Starting phenix.real_space_refine on Sat Aug 23 21:12:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xkw_38429/08_2025/8xkw_38429.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xkw_38429/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xkw_38429/08_2025/8xkw_38429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xkw_38429/08_2025/8xkw_38429.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xkw_38429/08_2025/8xkw_38429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xkw_38429/08_2025/8xkw_38429.map" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.75, per 1000 atoms: 0.19 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: 1.28 Conformation dependent library (CDL) restraints added in 342.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.21 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: 2.99 Time building geometry restraints manager: 1.70 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.310 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.400 ------------------------------------------------------------------------------- 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= 0.231 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 : 7.76 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG F 310 TYR 0.005 0.001 TYR A 114 PHE 0.006 0.001 PHE G 130 TRP 0.006 0.001 TRP C 36 HIS 0.003 0.001 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 7682) covalent geometry : angle 0.67723 (10418) hydrogen bonds : bond 0.15447 ( 503) hydrogen bonds : angle 8.21524 ( 1467) *********************** 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 : 0.386 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: 0.1467 time to fit residues: 13.3256 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 : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.052310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.046562 restraints weight = 188951.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.047744 restraints weight = 82299.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.048605 restraints weight = 47613.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.049082 restraints weight = 32205.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.049444 restraints weight = 25151.760| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 7682 Z= 0.336 Angle : 0.693 10.365 10418 Z= 0.380 Chirality : 0.062 0.466 1176 Planarity : 0.004 0.035 1334 Dihedral : 4.110 28.300 1008 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.86 % Allowed : 20.17 % Favored : 78.97 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.29), residues: 936 helix: 2.42 (0.28), residues: 340 sheet: -0.32 (0.27), residues: 408 loop : -1.08 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.006 0.001 TYR F 171 PHE 0.008 0.001 PHE A 104 TRP 0.005 0.001 TRP H 36 HIS 0.003 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00665 ( 7682) covalent geometry : angle 0.69251 (10418) hydrogen bonds : bond 0.04219 ( 503) hydrogen bonds : angle 6.48009 ( 1467) *********************** 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 68 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.432 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: 7 outliers final: 4 residues processed: 67 average time/residue: 0.1491 time to fit residues: 14.5410 Evaluate side-chains 64 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 27 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3538 r_free = 0.3538 target = 0.053047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.047493 restraints weight = 184545.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.048679 restraints weight = 78817.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.049470 restraints weight = 44419.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.050048 restraints weight = 30949.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.050164 restraints weight = 23380.380| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7682 Z= 0.117 Angle : 0.591 9.635 10418 Z= 0.316 Chirality : 0.061 0.443 1176 Planarity : 0.004 0.036 1334 Dihedral : 3.966 28.302 1008 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 20.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.29), residues: 936 helix: 3.03 (0.28), residues: 340 sheet: -0.36 (0.27), residues: 408 loop : -0.75 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 219 TYR 0.008 0.001 TYR A 171 PHE 0.007 0.001 PHE A 104 TRP 0.004 0.001 TRP C 42 HIS 0.002 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7682) covalent geometry : angle 0.59061 (10418) hydrogen bonds : bond 0.03176 ( 503) hydrogen bonds : angle 5.79750 ( 1467) *********************** 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 : 0.427 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: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1596 time to fit residues: 14.2089 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 : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 23 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 78 optimal weight: 0.4980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 GLN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 133 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.052360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.046868 restraints weight = 184935.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.048045 restraints weight = 78989.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.048758 restraints weight = 45211.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.049351 restraints weight = 32215.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.049693 restraints weight = 23969.359| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7682 Z= 0.193 Angle : 0.594 9.762 10418 Z= 0.318 Chirality : 0.060 0.443 1176 Planarity : 0.004 0.036 1334 Dihedral : 3.923 29.539 1008 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.86 % Allowed : 20.17 % Favored : 78.97 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.29), residues: 936 helix: 3.19 (0.28), residues: 340 sheet: -0.36 (0.27), residues: 402 loop : -0.73 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.005 0.001 TYR F 114 PHE 0.009 0.001 PHE F 104 TRP 0.005 0.001 TRP J 41 HIS 0.005 0.001 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 7682) covalent geometry : angle 0.59419 (10418) hydrogen bonds : bond 0.02912 ( 503) hydrogen bonds : angle 5.40897 ( 1467) *********************** 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 69 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.429 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: 3 residues processed: 67 average time/residue: 0.1583 time to fit residues: 15.3087 Evaluate side-chains 65 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 11 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.051882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.046373 restraints weight = 183513.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.047532 restraints weight = 79181.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.048334 restraints weight = 45105.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.048835 restraints weight = 31086.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.048988 restraints weight = 23879.564| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7682 Z= 0.200 Angle : 0.596 9.928 10418 Z= 0.318 Chirality : 0.060 0.446 1176 Planarity : 0.003 0.038 1334 Dihedral : 3.920 28.639 1008 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.86 % Allowed : 21.39 % Favored : 77.75 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.29), residues: 936 helix: 3.27 (0.28), residues: 340 sheet: -0.10 (0.27), residues: 390 loop : -1.04 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 219 TYR 0.007 0.001 TYR F 114 PHE 0.007 0.001 PHE G 130 TRP 0.005 0.001 TRP E 41 HIS 0.004 0.001 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 7682) covalent geometry : angle 0.59577 (10418) hydrogen bonds : bond 0.02789 ( 503) hydrogen bonds : angle 5.25104 ( 1467) *********************** 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 69 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.425 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: 5 residues processed: 66 average time/residue: 0.1576 time to fit residues: 14.8646 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 : 0.272 ------------------------------------------------------------------------------- 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 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 49 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3510 r_free = 0.3510 target = 0.051832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.046068 restraints weight = 177988.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.047227 restraints weight = 78726.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.048013 restraints weight = 46450.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.048570 restraints weight = 32521.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.048917 restraints weight = 25035.597| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7682 Z= 0.195 Angle : 0.594 9.768 10418 Z= 0.315 Chirality : 0.060 0.443 1176 Planarity : 0.003 0.038 1334 Dihedral : 3.901 29.467 1008 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.10 % Allowed : 21.64 % Favored : 77.26 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.30), residues: 936 helix: 3.33 (0.28), residues: 340 sheet: -0.17 (0.27), residues: 396 loop : -1.03 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.006 0.001 TYR F 114 PHE 0.007 0.001 PHE F 98 TRP 0.005 0.001 TRP J 41 HIS 0.005 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 7682) covalent geometry : angle 0.59405 (10418) hydrogen bonds : bond 0.02692 ( 503) hydrogen bonds : angle 5.10301 ( 1467) *********************** 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 72 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.441 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: 9 outliers final: 9 residues processed: 67 average time/residue: 0.1524 time to fit residues: 14.7286 Evaluate side-chains 72 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain E residue 54 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 I residue 61 LEU Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 81 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.051845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.046231 restraints weight = 178127.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.047419 restraints weight = 78427.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.048204 restraints weight = 45876.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.048737 restraints weight = 31739.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.049084 restraints weight = 24463.891| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2185 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= 0.171 Angle : 0.581 9.802 10418 Z= 0.308 Chirality : 0.060 0.442 1176 Planarity : 0.003 0.039 1334 Dihedral : 3.843 27.935 1008 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.22 % Allowed : 21.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.29), residues: 936 helix: 3.43 (0.28), residues: 340 sheet: -0.15 (0.26), residues: 390 loop : -0.90 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 219 TYR 0.006 0.001 TYR F 114 PHE 0.015 0.001 PHE G 130 TRP 0.005 0.001 TRP E 41 HIS 0.004 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7682) covalent geometry : angle 0.58135 (10418) hydrogen bonds : bond 0.02596 ( 503) hydrogen bonds : angle 4.98711 ( 1467) *********************** 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 72 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.330 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: 10 residues processed: 69 average time/residue: 0.1637 time to fit residues: 16.0839 Evaluate side-chains 72 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 18 SER 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 18 SER Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 131 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 38 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.050993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.045433 restraints weight = 182575.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.046537 restraints weight = 80658.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.047294 restraints weight = 47739.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.047802 restraints weight = 33327.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.048104 restraints weight = 25347.675| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7682 Z= 0.302 Angle : 0.650 10.382 10418 Z= 0.345 Chirality : 0.060 0.454 1176 Planarity : 0.004 0.037 1334 Dihedral : 4.077 28.767 1008 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.08 % Allowed : 20.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.29), residues: 936 helix: 3.03 (0.28), residues: 340 sheet: -0.48 (0.26), residues: 406 loop : -0.92 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 219 TYR 0.009 0.002 TYR F 114 PHE 0.009 0.001 PHE A 359 TRP 0.009 0.001 TRP F 145 HIS 0.005 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00597 ( 7682) covalent geometry : angle 0.65020 (10418) hydrogen bonds : bond 0.02854 ( 503) hydrogen bonds : angle 5.16252 ( 1467) *********************** 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 73 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.409 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: 0.9255 (mmt) cc_final: 0.9047 (mmt) outliers start: 17 outliers final: 14 residues processed: 70 average time/residue: 0.1265 time to fit residues: 12.8595 Evaluate side-chains 70 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 18 SER 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 A residue 271 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain J residue 18 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 Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.051664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.046026 restraints weight = 179266.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.047212 restraints weight = 79134.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.047976 restraints weight = 45601.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.048509 restraints weight = 31915.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.048833 restraints weight = 24322.078| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2491 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= 0.135 Angle : 0.587 9.532 10418 Z= 0.307 Chirality : 0.060 0.436 1176 Planarity : 0.003 0.040 1334 Dihedral : 3.918 27.233 1008 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.22 % Allowed : 21.76 % Favored : 77.02 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.29), residues: 936 helix: 3.44 (0.28), residues: 340 sheet: -0.18 (0.26), residues: 388 loop : -0.98 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 47 TYR 0.006 0.001 TYR E 30 PHE 0.015 0.001 PHE G 130 TRP 0.005 0.001 TRP C 36 HIS 0.003 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7682) covalent geometry : angle 0.58720 (10418) hydrogen bonds : bond 0.02565 ( 503) hydrogen bonds : angle 4.92533 ( 1467) *********************** 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 69 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.328 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: D 54 MET cc_start: 0.9600 (mmm) cc_final: 0.9289 (tpp) REVERT: I 54 MET cc_start: 0.9610 (mmm) cc_final: 0.9259 (tpp) outliers start: 10 outliers final: 10 residues processed: 67 average time/residue: 0.1345 time to fit residues: 13.0275 Evaluate side-chains 69 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 SER 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 A residue 351 THR Chi-restraints excluded: chain J residue 18 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 Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 81 optimal weight: 0.1980 chunk 24 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.051756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.046296 restraints weight = 182184.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.047489 restraints weight = 78163.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.048254 restraints weight = 44330.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.048780 restraints weight = 30490.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.049072 restraints weight = 23226.960| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7682 Z= 0.119 Angle : 0.582 9.519 10418 Z= 0.304 Chirality : 0.060 0.435 1176 Planarity : 0.003 0.041 1334 Dihedral : 3.820 28.536 1008 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.98 % Allowed : 22.49 % Favored : 76.53 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.29), residues: 936 helix: 3.44 (0.28), residues: 340 sheet: -0.16 (0.26), residues: 388 loop : -0.86 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.005 0.001 TYR E 30 PHE 0.009 0.001 PHE D 48 TRP 0.005 0.001 TRP C 42 HIS 0.003 0.001 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7682) covalent geometry : angle 0.58210 (10418) hydrogen bonds : bond 0.02433 ( 503) hydrogen bonds : angle 4.83514 ( 1467) ********************** 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 68 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.351 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: 0.9435 (mmt) cc_final: 0.8791 (mmt) REVERT: D 54 MET cc_start: 0.9600 (mmm) cc_final: 0.9211 (tpp) REVERT: I 54 MET cc_start: 0.9601 (mmm) cc_final: 0.9215 (tpp) outliers start: 8 outliers final: 8 residues processed: 66 average time/residue: 0.1403 time to fit residues: 13.2859 Evaluate side-chains 68 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 SER 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 A residue 136 SER Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 136 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 5 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.051637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.046034 restraints weight = 176304.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.047199 restraints weight = 77084.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.047932 restraints weight = 44719.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.048426 restraints weight = 31030.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.048792 restraints weight = 24205.077| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2657 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= 0.216 Angle : 0.617 9.962 10418 Z= 0.323 Chirality : 0.060 0.447 1176 Planarity : 0.003 0.039 1334 Dihedral : 3.861 27.249 1008 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.22 % Allowed : 22.49 % Favored : 76.28 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.30), residues: 936 helix: 3.46 (0.28), residues: 340 sheet: -0.41 (0.26), residues: 400 loop : -0.69 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.007 0.001 TYR E 30 PHE 0.015 0.001 PHE G 130 TRP 0.006 0.001 TRP F 145 HIS 0.004 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 7682) covalent geometry : angle 0.61670 (10418) hydrogen bonds : bond 0.02598 ( 503) hydrogen bonds : angle 4.87128 ( 1467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2007.22 seconds wall clock time: 35 minutes 13.36 seconds (2113.36 seconds total)