Starting phenix.real_space_refine on Sat Dec 28 09:55:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vwk_21419/12_2024/6vwk_21419_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vwk_21419/12_2024/6vwk_21419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vwk_21419/12_2024/6vwk_21419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vwk_21419/12_2024/6vwk_21419.map" model { file = "/net/cci-nas-00/data/ceres_data/6vwk_21419/12_2024/6vwk_21419_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vwk_21419/12_2024/6vwk_21419_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 86 5.16 5 C 5615 2.51 5 N 1328 2.21 5 O 1394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8423 Number of models: 1 Model: "" Number of chains: 13 Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "X" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 362 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Time building chain proxies: 5.58, per 1000 atoms: 0.66 Number of scatterers: 8423 At special positions: 0 Unit cell: (89.557, 99.268, 102.505, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 86 16.00 O 1394 8.00 N 1328 7.00 C 5615 6.00 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: 2.08 Conformation dependent library (CDL) restraints added in 1.2 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 1 sheets defined 90.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'I' and resid 3 through 42 removed outlier: 3.703A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 77 removed outlier: 3.722A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'J' and resid 4 through 42 Processing helix chain 'J' and resid 45 through 77 removed outlier: 3.750A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'L' and resid 4 through 42 Processing helix chain 'L' and resid 45 through 77 removed outlier: 3.716A pdb=" N LEU L 59 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) Proline residue: L 64 - end of helix Processing helix chain 'M' and resid 4 through 42 removed outlier: 3.743A pdb=" N GLN M 42 " --> pdb=" O GLY M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 77 removed outlier: 3.789A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) Proline residue: M 64 - end of helix Processing helix chain 'N' and resid 4 through 42 removed outlier: 3.589A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA N 40 " --> pdb=" O LEU N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 77 removed outlier: 3.837A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE N 63 " --> pdb=" O LEU N 59 " (cutoff:3.500A) Proline residue: N 64 - end of helix Processing helix chain 'O' and resid 4 through 42 removed outlier: 3.628A pdb=" N LEU O 8 " --> pdb=" O LEU O 4 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 77 removed outlier: 3.861A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) Proline residue: O 64 - end of helix Processing helix chain 'P' and resid 4 through 42 Processing helix chain 'P' and resid 45 through 77 removed outlier: 3.789A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.671A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 42 Processing helix chain 'Q' and resid 45 through 77 removed outlier: 3.602A pdb=" N LEU Q 59 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Proline residue: Q 64 - end of helix Processing helix chain 'R' and resid 4 through 42 Processing helix chain 'R' and resid 45 through 77 removed outlier: 3.811A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'S' and resid 4 through 42 removed outlier: 3.808A pdb=" N LEU S 8 " --> pdb=" O LEU S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 3.767A pdb=" N LEU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 77 removed outlier: 3.541A pdb=" N ALA S 67 " --> pdb=" O ILE S 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 25 Processing helix chain 'X' and resid 25 through 46 Processing helix chain 'Y' and resid 2 through 50 Proline residue: Y 27 - end of helix Processing helix chain 'a' and resid 7 through 16 Processing helix chain 'a' and resid 43 through 67 Processing helix chain 'a' and resid 73 through 94 Processing helix chain 'a' and resid 100 through 118 Processing helix chain 'a' and resid 119 through 121 No H-bonds generated for 'chain 'a' and resid 119 through 121' Processing helix chain 'a' and resid 124 through 133 Processing helix chain 'a' and resid 146 through 169 removed outlier: 3.878A pdb=" N THR a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) Processing helix chain 'a' and resid 172 through 180 Processing helix chain 'a' and resid 185 through 187 No H-bonds generated for 'chain 'a' and resid 185 through 187' Processing helix chain 'a' and resid 188 through 229 Proline residue: a 204 - end of helix removed outlier: 3.568A pdb=" N PHE a 222 " --> pdb=" O GLY a 218 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 269 removed outlier: 4.692A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.892A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR a 250 " --> pdb=" O ILE a 246 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 20 through 22 813 hydrogen bonds defined for protein. 2439 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: 2.58 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1336 1.32 - 1.44: 2020 1.44 - 1.57: 5049 1.57 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 8577 Sorted by residual: bond pdb=" C ARG a 210 " pdb=" O ARG a 210 " ideal model delta sigma weight residual 1.236 1.196 0.041 1.15e-02 7.56e+03 1.24e+01 bond pdb=" N VAL S 60 " pdb=" CA VAL S 60 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.31e+00 bond pdb=" C LEU S 8 " pdb=" O LEU S 8 " ideal model delta sigma weight residual 1.236 1.202 0.034 1.26e-02 6.30e+03 7.37e+00 bond pdb=" N MET S 11 " pdb=" CA MET S 11 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.33e-02 5.65e+03 6.72e+00 bond pdb=" C ASP S 7 " pdb=" O ASP S 7 " ideal model delta sigma weight residual 1.237 1.267 -0.031 1.19e-02 7.06e+03 6.61e+00 ... (remaining 8572 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 9466 1.56 - 3.12: 1802 3.12 - 4.68: 274 4.68 - 6.24: 70 6.24 - 7.80: 14 Bond angle restraints: 11626 Sorted by residual: angle pdb=" N ALA M 62 " pdb=" CA ALA M 62 " pdb=" C ALA M 62 " ideal model delta sigma weight residual 111.07 116.01 -4.94 1.07e+00 8.73e-01 2.13e+01 angle pdb=" N ALA Q 62 " pdb=" CA ALA Q 62 " pdb=" C ALA Q 62 " ideal model delta sigma weight residual 111.28 116.29 -5.01 1.09e+00 8.42e-01 2.11e+01 angle pdb=" CA VAL S 60 " pdb=" C VAL S 60 " pdb=" O VAL S 60 " ideal model delta sigma weight residual 121.17 116.64 4.53 1.06e+00 8.90e-01 1.83e+01 angle pdb=" N PRO X 27 " pdb=" CA PRO X 27 " pdb=" C PRO X 27 " ideal model delta sigma weight residual 110.70 115.88 -5.18 1.22e+00 6.72e-01 1.80e+01 angle pdb=" N PHE R 76 " pdb=" CA PHE R 76 " pdb=" C PHE R 76 " ideal model delta sigma weight residual 111.40 116.56 -5.16 1.22e+00 6.72e-01 1.79e+01 ... (remaining 11621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 4676 17.07 - 34.15: 306 34.15 - 51.22: 55 51.22 - 68.29: 14 68.29 - 85.36: 5 Dihedral angle restraints: 5056 sinusoidal: 1884 harmonic: 3172 Sorted by residual: dihedral pdb=" CA LEU X 3 " pdb=" C LEU X 3 " pdb=" N ASN X 4 " pdb=" CA ASN X 4 " ideal model delta harmonic sigma weight residual -180.00 -151.82 -28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA MET a 6 " pdb=" C MET a 6 " pdb=" N THR a 7 " pdb=" CA THR a 7 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ARG a 140 " pdb=" C ARG a 140 " pdb=" N VAL a 141 " pdb=" CA VAL a 141 " ideal model delta harmonic sigma weight residual -180.00 -152.75 -27.25 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 5053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1148 0.078 - 0.157: 213 0.157 - 0.235: 33 0.235 - 0.314: 17 0.314 - 0.392: 4 Chirality restraints: 1415 Sorted by residual: chirality pdb=" CA PHE S 76 " pdb=" N PHE S 76 " pdb=" C PHE S 76 " pdb=" CB PHE S 76 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA PHE P 76 " pdb=" N PHE P 76 " pdb=" C PHE P 76 " pdb=" CB PHE P 76 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA PHE J 76 " pdb=" N PHE J 76 " pdb=" C PHE J 76 " pdb=" CB PHE J 76 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 1412 not shown) Planarity restraints: 1434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU O 8 " -0.027 2.00e-02 2.50e+03 5.49e-02 3.02e+01 pdb=" C LEU O 8 " 0.095 2.00e-02 2.50e+03 pdb=" O LEU O 8 " -0.036 2.00e-02 2.50e+03 pdb=" N LEU O 9 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET Y 22 " 0.024 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C MET Y 22 " -0.081 2.00e-02 2.50e+03 pdb=" O MET Y 22 " 0.030 2.00e-02 2.50e+03 pdb=" N LYS Y 23 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 21 " -0.022 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C ALA J 21 " 0.075 2.00e-02 2.50e+03 pdb=" O ALA J 21 " -0.028 2.00e-02 2.50e+03 pdb=" N ILE J 22 " -0.026 2.00e-02 2.50e+03 ... (remaining 1431 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 2295 2.86 - 3.37: 8720 3.37 - 3.88: 14108 3.88 - 4.39: 15509 4.39 - 4.90: 27755 Nonbonded interactions: 68387 Sorted by model distance: nonbonded pdb=" O ASN a 33 " pdb=" OD1 ASN a 33 " model vdw 2.355 3.040 nonbonded pdb=" O SER a 165 " pdb=" O LYS a 169 " model vdw 2.367 3.040 nonbonded pdb=" O ASN N 5 " pdb=" OD2 ASP O 7 " model vdw 2.395 3.040 nonbonded pdb=" O LEU L 4 " pdb=" OD1 ASP L 7 " model vdw 2.418 3.040 nonbonded pdb=" OD1 ASN O 5 " pdb=" N MET O 6 " model vdw 2.510 3.120 ... (remaining 68382 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 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'X' selection = (chain 'Y' and resid 1 through 47) } 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 individual isotropic 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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.310 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 : 0.010 0.064 8577 Z= 0.640 Angle : 1.305 7.796 11626 Z= 0.848 Chirality : 0.069 0.392 1415 Planarity : 0.013 0.063 1434 Dihedral : 12.707 85.363 3032 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.59 % Allowed : 5.19 % Favored : 94.21 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.22), residues: 1107 helix: 0.01 (0.14), residues: 974 sheet: None (None), residues: 0 loop : -0.96 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.006 TRP Y 26 HIS 0.020 0.007 HIS a 15 PHE 0.032 0.004 PHE L 76 TYR 0.052 0.007 TYR O 10 ARG 0.047 0.009 ARG Y 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 168 time to evaluate : 0.952 Fit side-chains REVERT: I 6 MET cc_start: 0.5274 (mtm) cc_final: 0.4821 (mmp) REVERT: J 11 MET cc_start: 0.8069 (tpp) cc_final: 0.7832 (tpt) REVERT: L 11 MET cc_start: 0.8456 (tpt) cc_final: 0.7974 (tpt) REVERT: M 6 MET cc_start: 0.5909 (mtt) cc_final: 0.5557 (mtm) REVERT: Q 28 ILE cc_start: 0.9184 (mt) cc_final: 0.8977 (mp) REVERT: S 6 MET cc_start: 0.5895 (mmt) cc_final: 0.5233 (mmt) REVERT: S 11 MET cc_start: 0.8581 (tpp) cc_final: 0.8263 (tpt) REVERT: S 65 MET cc_start: 0.8400 (mmt) cc_final: 0.8186 (mmt) REVERT: Y 16 LEU cc_start: 0.8865 (mp) cc_final: 0.8557 (mp) REVERT: a 257 MET cc_start: 0.8137 (ttp) cc_final: 0.7927 (ttt) outliers start: 5 outliers final: 2 residues processed: 172 average time/residue: 0.2317 time to fit residues: 53.5022 Evaluate side-chains 133 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain a residue 149 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 5 ASN S 3 ASN a 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8577 Z= 0.293 Angle : 0.714 8.231 11626 Z= 0.371 Chirality : 0.045 0.351 1415 Planarity : 0.006 0.050 1434 Dihedral : 4.990 34.844 1178 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.53 % Allowed : 9.09 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 2.19 (0.23), residues: 1107 helix: 1.73 (0.15), residues: 976 sheet: None (None), residues: 0 loop : -0.44 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP a 111 HIS 0.007 0.002 HIS a 132 PHE 0.017 0.002 PHE a 75 TYR 0.023 0.002 TYR M 10 ARG 0.007 0.001 ARG Q 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.949 Fit side-chains REVERT: J 11 MET cc_start: 0.7968 (tpp) cc_final: 0.7710 (tpt) REVERT: L 11 MET cc_start: 0.8313 (tpt) cc_final: 0.7655 (tpt) REVERT: M 6 MET cc_start: 0.5572 (mtt) cc_final: 0.5320 (mtt) REVERT: Q 41 ARG cc_start: 0.8118 (ttm110) cc_final: 0.7724 (ttm-80) REVERT: S 6 MET cc_start: 0.5654 (mmt) cc_final: 0.5187 (mmt) REVERT: X 2 ASN cc_start: 0.6232 (t0) cc_final: 0.5847 (p0) REVERT: Y 18 VAL cc_start: 0.8018 (t) cc_final: 0.7753 (t) REVERT: a 116 ASN cc_start: 0.8595 (m-40) cc_final: 0.8039 (m110) outliers start: 13 outliers final: 7 residues processed: 148 average time/residue: 0.2029 time to fit residues: 41.6681 Evaluate side-chains 135 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain a residue 265 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 0.0870 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 76 optimal weight: 0.8980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 14 HIS a 20 GLN a 245 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8577 Z= 0.223 Angle : 0.621 8.028 11626 Z= 0.314 Chirality : 0.041 0.305 1415 Planarity : 0.005 0.047 1434 Dihedral : 4.449 36.765 1176 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.89 % Allowed : 9.80 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 3.04 (0.24), residues: 1107 helix: 2.38 (0.15), residues: 957 sheet: None (None), residues: 0 loop : -0.50 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 111 HIS 0.003 0.001 HIS a 132 PHE 0.013 0.001 PHE a 75 TYR 0.024 0.002 TYR M 10 ARG 0.006 0.000 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.948 Fit side-chains REVERT: J 11 MET cc_start: 0.7908 (tpp) cc_final: 0.7659 (tpt) REVERT: J 57 MET cc_start: 0.8292 (tmm) cc_final: 0.7821 (ttp) REVERT: L 11 MET cc_start: 0.8268 (tpt) cc_final: 0.7592 (tpt) REVERT: M 6 MET cc_start: 0.5260 (mtt) cc_final: 0.4921 (mtt) REVERT: S 6 MET cc_start: 0.5556 (mmt) cc_final: 0.5132 (mmt) REVERT: X 2 ASN cc_start: 0.6646 (t0) cc_final: 0.6308 (p0) REVERT: X 24 TYR cc_start: 0.7882 (m-10) cc_final: 0.7666 (m-10) REVERT: Y 18 VAL cc_start: 0.7980 (t) cc_final: 0.7696 (t) REVERT: a 116 ASN cc_start: 0.8521 (m-40) cc_final: 0.8034 (m110) outliers start: 16 outliers final: 8 residues processed: 148 average time/residue: 0.2053 time to fit residues: 43.0060 Evaluate side-chains 140 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 245 HIS Chi-restraints excluded: chain a residue 246 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 95 optimal weight: 0.0970 chunk 101 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8577 Z= 0.240 Angle : 0.617 8.358 11626 Z= 0.309 Chirality : 0.041 0.318 1415 Planarity : 0.005 0.048 1434 Dihedral : 4.344 40.086 1176 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.48 % Allowed : 10.63 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 3.22 (0.23), residues: 1107 helix: 2.52 (0.15), residues: 957 sheet: None (None), residues: 0 loop : -0.55 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 241 HIS 0.009 0.002 HIS a 245 PHE 0.012 0.001 PHE a 85 TYR 0.021 0.001 TYR M 10 ARG 0.004 0.000 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: J 11 MET cc_start: 0.7891 (tpp) cc_final: 0.7610 (tpt) REVERT: J 57 MET cc_start: 0.8281 (tmm) cc_final: 0.7854 (ttp) REVERT: L 11 MET cc_start: 0.8264 (tpt) cc_final: 0.7585 (tpt) REVERT: R 17 MET cc_start: 0.7963 (mmm) cc_final: 0.7291 (mmm) REVERT: X 1 MET cc_start: 0.4873 (mtt) cc_final: 0.4319 (ttm) REVERT: X 24 TYR cc_start: 0.7953 (m-10) cc_final: 0.7621 (m-10) REVERT: Y 18 VAL cc_start: 0.7909 (t) cc_final: 0.7638 (t) REVERT: a 116 ASN cc_start: 0.8548 (m-40) cc_final: 0.8100 (m110) outliers start: 21 outliers final: 12 residues processed: 148 average time/residue: 0.1830 time to fit residues: 38.6301 Evaluate side-chains 144 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain O residue 16 MET Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 245 HIS Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain a residue 259 LEU Chi-restraints excluded: chain a residue 265 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 91 optimal weight: 0.0980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8577 Z= 0.240 Angle : 0.611 8.541 11626 Z= 0.304 Chirality : 0.040 0.319 1415 Planarity : 0.005 0.048 1434 Dihedral : 4.291 45.360 1176 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.36 % Allowed : 11.10 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 3.38 (0.23), residues: 1107 helix: 2.63 (0.15), residues: 957 sheet: None (None), residues: 0 loop : -0.59 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 231 HIS 0.002 0.001 HIS a 95 PHE 0.012 0.001 PHE a 85 TYR 0.017 0.001 TYR M 10 ARG 0.003 0.000 ARG a 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: J 11 MET cc_start: 0.7847 (tpp) cc_final: 0.7554 (tpt) REVERT: J 57 MET cc_start: 0.8355 (tmm) cc_final: 0.7872 (ttp) REVERT: L 11 MET cc_start: 0.8255 (tpt) cc_final: 0.7543 (tpt) REVERT: R 17 MET cc_start: 0.7966 (mmm) cc_final: 0.7465 (mmm) REVERT: R 28 ILE cc_start: 0.8233 (mt) cc_final: 0.8000 (mm) REVERT: R 57 MET cc_start: 0.8314 (ttp) cc_final: 0.7951 (ttt) REVERT: X 1 MET cc_start: 0.5065 (mtt) cc_final: 0.4692 (ttm) REVERT: X 24 TYR cc_start: 0.7769 (m-10) cc_final: 0.7413 (m-10) REVERT: Y 18 VAL cc_start: 0.7950 (t) cc_final: 0.7663 (t) REVERT: a 116 ASN cc_start: 0.8574 (m-40) cc_final: 0.8091 (m110) outliers start: 20 outliers final: 10 residues processed: 141 average time/residue: 0.1924 time to fit residues: 38.2225 Evaluate side-chains 143 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain O residue 16 MET Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain a residue 265 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 ASN J 5 ASN a 15 HIS a 245 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8577 Z= 0.251 Angle : 0.616 8.711 11626 Z= 0.305 Chirality : 0.040 0.320 1415 Planarity : 0.005 0.048 1434 Dihedral : 4.308 50.864 1176 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.36 % Allowed : 12.40 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 3.40 (0.23), residues: 1107 helix: 2.65 (0.15), residues: 957 sheet: None (None), residues: 0 loop : -0.61 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 241 HIS 0.002 0.001 HIS a 95 PHE 0.013 0.001 PHE a 85 TYR 0.014 0.001 TYR a 11 ARG 0.007 0.000 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: I 57 MET cc_start: 0.7840 (tmm) cc_final: 0.7563 (ttp) REVERT: J 3 ASN cc_start: 0.5505 (OUTLIER) cc_final: 0.5281 (m-40) REVERT: J 11 MET cc_start: 0.7868 (tpp) cc_final: 0.7560 (tpt) REVERT: L 11 MET cc_start: 0.8250 (tpt) cc_final: 0.7523 (tpt) REVERT: N 16 MET cc_start: 0.7972 (ttm) cc_final: 0.7757 (ttp) REVERT: O 42 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7027 (mm-40) REVERT: O 57 MET cc_start: 0.8248 (tmm) cc_final: 0.7967 (ttp) REVERT: R 28 ILE cc_start: 0.8239 (mt) cc_final: 0.8019 (mm) REVERT: R 57 MET cc_start: 0.8297 (ttp) cc_final: 0.7927 (ttt) REVERT: R 75 MET cc_start: 0.8663 (ttp) cc_final: 0.8113 (mtp) REVERT: X 1 MET cc_start: 0.5092 (mtt) cc_final: 0.4791 (ttm) REVERT: X 24 TYR cc_start: 0.7712 (m-10) cc_final: 0.7384 (m-10) REVERT: Y 18 VAL cc_start: 0.7976 (t) cc_final: 0.7702 (t) REVERT: a 6 MET cc_start: 0.7030 (mmp) cc_final: 0.6784 (mmt) REVERT: a 116 ASN cc_start: 0.8576 (m-40) cc_final: 0.8098 (m110) outliers start: 20 outliers final: 14 residues processed: 142 average time/residue: 0.1973 time to fit residues: 39.7437 Evaluate side-chains 144 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 3 ASN Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain O residue 16 MET Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 245 HIS Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain a residue 265 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 0.0030 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 chunk 62 optimal weight: 0.5980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8577 Z= 0.215 Angle : 0.599 8.734 11626 Z= 0.295 Chirality : 0.039 0.306 1415 Planarity : 0.005 0.048 1434 Dihedral : 4.275 50.781 1176 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.36 % Allowed : 11.81 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 3.52 (0.23), residues: 1107 helix: 2.75 (0.15), residues: 957 sheet: None (None), residues: 0 loop : -0.67 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 241 HIS 0.011 0.002 HIS a 245 PHE 0.011 0.001 PHE a 85 TYR 0.013 0.001 TYR a 11 ARG 0.007 0.000 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: I 57 MET cc_start: 0.7821 (tmm) cc_final: 0.7544 (ttp) REVERT: J 11 MET cc_start: 0.7884 (tpp) cc_final: 0.7562 (tpt) REVERT: L 11 MET cc_start: 0.8247 (tpt) cc_final: 0.7518 (tpt) REVERT: R 17 MET cc_start: 0.7919 (mmm) cc_final: 0.7347 (mmm) REVERT: R 57 MET cc_start: 0.8316 (ttp) cc_final: 0.7940 (ttt) REVERT: R 75 MET cc_start: 0.8655 (ttp) cc_final: 0.8127 (mtp) REVERT: S 57 MET cc_start: 0.8191 (tmt) cc_final: 0.7965 (tmt) REVERT: X 1 MET cc_start: 0.5170 (mtt) cc_final: 0.4872 (ttm) REVERT: X 24 TYR cc_start: 0.7709 (m-10) cc_final: 0.7339 (m-10) REVERT: Y 18 VAL cc_start: 0.7959 (t) cc_final: 0.7682 (t) REVERT: a 116 ASN cc_start: 0.8571 (m-40) cc_final: 0.8077 (m110) outliers start: 20 outliers final: 14 residues processed: 144 average time/residue: 0.1867 time to fit residues: 38.4782 Evaluate side-chains 142 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 245 HIS Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain a residue 259 LEU Chi-restraints excluded: chain a residue 265 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.5980 chunk 60 optimal weight: 0.0070 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 79 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 ASN a 15 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8577 Z= 0.241 Angle : 0.617 7.981 11626 Z= 0.304 Chirality : 0.039 0.303 1415 Planarity : 0.005 0.048 1434 Dihedral : 4.273 50.711 1176 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.01 % Allowed : 12.99 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 3.51 (0.23), residues: 1107 helix: 2.73 (0.15), residues: 958 sheet: None (None), residues: 0 loop : -0.66 (0.47), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 241 HIS 0.016 0.002 HIS a 15 PHE 0.012 0.001 PHE a 85 TYR 0.011 0.001 TYR a 11 ARG 0.008 0.000 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: I 6 MET cc_start: 0.4801 (ppp) cc_final: 0.3716 (mtm) REVERT: I 57 MET cc_start: 0.7818 (tmm) cc_final: 0.7545 (ttp) REVERT: J 3 ASN cc_start: 0.5896 (OUTLIER) cc_final: 0.5611 (m-40) REVERT: J 11 MET cc_start: 0.7895 (tpp) cc_final: 0.7598 (tpt) REVERT: O 42 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7023 (mm-40) REVERT: O 57 MET cc_start: 0.8055 (ttp) cc_final: 0.7811 (ttp) REVERT: R 17 MET cc_start: 0.7917 (mmm) cc_final: 0.7374 (mmm) REVERT: R 57 MET cc_start: 0.8206 (ttp) cc_final: 0.7739 (ttt) REVERT: R 75 MET cc_start: 0.8678 (ttp) cc_final: 0.8160 (mtp) REVERT: S 57 MET cc_start: 0.8201 (tmt) cc_final: 0.7965 (tmt) REVERT: X 1 MET cc_start: 0.5193 (mtt) cc_final: 0.4886 (ttm) REVERT: X 24 TYR cc_start: 0.7709 (m-10) cc_final: 0.7346 (m-10) REVERT: Y 18 VAL cc_start: 0.7970 (t) cc_final: 0.7715 (t) REVERT: a 6 MET cc_start: 0.7129 (mmt) cc_final: 0.6490 (tpt) REVERT: a 116 ASN cc_start: 0.8571 (m-40) cc_final: 0.8094 (m110) outliers start: 17 outliers final: 14 residues processed: 144 average time/residue: 0.1931 time to fit residues: 39.0501 Evaluate side-chains 145 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 3 ASN Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain a residue 259 LEU Chi-restraints excluded: chain a residue 265 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 93 optimal weight: 0.0050 chunk 61 optimal weight: 0.5980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 ASN a 15 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8577 Z= 0.236 Angle : 0.606 7.682 11626 Z= 0.300 Chirality : 0.039 0.299 1415 Planarity : 0.005 0.049 1434 Dihedral : 4.259 50.672 1176 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.13 % Allowed : 13.58 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 3.56 (0.23), residues: 1107 helix: 2.77 (0.15), residues: 958 sheet: None (None), residues: 0 loop : -0.67 (0.47), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 241 HIS 0.009 0.001 HIS a 15 PHE 0.011 0.001 PHE a 85 TYR 0.011 0.001 TYR a 11 ARG 0.009 0.000 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: I 6 MET cc_start: 0.4850 (ppp) cc_final: 0.3648 (mtm) REVERT: I 57 MET cc_start: 0.7812 (tmm) cc_final: 0.7547 (ttp) REVERT: J 3 ASN cc_start: 0.5894 (OUTLIER) cc_final: 0.5408 (m-40) REVERT: J 11 MET cc_start: 0.7879 (tpp) cc_final: 0.7587 (tpt) REVERT: O 42 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7042 (mm-40) REVERT: O 57 MET cc_start: 0.8058 (ttp) cc_final: 0.7792 (ttp) REVERT: R 17 MET cc_start: 0.7927 (mmm) cc_final: 0.7410 (mmm) REVERT: R 75 MET cc_start: 0.8683 (ttp) cc_final: 0.8170 (mtp) REVERT: S 57 MET cc_start: 0.8196 (tmt) cc_final: 0.7963 (tmt) REVERT: X 24 TYR cc_start: 0.7694 (m-10) cc_final: 0.7351 (m-10) REVERT: Y 18 VAL cc_start: 0.7977 (t) cc_final: 0.7714 (t) REVERT: a 6 MET cc_start: 0.7088 (mmt) cc_final: 0.6455 (tpt) REVERT: a 116 ASN cc_start: 0.8567 (m-40) cc_final: 0.8093 (m110) outliers start: 18 outliers final: 14 residues processed: 146 average time/residue: 0.1941 time to fit residues: 40.1100 Evaluate side-chains 148 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 3 ASN Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain R residue 44 ASP Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain a residue 259 LEU Chi-restraints excluded: chain a residue 265 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.6980 chunk 60 optimal weight: 0.0170 chunk 47 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 ASN a 15 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8577 Z= 0.243 Angle : 0.617 8.696 11626 Z= 0.306 Chirality : 0.039 0.297 1415 Planarity : 0.005 0.049 1434 Dihedral : 4.262 50.717 1176 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.89 % Allowed : 13.70 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 3.55 (0.23), residues: 1107 helix: 2.76 (0.15), residues: 959 sheet: None (None), residues: 0 loop : -0.64 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 241 HIS 0.006 0.001 HIS a 15 PHE 0.012 0.001 PHE a 85 TYR 0.010 0.001 TYR a 11 ARG 0.009 0.000 ARG I 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: I 6 MET cc_start: 0.4870 (ppp) cc_final: 0.3660 (mtm) REVERT: I 57 MET cc_start: 0.7814 (tmm) cc_final: 0.7545 (ttp) REVERT: J 11 MET cc_start: 0.7903 (tpp) cc_final: 0.7610 (tpt) REVERT: O 42 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7057 (mm-40) REVERT: O 57 MET cc_start: 0.8060 (ttp) cc_final: 0.7793 (ttp) REVERT: R 17 MET cc_start: 0.7925 (mmm) cc_final: 0.7404 (mmm) REVERT: R 57 MET cc_start: 0.8080 (ttp) cc_final: 0.7729 (ttp) REVERT: R 75 MET cc_start: 0.8686 (ttp) cc_final: 0.8186 (mtp) REVERT: S 57 MET cc_start: 0.8197 (tmt) cc_final: 0.7966 (tmt) REVERT: X 24 TYR cc_start: 0.7735 (m-10) cc_final: 0.7371 (m-10) REVERT: Y 18 VAL cc_start: 0.7987 (t) cc_final: 0.7717 (t) REVERT: a 6 MET cc_start: 0.7105 (mmt) cc_final: 0.6412 (tpt) REVERT: a 116 ASN cc_start: 0.8600 (m-40) cc_final: 0.8128 (m110) outliers start: 16 outliers final: 14 residues processed: 142 average time/residue: 0.2014 time to fit residues: 40.6578 Evaluate side-chains 146 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain R residue 44 ASP Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain a residue 259 LEU Chi-restraints excluded: chain a residue 265 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.130986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.109992 restraints weight = 10149.719| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.22 r_work: 0.3080 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8577 Z= 0.247 Angle : 0.619 9.160 11626 Z= 0.305 Chirality : 0.039 0.295 1415 Planarity : 0.005 0.049 1434 Dihedral : 4.247 50.738 1176 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.77 % Allowed : 14.05 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 3.53 (0.23), residues: 1107 helix: 2.75 (0.15), residues: 959 sheet: None (None), residues: 0 loop : -0.66 (0.46), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 241 HIS 0.009 0.002 HIS a 15 PHE 0.011 0.001 PHE a 85 TYR 0.013 0.001 TYR a 11 ARG 0.009 0.000 ARG I 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1913.56 seconds wall clock time: 35 minutes 31.30 seconds (2131.30 seconds total)