Starting phenix.real_space_refine on Mon Jan 20 04:43:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xkw_38429/01_2025/8xkw_38429.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xkw_38429/01_2025/8xkw_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_38429/01_2025/8xkw_38429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xkw_38429/01_2025/8xkw_38429.map" model { file = "/net/cci-nas-00/data/ceres_data/8xkw_38429/01_2025/8xkw_38429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xkw_38429/01_2025/8xkw_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-5571/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: 6.96, per 1000 atoms: 0.47 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: 3.53 Conformation dependent library (CDL) restraints added in 1.1 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: 1.05 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: 5.90 Time building geometry restraints manager: 4.28 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: 0.01 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: 2.880 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: 0.280 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 32.260 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.450 ------------------------------------------------------------------------------- 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 : 1.142 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: 0.3820 time to fit residues: 34.5194 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 : 1.142 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.052726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.047095 restraints weight = 183871.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.048293 restraints weight = 78819.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.048987 restraints weight = 44720.388| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 : 1.126 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: 0.3589 time to fit residues: 34.8307 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 : 1.245 ------------------------------------------------------------------------------- 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 11 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.052380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.046961 restraints weight = 185632.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.048096 restraints weight = 78239.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.048926 restraints weight = 44759.485| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7682 Z= 0.265 Angle : 0.605 9.712 10418 Z= 0.326 Chirality : 0.060 0.445 1176 Planarity : 0.004 0.037 1334 Dihedral : 4.003 29.178 1008 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.24 % Allowed : 20.42 % 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: 1.08 (0.29), residues: 936 helix: 3.04 (0.28), residues: 340 sheet: -0.42 (0.27), residues: 408 loop : -0.83 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 41 HIS 0.006 0.001 HIS A 102 PHE 0.010 0.001 PHE A 104 TYR 0.009 0.001 TYR A 171 ARG 0.003 0.000 ARG A 219 *********************** 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 64 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 1.190 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 outliers start: 2 outliers final: 1 residues processed: 63 average time/residue: 0.3803 time to fit residues: 34.2084 Evaluate side-chains 63 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 85 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.052010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.046488 restraints weight = 185024.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.047645 restraints weight = 79197.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.048402 restraints weight = 45321.603| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1587 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= 0.257 Angle : 0.596 9.846 10418 Z= 0.319 Chirality : 0.060 0.445 1176 Planarity : 0.003 0.038 1334 Dihedral : 3.942 29.552 1008 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.98 % Allowed : 21.15 % Favored : 77.87 % 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: 1.26 (0.30), residues: 936 helix: 3.17 (0.28), residues: 340 sheet: -0.32 (0.27), residues: 402 loop : -0.71 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 41 HIS 0.004 0.001 HIS A 102 PHE 0.014 0.001 PHE B 130 TYR 0.006 0.001 TYR F 114 ARG 0.004 0.000 ARG F 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 71 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 1.216 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: 8 outliers final: 4 residues processed: 67 average time/residue: 0.3531 time to fit residues: 33.7437 Evaluate side-chains 66 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 F residue 131 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 81 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 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** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.052377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.046786 restraints weight = 181660.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.047972 restraints weight = 79243.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.048788 restraints weight = 45799.029| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7682 Z= 0.165 Angle : 0.569 9.699 10418 Z= 0.302 Chirality : 0.060 0.441 1176 Planarity : 0.003 0.039 1334 Dihedral : 3.815 28.801 1008 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.61 % Allowed : 21.52 % Favored : 77.87 % 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: 3.44 (0.28), residues: 340 sheet: -0.08 (0.27), residues: 390 loop : -0.89 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 36 HIS 0.003 0.001 HIS A 102 PHE 0.006 0.001 PHE F 104 TYR 0.006 0.001 TYR A 171 ARG 0.002 0.000 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 70 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 1.338 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: 5 outliers final: 4 residues processed: 68 average time/residue: 0.3669 time to fit residues: 36.3720 Evaluate side-chains 69 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 131 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 75 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.052142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.046415 restraints weight = 178787.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.047610 restraints weight = 79509.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.048338 restraints weight = 46070.176| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1979 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= 0.209 Angle : 0.577 9.834 10418 Z= 0.304 Chirality : 0.060 0.443 1176 Planarity : 0.003 0.038 1334 Dihedral : 3.783 29.025 1008 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.61 % Allowed : 22.49 % Favored : 76.89 % 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: 3.52 (0.28), residues: 340 sheet: -0.09 (0.27), residues: 390 loop : -0.85 (0.44), residues: 206 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 0.006 0.001 PHE F 104 TYR 0.005 0.001 TYR F 114 ARG 0.002 0.000 ARG F 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 69 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 1.192 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: 5 outliers final: 5 residues processed: 65 average time/residue: 0.3714 time to fit residues: 34.9318 Evaluate side-chains 69 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 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 6 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.051397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.045743 restraints weight = 181514.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.046899 restraints weight = 79829.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.047654 restraints weight = 46824.804| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7682 Z= 0.331 Angle : 0.626 10.260 10418 Z= 0.332 Chirality : 0.060 0.452 1176 Planarity : 0.004 0.038 1334 Dihedral : 3.955 28.505 1008 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.47 % Allowed : 21.64 % Favored : 76.89 % 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: 1.35 (0.29), residues: 936 helix: 3.32 (0.28), residues: 340 sheet: -0.15 (0.27), residues: 396 loop : -1.13 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 145 HIS 0.005 0.001 HIS A 102 PHE 0.008 0.001 PHE F 98 TYR 0.008 0.001 TYR F 114 ARG 0.004 0.001 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 73 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 1.216 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 outliers start: 12 outliers final: 10 residues processed: 70 average time/residue: 0.3530 time to fit residues: 35.4833 Evaluate side-chains 68 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 108 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.051896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.046197 restraints weight = 176813.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.047388 restraints weight = 78243.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.048163 restraints weight = 45507.968| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7682 Z= 0.174 Angle : 0.580 9.646 10418 Z= 0.303 Chirality : 0.060 0.439 1176 Planarity : 0.003 0.040 1334 Dihedral : 3.829 28.351 1008 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.22 % Allowed : 21.88 % Favored : 76.89 % 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: 1.59 (0.30), residues: 936 helix: 3.55 (0.28), residues: 340 sheet: -0.10 (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 C 36 HIS 0.002 0.001 HIS F 102 PHE 0.014 0.001 PHE G 130 TYR 0.005 0.001 TYR A 171 ARG 0.002 0.000 ARG A 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 71 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 1.236 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 outliers start: 10 outliers final: 8 residues processed: 68 average time/residue: 0.3624 time to fit residues: 35.4834 Evaluate side-chains 69 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 271 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 30 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.051830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.046138 restraints weight = 178195.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.047327 restraints weight = 78851.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.048117 restraints weight = 45292.898| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2444 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= 0.187 Angle : 0.577 9.724 10418 Z= 0.302 Chirality : 0.060 0.438 1176 Planarity : 0.003 0.040 1334 Dihedral : 3.735 28.222 1008 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.49 % Allowed : 22.86 % Favored : 76.65 % 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: 1.66 (0.30), residues: 936 helix: 3.63 (0.28), residues: 340 sheet: -0.05 (0.27), residues: 388 loop : -0.91 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 42 HIS 0.003 0.001 HIS F 102 PHE 0.006 0.001 PHE F 98 TYR 0.006 0.001 TYR E 30 ARG 0.002 0.000 ARG A 219 *********************** 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 65 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 1.152 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: 0.9231 (mmt) cc_final: 0.8723 (mmt) outliers start: 4 outliers final: 4 residues processed: 63 average time/residue: 0.3788 time to fit residues: 33.9076 Evaluate side-chains 63 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 271 ILE 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 42 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 48 optimal weight: 0.2980 chunk 5 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.052108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.046387 restraints weight = 175697.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.047585 restraints weight = 77008.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.048359 restraints weight = 44545.222| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7682 Z= 0.145 Angle : 0.572 9.581 10418 Z= 0.296 Chirality : 0.059 0.437 1176 Planarity : 0.003 0.041 1334 Dihedral : 3.663 27.662 1008 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.73 % Allowed : 22.49 % Favored : 76.77 % 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: 1.77 (0.30), residues: 936 helix: 3.69 (0.28), residues: 340 sheet: 0.02 (0.27), residues: 386 loop : -0.83 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 36 HIS 0.002 0.001 HIS F 102 PHE 0.018 0.001 PHE G 130 TYR 0.004 0.001 TYR F 114 ARG 0.001 0.000 ARG F 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 66 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 1.143 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 outliers start: 6 outliers final: 6 residues processed: 64 average time/residue: 0.3683 time to fit residues: 33.9662 Evaluate side-chains 66 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 53 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 108 SER 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 9 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3526 r_free = 0.3526 target = 0.052343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.046639 restraints weight = 176546.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.047844 restraints weight = 77119.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.048669 restraints weight = 44493.283| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7682 Z= 0.137 Angle : 0.571 9.473 10418 Z= 0.295 Chirality : 0.059 0.435 1176 Planarity : 0.003 0.041 1334 Dihedral : 3.577 27.995 1008 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.61 % Allowed : 22.49 % Favored : 76.89 % 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: 3.81 (0.29), residues: 340 sheet: -0.15 (0.27), residues: 398 loop : -0.41 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 32 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 C 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3733.25 seconds wall clock time: 67 minutes 9.12 seconds (4029.12 seconds total)