chains 123 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 27 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** 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 = 0.4137 r_free = 0.4137 target = 0.145868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.124090 restraints weight = 9427.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.127459 restraints weight = 5507.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.129651 restraints weight = 3868.034| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.7888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 3471 Z= 0.323 Angle : 0.825 11.231 4718 Z= 0.424 Chirality : 0.052 0.276 539 Planarity : 0.006 0.061 592 Dihedral : 5.535 26.412 559 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.37 % Favored : 91.38 % Rotamer: Outliers : 4.64 % Allowed : 30.33 % Favored : 65.03 % 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: -1.93 (0.41), residues: 406 helix: None (None), residues: 0 sheet: -0.80 (0.42), residues: 165 loop : -1.66 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 104 HIS 0.002 0.001 HIS A 245 PHE 0.022 0.003 PHE A 106 TYR 0.027 0.002 TYR H 100H ARG 0.006 0.001 ARG H 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1722.90 seconds wall clock time: 31 minutes 45.15 seconds (1905.15 seconds total)