Starting phenix.real_space_refine on Tue Dec 31 04:04:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xkw_38429/12_2024/8xkw_38429.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xkw_38429/12_2024/8xkw_38429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xkw_38429/12_2024/8xkw_38429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xkw_38429/12_2024/8xkw_38429.map" model { file = "/net/cci-nas-00/data/ceres_data/8xkw_38429/12_2024/8xkw_38429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xkw_38429/12_2024/8xkw_38429.cif" } resolution = 3.64 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= 0.002 sd= 0.034 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: 5 Type Number sf(0) Gaussians S 24 5.16 5 C 4814 2.51 5 N 1264 2.21 5 O 1418 1.98 5 H 7182 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14702 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 784 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "C" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 638 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "D" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 540 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "E" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 719 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 41} Chain: "A" Number of atoms: 4670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4670 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 1 Chain: "G" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 784 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "H" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 638 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "I" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 540 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "J" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 719 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 41} Chain: "F" Number of atoms: 4670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4670 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 1 Time building chain proxies: 7.71, per 1000 atoms: 0.52 Number of scatterers: 14702 At special positions: 0 Unit cell: (126.14, 109.18, 92.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 O 1418 8.00 N 1264 7.00 C 4814 6.00 H 7182 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 1.2 seconds 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 37.4% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'B' and resid 86 through 135 Proline residue: B 112 - end of helix Processing helix chain 'C' and resid 14 through 49 Proline residue: C 39 - end of helix Processing helix chain 'D' and resid 30 through 51 removed outlier: 3.778A pdb=" N THR D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 58 removed outlier: 3.834A pdb=" N ASP D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 44 removed outlier: 6.028A pdb=" N ILE E 33 " --> pdb=" O HIS E 29 " (cutoff:3.500A) Proline residue: E 34 - end of helix Processing helix chain 'E' and resid 49 through 55 Processing helix chain 'A' and resid 50 through 54 removed outlier: 3.880A pdb=" N SER A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 50 through 54' Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'G' and resid 87 through 135 Proline residue: G 112 - end of helix Processing helix chain 'H' and resid 14 through 49 Proline residue: H 39 - end of helix Processing helix chain 'I' and resid 30 through 51 removed outlier: 3.778A pdb=" N THR I 34 " --> pdb=" O SER I 30 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE I 35 " --> pdb=" O PRO I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 58 removed outlier: 3.834A pdb=" N ASP I 55 " --> pdb=" O SER I 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 44 removed outlier: 6.028A pdb=" N ILE J 33 " --> pdb=" O HIS J 29 " (cutoff:3.500A) Proline residue: J 34 - end of helix Processing helix chain 'J' and resid 49 through 55 Processing helix chain 'F' and resid 50 through 54 removed outlier: 3.880A pdb=" N SER F 54 " --> pdb=" O SER F 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 50 through 54' Processing helix chain 'F' and resid 63 through 66 Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 364 through 373 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 93 removed outlier: 6.585A pdb=" N PHE A 98 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N CYS A 165 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR A 194 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 257 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ARG A 85 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 85 through 93 removed outlier: 6.585A pdb=" N PHE F 98 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N CYS F 165 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N THR F 194 " --> pdb=" O PRO F 185 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU F 209 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA F 254 " --> pdb=" O GLN F 250 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA F 257 " --> pdb=" O THR F 273 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS F 323 " --> pdb=" O ASP F 319 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ARG F 85 " --> pdb=" O LEU F 357 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1467 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: 5.47 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 3.89: 14842 3.89 - 6.95: 8 6.95 - 10.00: 13 10.00 - 13.06: 0 13.06 - 16.12: 1 Warning: very large bond lengths. Bond restraints: 14864 Sorted by residual: bond pdb=" CB MET G 126 " pdb=" HB1 MET G 126 " ideal model delta sigma weight residual 0.970 16.116 -15.146 2.00e-02 2.50e+03 5.74e+05 bond pdb=" CG GLN F 358 " pdb=" HG1 GLN F 358 " ideal model delta sigma weight residual 0.970 9.352 -8.382 2.00e-02 2.50e+03 1.76e+05 bond pdb=" CG GLN A 358 " pdb=" HG1 GLN A 358 " ideal model delta sigma weight residual 0.970 9.352 -8.382 2.00e-02 2.50e+03 1.76e+05 bond pdb=" CB MET B 126 " pdb=" HB1 MET B 126 " ideal model delta sigma weight residual 0.970 9.286 -8.316 2.00e-02 2.50e+03 1.73e+05 bond pdb=" CB GLN F 169 " pdb=" HB1 GLN F 169 " ideal model delta sigma weight residual 0.970 8.815 -7.845 2.00e-02 2.50e+03 1.54e+05 ... (remaining 14859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 19.32: 26523 19.32 - 38.64: 107 38.64 - 57.97: 18 57.97 - 77.29: 13 77.29 - 96.61: 11 Bond angle restraints: 26672 Sorted by residual: angle pdb=" HB1 GLN F 169 " pdb=" CB GLN F 169 " pdb=" HB2 GLN F 169 " ideal model delta sigma weight residual 110.00 13.39 96.61 3.00e+00 1.11e-01 1.04e+03 angle pdb=" HB1 GLN A 169 " pdb=" CB GLN A 169 " pdb=" HB2 GLN A 169 " ideal model delta sigma weight residual 110.00 13.40 96.60 3.00e+00 1.11e-01 1.04e+03 angle pdb=" CB GLU F 298 " pdb=" CG GLU F 298 " pdb=" HG1 GLU F 298 " ideal model delta sigma weight residual 109.00 16.71 92.29 3.00e+00 1.11e-01 9.46e+02 angle pdb=" CB GLU A 298 " pdb=" CG GLU A 298 " pdb=" HG1 GLU A 298 " ideal model delta sigma weight residual 109.00 16.74 92.26 3.00e+00 1.11e-01 9.46e+02 angle pdb=" HG1 MET B 126 " pdb=" CG MET B 126 " pdb=" HG3 MET B 126 " ideal model delta sigma weight residual 110.00 25.52 84.48 3.00e+00 1.11e-01 7.93e+02 ... (remaining 26667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6264 17.76 - 35.51: 632 35.51 - 53.27: 146 53.27 - 71.02: 32 71.02 - 88.78: 8 Dihedral angle restraints: 7082 sinusoidal: 3760 harmonic: 3322 Sorted by residual: dihedral pdb=" CA ASN A 95 " pdb=" C ASN A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ASN F 95 " pdb=" C ASN F 95 " pdb=" N PRO F 96 " pdb=" CA PRO F 96 " ideal model delta harmonic sigma weight residual 180.00 154.66 25.34 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" C GLU F 360 " pdb=" N GLU F 360 " pdb=" CA GLU F 360 " pdb=" CB GLU F 360 " ideal model delta harmonic sigma weight residual -122.60 -134.01 11.41 0 2.50e+00 1.60e-01 2.08e+01 ... (remaining 7079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1063 0.077 - 0.154: 87 0.154 - 0.231: 4 0.231 - 0.308: 4 0.308 - 0.385: 18 Chirality restraints: 1176 Sorted by residual: chirality pdb=" CA HIS A 49 " pdb=" N HIS A 49 " pdb=" C HIS A 49 " pdb=" CB HIS A 49 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA HIS F 49 " pdb=" N HIS F 49 " pdb=" C HIS F 49 " pdb=" CB HIS F 49 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA THR A 351 " pdb=" N THR A 351 " pdb=" C THR A 351 " pdb=" CB THR A 351 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 1173 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 358 " -0.036 2.00e-02 2.50e+03 4.41e-01 2.92e+03 pdb=" CD GLN A 358 " 0.000 2.00e-02 2.50e+03 pdb=" OE1 GLN A 358 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 GLN A 358 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 358 " -0.764 2.00e-02 2.50e+03 pdb="HE22 GLN A 358 " 0.763 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 358 " 0.036 2.00e-02 2.50e+03 4.41e-01 2.92e+03 pdb=" CD GLN F 358 " 0.000 2.00e-02 2.50e+03 pdb=" OE1 GLN F 358 " -0.036 2.00e-02 2.50e+03 pdb=" NE2 GLN F 358 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN F 358 " 0.763 2.00e-02 2.50e+03 pdb="HE22 GLN F 358 " -0.762 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 49 " 0.170 2.00e-02 2.50e+03 1.87e-01 5.22e+02 pdb=" CG ASN E 49 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN E 49 " -0.163 2.00e-02 2.50e+03 pdb=" ND2 ASN E 49 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN E 49 " 0.281 2.00e-02 2.50e+03 pdb="HD22 ASN E 49 " -0.272 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 316 2.08 - 2.71: 23559 2.71 - 3.34: 42061 3.34 - 3.97: 51043 3.97 - 4.60: 78407 Nonbonded interactions: 195386 Sorted by model distance: nonbonded pdb=" HB1 MET G 126 " pdb=" HZ2 LYS F 331 " model vdw 1.455 2.270 nonbonded pdb=" H THR F 351 " pdb=" HA THR F 351 " model vdw 1.561 1.816 nonbonded pdb=" H THR A 351 " pdb=" HA THR A 351 " model vdw 1.561 1.816 nonbonded pdb=" H ILE A 256 " pdb=" HA ILE A 256 " model vdw 1.580 1.816 nonbonded pdb=" H ILE F 256 " pdb=" HA ILE F 256 " model vdw 1.580 1.816 ... (remaining 195381 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 0.250 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 33.560 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.004 0.047 7682 Z= 0.243 Angle : 0.677 9.125 10418 Z= 0.423 Chirality : 0.062 0.385 1176 Planarity : 0.004 0.040 1334 Dihedral : 15.659 88.780 2746 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.24 % Allowed : 20.54 % Favored : 79.22 % Cbeta Deviations : 0.22 % 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: 1.25 (0.29), residues: 936 helix: 2.63 (0.29), residues: 340 sheet: 0.20 (0.27), residues: 400 loop : -0.96 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 36 HIS 0.003 0.001 HIS F 102 PHE 0.006 0.001 PHE G 130 TYR 0.005 0.001 TYR A 114 ARG 0.002 0.000 ARG F 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 353 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 1.241 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.3795 time to fit residues: 34.3376 Evaluate side-chains 60 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 ASN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 GLN J 49 ASN ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7682 Z= 0.270 Angle : 0.640 10.188 10418 Z= 0.348 Chirality : 0.061 0.458 1176 Planarity : 0.004 0.037 1334 Dihedral : 4.014 28.114 1008 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.49 % Allowed : 20.17 % Favored : 79.34 % Cbeta Deviations : 0.45 % 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: 0.96 (0.29), residues: 936 helix: 2.71 (0.29), residues: 340 sheet: -0.29 (0.26), residues: 408 loop : -0.92 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 36 HIS 0.002 0.001 HIS A 346 PHE 0.008 0.001 PHE G 130 TYR 0.005 0.001 TYR F 171 ARG 0.002 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 353 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 1.241 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 67 average time/residue: 0.3673 time to fit residues: 35.2328 Evaluate side-chains 65 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain J residue 18 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7682 Z= 0.173 Angle : 0.582 9.521 10418 Z= 0.311 Chirality : 0.060 0.441 1176 Planarity : 0.004 0.037 1334 Dihedral : 3.882 28.832 1008 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 20.78 % Favored : 79.22 % Cbeta Deviations : 0.45 % 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: 1.24 (0.29), residues: 936 helix: 3.18 (0.28), residues: 340 sheet: -0.37 (0.27), residues: 408 loop : -0.71 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 41 HIS 0.003 0.001 HIS A 102 PHE 0.009 0.001 PHE A 104 TYR 0.008 0.001 TYR A 171 ARG 0.002 0.000 ARG F 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 353 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.196 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 126 MET cc_start: 0.9372 (mmm) cc_final: 0.9090 (mmt) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.3746 time to fit residues: 33.4952 Evaluate side-chains 62 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 GLN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 133 GLN J 52 ASN ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7682 Z= 0.178 Angle : 0.567 9.614 10418 Z= 0.301 Chirality : 0.060 0.440 1176 Planarity : 0.003 0.037 1334 Dihedral : 3.763 29.149 1008 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.12 % Allowed : 20.42 % Favored : 79.46 % Cbeta Deviations : 0.45 % 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: 1.41 (0.30), residues: 936 helix: 3.40 (0.28), residues: 340 sheet: -0.33 (0.27), residues: 402 loop : -0.63 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 41 HIS 0.004 0.001 HIS A 102 PHE 0.007 0.001 PHE F 104 TYR 0.004 0.001 TYR A 171 ARG 0.002 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 353 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 1.174 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 64 average time/residue: 0.3725 time to fit residues: 33.9729 Evaluate side-chains 65 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7682 Z= 0.307 Angle : 0.618 10.052 10418 Z= 0.330 Chirality : 0.060 0.449 1176 Planarity : 0.004 0.036 1334 Dihedral : 3.940 28.789 1008 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.34 % Allowed : 20.42 % Favored : 78.24 % Cbeta Deviations : 0.45 % 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 (0.30), residues: 936 helix: 3.30 (0.28), residues: 340 sheet: -0.40 (0.27), residues: 408 loop : -0.64 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 145 HIS 0.006 0.001 HIS F 102 PHE 0.009 0.001 PHE F 104 TYR 0.007 0.001 TYR F 114 ARG 0.004 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 353 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 1.238 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 70 average time/residue: 0.3719 time to fit residues: 37.5822 Evaluate side-chains 68 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7682 Z= 0.177 Angle : 0.575 9.860 10418 Z= 0.303 Chirality : 0.060 0.445 1176 Planarity : 0.003 0.038 1334 Dihedral : 3.799 28.283 1008 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.86 % Allowed : 21.15 % Favored : 78.00 % Cbeta Deviations : 0.45 % 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: 1.58 (0.30), residues: 936 helix: 3.49 (0.28), residues: 340 sheet: -0.06 (0.27), residues: 390 loop : -0.86 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 41 HIS 0.003 0.001 HIS F 102 PHE 0.011 0.001 PHE G 130 TYR 0.006 0.001 TYR F 171 ARG 0.002 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 353 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 1.128 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: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 66 average time/residue: 0.3688 time to fit residues: 34.8088 Evaluate side-chains 71 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain F residue 131 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7682 Z= 0.232 Angle : 0.586 9.958 10418 Z= 0.309 Chirality : 0.060 0.444 1176 Planarity : 0.003 0.038 1334 Dihedral : 3.765 28.398 1008 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.86 % Allowed : 22.13 % Favored : 77.02 % Cbeta Deviations : 0.45 % 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: 1.53 (0.30), residues: 936 helix: 3.49 (0.28), residues: 340 sheet: -0.11 (0.27), residues: 396 loop : -0.96 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 41 HIS 0.004 0.001 HIS F 102 PHE 0.006 0.001 PHE A 104 TYR 0.005 0.001 TYR F 114 ARG 0.003 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 353 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 1.214 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.9300 (mmt) cc_final: 0.8945 (mmt) outliers start: 7 outliers final: 7 residues processed: 66 average time/residue: 0.3812 time to fit residues: 36.3173 Evaluate side-chains 68 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 271 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.0970 chunk 17 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7682 Z= 0.161 Angle : 0.568 9.703 10418 Z= 0.297 Chirality : 0.060 0.438 1176 Planarity : 0.003 0.039 1334 Dihedral : 3.690 27.949 1008 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.73 % Allowed : 22.25 % Favored : 77.02 % Cbeta Deviations : 0.45 % 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 (0.30), residues: 936 helix: 3.61 (0.28), residues: 340 sheet: -0.01 (0.27), residues: 390 loop : -0.78 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 36 HIS 0.003 0.001 HIS F 102 PHE 0.016 0.001 PHE G 130 TYR 0.004 0.001 TYR F 114 ARG 0.002 0.000 ARG F 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 353 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 1.272 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: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.8999 (mmt) cc_final: 0.8751 (mmt) REVERT: G 126 MET cc_start: 0.9416 (tpp) cc_final: 0.9168 (mmm) outliers start: 6 outliers final: 6 residues processed: 64 average time/residue: 0.3768 time to fit residues: 34.8386 Evaluate side-chains 67 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain F residue 131 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 74 optimal weight: 0.0770 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7682 Z= 0.129 Angle : 0.558 9.358 10418 Z= 0.291 Chirality : 0.060 0.429 1176 Planarity : 0.003 0.040 1334 Dihedral : 3.569 27.787 1008 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.61 % Allowed : 22.00 % Favored : 77.38 % Cbeta Deviations : 0.45 % 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 (0.30), residues: 936 helix: 3.73 (0.28), residues: 340 sheet: -0.14 (0.27), residues: 402 loop : -0.29 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 260 HIS 0.002 0.001 HIS A 102 PHE 0.023 0.001 PHE B 130 TYR 0.004 0.001 TYR F 307 ARG 0.001 0.000 ARG E 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 353 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 1.313 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: symmetry clash outliers start: 5 outliers final: 5 residues processed: 64 average time/residue: 0.3758 time to fit residues: 34.4001 Evaluate side-chains 67 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain F residue 131 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 7 optimal weight: 0.0980 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7682 Z= 0.174 Angle : 0.565 9.802 10418 Z= 0.295 Chirality : 0.059 0.441 1176 Planarity : 0.003 0.039 1334 Dihedral : 3.534 27.110 1008 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.61 % Allowed : 22.00 % Favored : 77.38 % Cbeta Deviations : 0.45 % 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: 1.90 (0.30), residues: 936 helix: 3.76 (0.28), residues: 340 sheet: 0.09 (0.27), residues: 390 loop : -0.68 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 145 HIS 0.002 0.001 HIS A 102 PHE 0.018 0.001 PHE G 130 TYR 0.004 0.001 TYR F 114 ARG 0.001 0.000 ARG A 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 353 is missing expected H atoms. Skipping. Residue ILE 353 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 1.260 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: symmetry clash REVERT: B 126 MET cc_start: 0.9279 (mmt) cc_final: 0.8898 (mmt) outliers start: 5 outliers final: 5 residues processed: 64 average time/residue: 0.3748 time to fit residues: 34.2134 Evaluate side-chains 66 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain F residue 131 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 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 = 0.3530 r_free = 0.3530 target = 0.052548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.046942 restraints weight = 175587.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.048153 restraints weight = 77196.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.048844 restraints weight = 44601.103| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7682 Z= 0.147 Angle : 0.567 9.588 10418 Z= 0.293 Chirality : 0.059 0.436 1176 Planarity : 0.003 0.038 1334 Dihedral : 3.531 27.443 1008 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.61 % Allowed : 22.25 % Favored : 77.14 % Cbeta Deviations : 0.45 % 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: 1.87 (0.30), residues: 936 helix: 3.75 (0.29), residues: 340 sheet: -0.12 (0.27), residues: 402 loop : -0.28 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 36 HIS 0.002 0.001 HIS A 102 PHE 0.005 0.001 PHE F 104 TYR 0.004 0.001 TYR J 38 ARG 0.001 0.000 ARG A 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2988.98 seconds wall clock time: 54 minutes 30.69 seconds (3270.69 seconds total)