Starting phenix.real_space_refine on Tue Mar 3 19:15:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vwk_21419/03_2026/6vwk_21419_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vwk_21419/03_2026/6vwk_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_21419/03_2026/6vwk_21419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vwk_21419/03_2026/6vwk_21419.map" model { file = "/net/cci-nas-00/data/ceres_data/6vwk_21419/03_2026/6vwk_21419_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vwk_21419/03_2026/6vwk_21419_neut.cif" } resolution = 3.3 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= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.94, per 1000 atoms: 0.23 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: 0.80 Conformation dependent library (CDL) restraints added in 381.3 milliseconds 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: 0.29 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: 1.30 Time building geometry restraints manager: 1.03 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.340 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.800 ------------------------------------------------------------------------------- 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= 0.565 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.047 0.009 ARG Y 36 TYR 0.052 0.007 TYR O 10 PHE 0.032 0.004 PHE L 76 TRP 0.030 0.006 TRP Y 26 HIS 0.020 0.007 HIS a 15 Details of bonding type rmsd covalent geometry : bond 0.00984 ( 8577) covalent geometry : angle 1.30490 (11626) hydrogen bonds : bond 0.15047 ( 813) hydrogen bonds : angle 5.96313 ( 2439) *********************** 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 : 0.275 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: 0.7831 (tpt) REVERT: L 11 MET cc_start: 0.8457 (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: 0.0989 time to fit residues: 23.2157 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 : 0.252 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 5 ASN R 52 GLN S 3 ASN a 14 HIS a 15 HIS a 132 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.124773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.106325 restraints weight = 10222.120| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 0.96 r_work: 0.3036 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8577 Z= 0.206 Angle : 0.721 8.311 11626 Z= 0.373 Chirality : 0.045 0.350 1415 Planarity : 0.006 0.048 1434 Dihedral : 5.001 35.001 1178 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.53 % Allowed : 8.97 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 are not related in a simple way. 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 ARG 0.005 0.001 ARG a 210 TYR 0.022 0.002 TYR M 10 PHE 0.018 0.002 PHE a 75 TRP 0.015 0.002 TRP a 111 HIS 0.007 0.002 HIS a 132 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 8577) covalent geometry : angle 0.72143 (11626) hydrogen bonds : bond 0.07366 ( 813) hydrogen bonds : angle 4.57218 ( 2439) *********************** 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 : 0.348 Fit side-chains REVERT: J 11 MET cc_start: 0.8130 (tpp) cc_final: 0.7865 (tpt) REVERT: L 11 MET cc_start: 0.8422 (tpt) cc_final: 0.7794 (tpt) REVERT: M 6 MET cc_start: 0.5900 (mtt) cc_final: 0.5571 (mtt) REVERT: Q 41 ARG cc_start: 0.8245 (ttm110) cc_final: 0.7864 (ttm-80) REVERT: S 6 MET cc_start: 0.6035 (mmt) cc_final: 0.5496 (mmt) REVERT: X 2 ASN cc_start: 0.6286 (t0) cc_final: 0.5798 (p0) REVERT: Y 18 VAL cc_start: 0.8051 (t) cc_final: 0.7769 (t) REVERT: a 116 ASN cc_start: 0.8685 (m-40) cc_final: 0.8150 (m110) outliers start: 13 outliers final: 6 residues processed: 148 average time/residue: 0.0881 time to fit residues: 18.4528 Evaluate side-chains 133 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 61 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 97 optimal weight: 0.0980 chunk 30 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 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 20 GLN a 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.126656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.108920 restraints weight = 10055.857| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 0.90 r_work: 0.3066 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8577 Z= 0.168 Angle : 0.631 7.884 11626 Z= 0.320 Chirality : 0.041 0.303 1415 Planarity : 0.005 0.047 1434 Dihedral : 4.518 39.569 1176 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.01 % Allowed : 10.04 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 are not related in a simple way. whole: 2.90 (0.24), residues: 1107 helix: 2.22 (0.15), residues: 977 sheet: None (None), residues: 0 loop : -0.42 (0.55), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 41 TYR 0.025 0.002 TYR M 10 PHE 0.013 0.001 PHE a 75 TRP 0.009 0.001 TRP a 111 HIS 0.002 0.001 HIS a 95 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8577) covalent geometry : angle 0.63070 (11626) hydrogen bonds : bond 0.06290 ( 813) hydrogen bonds : angle 4.26482 ( 2439) *********************** 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 153 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.289 Fit side-chains REVERT: J 11 MET cc_start: 0.8091 (tpp) cc_final: 0.7824 (tpt) REVERT: J 57 MET cc_start: 0.8445 (tmm) cc_final: 0.8042 (ttp) REVERT: L 11 MET cc_start: 0.8417 (tpt) cc_final: 0.7772 (tpt) REVERT: M 6 MET cc_start: 0.5769 (mtt) cc_final: 0.5460 (mtt) REVERT: P 37 GLU cc_start: 0.7848 (tt0) cc_final: 0.7642 (tt0) REVERT: X 2 ASN cc_start: 0.6733 (t0) cc_final: 0.6308 (p0) REVERT: X 24 TYR cc_start: 0.8197 (m-10) cc_final: 0.7954 (m-10) REVERT: Y 18 VAL cc_start: 0.8011 (t) cc_final: 0.7727 (t) REVERT: a 46 MET cc_start: 0.7275 (mmm) cc_final: 0.6920 (mtp) REVERT: a 116 ASN cc_start: 0.8589 (m-40) cc_final: 0.8106 (m110) outliers start: 17 outliers final: 10 residues processed: 146 average time/residue: 0.0839 time to fit residues: 17.5469 Evaluate side-chains 141 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J 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 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 265 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 58 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 20 optimal weight: 0.0040 chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.129481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.109252 restraints weight = 10162.788| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.09 r_work: 0.3087 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2636 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= 0.171 Angle : 0.626 8.223 11626 Z= 0.313 Chirality : 0.041 0.322 1415 Planarity : 0.005 0.049 1434 Dihedral : 4.418 44.503 1176 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.60 % Allowed : 10.63 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 are not related in a simple way. whole: 3.10 (0.23), residues: 1107 helix: 2.42 (0.15), residues: 958 sheet: None (None), residues: 0 loop : -0.51 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 41 TYR 0.021 0.001 TYR M 10 PHE 0.013 0.001 PHE a 85 TRP 0.007 0.001 TRP a 241 HIS 0.010 0.002 HIS a 245 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8577) covalent geometry : angle 0.62571 (11626) hydrogen bonds : bond 0.06165 ( 813) hydrogen bonds : angle 4.20459 ( 2439) *********************** 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: 22 poor density : 134 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: J 11 MET cc_start: 0.8019 (tpp) cc_final: 0.7727 (tpt) REVERT: J 57 MET cc_start: 0.8418 (tmm) cc_final: 0.8075 (ttp) REVERT: L 11 MET cc_start: 0.8360 (tpt) cc_final: 0.7666 (tpt) REVERT: O 57 MET cc_start: 0.8784 (tmm) cc_final: 0.8510 (ttp) REVERT: P 37 GLU cc_start: 0.7910 (tt0) cc_final: 0.7678 (tt0) REVERT: R 17 MET cc_start: 0.8434 (mmm) cc_final: 0.7887 (mmm) REVERT: R 57 MET cc_start: 0.8557 (ttp) cc_final: 0.8111 (ttt) REVERT: X 1 MET cc_start: 0.5308 (mtt) cc_final: 0.4644 (ttm) REVERT: X 24 TYR cc_start: 0.8316 (m-10) cc_final: 0.7949 (m-10) REVERT: Y 18 VAL cc_start: 0.7958 (t) cc_final: 0.7678 (t) REVERT: a 46 MET cc_start: 0.7256 (mmm) cc_final: 0.6875 (mtp) REVERT: a 116 ASN cc_start: 0.8668 (m-40) cc_final: 0.8181 (m110) outliers start: 22 outliers final: 13 residues processed: 147 average time/residue: 0.0742 time to fit residues: 15.7709 Evaluate side-chains 145 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain J 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 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 59 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 0.0020 chunk 32 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.129255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.109858 restraints weight = 10155.493| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.04 r_work: 0.3079 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8577 Z= 0.171 Angle : 0.621 8.482 11626 Z= 0.309 Chirality : 0.041 0.317 1415 Planarity : 0.005 0.049 1434 Dihedral : 4.383 49.412 1176 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.36 % Allowed : 11.57 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 are not related in a simple way. whole: 3.18 (0.23), residues: 1107 helix: 2.49 (0.15), residues: 957 sheet: None (None), residues: 0 loop : -0.55 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 210 TYR 0.017 0.001 TYR M 10 PHE 0.013 0.001 PHE a 85 TRP 0.006 0.001 TRP a 231 HIS 0.018 0.003 HIS a 15 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8577) covalent geometry : angle 0.62118 (11626) hydrogen bonds : bond 0.06072 ( 813) hydrogen bonds : angle 4.15852 ( 2439) *********************** 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 : 0.293 Fit side-chains revert: symmetry clash REVERT: I 57 MET cc_start: 0.8124 (tmm) cc_final: 0.7879 (ttp) REVERT: J 11 MET cc_start: 0.8036 (tpp) cc_final: 0.7716 (tpt) REVERT: L 11 MET cc_start: 0.8356 (tpt) cc_final: 0.7650 (tpt) REVERT: P 37 GLU cc_start: 0.7921 (tt0) cc_final: 0.7709 (tt0) REVERT: R 57 MET cc_start: 0.8628 (ttp) cc_final: 0.8325 (ttt) REVERT: X 1 MET cc_start: 0.5614 (mtt) cc_final: 0.5048 (ttm) REVERT: X 24 TYR cc_start: 0.8177 (m-10) cc_final: 0.7698 (m-10) REVERT: Y 18 VAL cc_start: 0.7987 (t) cc_final: 0.7706 (t) REVERT: a 46 MET cc_start: 0.7235 (mmm) cc_final: 0.6894 (mtp) REVERT: a 116 ASN cc_start: 0.8668 (m-40) cc_final: 0.8177 (m110) outliers start: 20 outliers final: 12 residues processed: 141 average time/residue: 0.0760 time to fit residues: 15.5783 Evaluate side-chains 143 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 82 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 0.0980 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 15 HIS a 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.129046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.109518 restraints weight = 10149.645| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.08 r_work: 0.3091 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8577 Z= 0.172 Angle : 0.626 8.748 11626 Z= 0.310 Chirality : 0.041 0.320 1415 Planarity : 0.005 0.048 1434 Dihedral : 4.341 51.292 1176 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.48 % Allowed : 12.40 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 are not related in a simple way. whole: 3.23 (0.23), residues: 1107 helix: 2.53 (0.15), residues: 957 sheet: None (None), residues: 0 loop : -0.60 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 41 TYR 0.013 0.001 TYR a 11 PHE 0.013 0.001 PHE a 85 TRP 0.006 0.001 TRP a 231 HIS 0.005 0.001 HIS a 15 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8577) covalent geometry : angle 0.62588 (11626) hydrogen bonds : bond 0.06032 ( 813) hydrogen bonds : angle 4.13676 ( 2439) *********************** 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 155 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: I 57 MET cc_start: 0.8123 (tmm) cc_final: 0.7870 (ttp) REVERT: J 11 MET cc_start: 0.7997 (tpp) cc_final: 0.7670 (tpt) REVERT: J 57 MET cc_start: 0.8450 (tmm) cc_final: 0.8108 (ttp) REVERT: L 11 MET cc_start: 0.8309 (tpt) cc_final: 0.7583 (tpt) REVERT: N 16 MET cc_start: 0.8253 (ttm) cc_final: 0.7973 (ttp) REVERT: O 42 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7110 (mm-40) REVERT: O 57 MET cc_start: 0.8653 (tmm) cc_final: 0.8059 (ttt) REVERT: P 6 MET cc_start: 0.4817 (ptt) cc_final: 0.4378 (mtp) REVERT: R 17 MET cc_start: 0.8405 (mmm) cc_final: 0.7958 (mmm) REVERT: R 57 MET cc_start: 0.8629 (ttp) cc_final: 0.8332 (ttt) REVERT: R 75 MET cc_start: 0.8912 (ttp) cc_final: 0.8448 (mtp) REVERT: X 1 MET cc_start: 0.5611 (mtt) cc_final: 0.5015 (ttm) REVERT: X 24 TYR cc_start: 0.8182 (m-10) cc_final: 0.7779 (m-10) REVERT: Y 18 VAL cc_start: 0.8041 (t) cc_final: 0.7763 (t) REVERT: a 6 MET cc_start: 0.6989 (mmp) cc_final: 0.6757 (mmt) REVERT: a 40 THR cc_start: 0.7109 (OUTLIER) cc_final: 0.6834 (p) REVERT: a 46 MET cc_start: 0.7235 (mmm) cc_final: 0.6893 (mtp) REVERT: a 116 ASN cc_start: 0.8669 (m-40) cc_final: 0.8204 (m110) outliers start: 21 outliers final: 14 residues processed: 147 average time/residue: 0.0778 time to fit residues: 16.6584 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 : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain J residue 37 GLU 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 O residue 16 MET Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 40 THR 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 85 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 89 optimal weight: 0.0970 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.129724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.109287 restraints weight = 10355.703| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.14 r_work: 0.3078 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3031 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= 0.163 Angle : 0.615 8.800 11626 Z= 0.304 Chirality : 0.040 0.307 1415 Planarity : 0.005 0.048 1434 Dihedral : 4.317 51.041 1176 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.36 % Allowed : 12.87 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 are not related in a simple way. whole: 3.32 (0.23), residues: 1107 helix: 2.60 (0.15), residues: 958 sheet: None (None), residues: 0 loop : -0.71 (0.47), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 41 TYR 0.014 0.001 TYR a 11 PHE 0.012 0.001 PHE a 85 TRP 0.007 0.001 TRP a 241 HIS 0.010 0.002 HIS a 245 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8577) covalent geometry : angle 0.61456 (11626) hydrogen bonds : bond 0.05886 ( 813) hydrogen bonds : angle 4.11317 ( 2439) *********************** 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 152 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: I 6 MET cc_start: 0.4884 (mtm) cc_final: 0.3924 (ppp) REVERT: I 16 MET cc_start: 0.8352 (ttm) cc_final: 0.8045 (ttp) REVERT: I 57 MET cc_start: 0.8141 (tmm) cc_final: 0.7890 (ttp) REVERT: J 11 MET cc_start: 0.8068 (tpp) cc_final: 0.7771 (tpt) REVERT: N 16 MET cc_start: 0.8279 (ttp) cc_final: 0.7987 (ttp) REVERT: O 42 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7127 (mm-40) REVERT: P 6 MET cc_start: 0.4904 (ptt) cc_final: 0.4487 (mtp) REVERT: R 17 MET cc_start: 0.8523 (mmm) cc_final: 0.8067 (mmm) REVERT: R 57 MET cc_start: 0.8669 (ttp) cc_final: 0.8388 (ttt) REVERT: R 75 MET cc_start: 0.8977 (ttp) cc_final: 0.8507 (mtp) REVERT: X 1 MET cc_start: 0.5747 (mtt) cc_final: 0.5132 (ttm) REVERT: X 24 TYR cc_start: 0.8230 (m-10) cc_final: 0.7787 (m-10) REVERT: Y 18 VAL cc_start: 0.8071 (t) cc_final: 0.7785 (t) REVERT: a 40 THR cc_start: 0.7089 (OUTLIER) cc_final: 0.6817 (p) REVERT: a 46 MET cc_start: 0.7261 (mmm) cc_final: 0.6903 (mtp) REVERT: a 116 ASN cc_start: 0.8696 (m-40) cc_final: 0.8222 (m110) outliers start: 20 outliers final: 15 residues processed: 145 average time/residue: 0.0854 time to fit residues: 17.9541 Evaluate side-chains 147 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 37 GLU 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 O residue 16 MET Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain a residue 40 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.128928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.108608 restraints weight = 10131.676| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.16 r_work: 0.3070 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8577 Z= 0.177 Angle : 0.627 8.918 11626 Z= 0.310 Chirality : 0.040 0.308 1415 Planarity : 0.005 0.048 1434 Dihedral : 4.313 51.135 1176 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.36 % Allowed : 13.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.23), residues: 1107 helix: 2.53 (0.15), residues: 958 sheet: None (None), residues: 0 loop : -0.69 (0.47), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 41 TYR 0.014 0.001 TYR a 11 PHE 0.013 0.001 PHE a 85 TRP 0.007 0.001 TRP a 241 HIS 0.002 0.001 HIS a 95 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 8577) covalent geometry : angle 0.62698 (11626) hydrogen bonds : bond 0.06067 ( 813) hydrogen bonds : angle 4.14082 ( 2439) *********************** 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 151 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: I 6 MET cc_start: 0.4942 (mtm) cc_final: 0.3923 (ppp) REVERT: I 57 MET cc_start: 0.8133 (tmm) cc_final: 0.7886 (ttp) REVERT: J 11 MET cc_start: 0.8135 (tpp) cc_final: 0.7824 (tpt) REVERT: J 41 ARG cc_start: 0.7290 (ttm-80) cc_final: 0.6834 (ttm-80) REVERT: O 42 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7213 (mm-40) REVERT: O 57 MET cc_start: 0.8623 (tmm) cc_final: 0.8410 (ttp) REVERT: P 6 MET cc_start: 0.4834 (ptt) cc_final: 0.4319 (mtp) REVERT: P 37 GLU cc_start: 0.7846 (tt0) cc_final: 0.7617 (tt0) REVERT: R 17 MET cc_start: 0.8557 (mmm) cc_final: 0.8053 (mmm) REVERT: R 57 MET cc_start: 0.8663 (ttp) cc_final: 0.8403 (ttt) REVERT: R 75 MET cc_start: 0.8945 (ttp) cc_final: 0.8518 (mtp) REVERT: X 1 MET cc_start: 0.5312 (mtt) cc_final: 0.4784 (ttm) REVERT: X 24 TYR cc_start: 0.8227 (m-10) cc_final: 0.7841 (m-10) REVERT: Y 18 VAL cc_start: 0.8071 (t) cc_final: 0.7807 (t) REVERT: a 6 MET cc_start: 0.7171 (mmt) cc_final: 0.6350 (tpt) REVERT: a 40 THR cc_start: 0.7052 (OUTLIER) cc_final: 0.6761 (p) REVERT: a 46 MET cc_start: 0.7281 (mmm) cc_final: 0.6890 (mtp) REVERT: a 116 ASN cc_start: 0.8684 (m-40) cc_final: 0.8160 (m110) outliers start: 20 outliers final: 16 residues processed: 143 average time/residue: 0.0905 time to fit residues: 18.3289 Evaluate side-chains 148 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 37 GLU 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 O residue 16 MET Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 40 THR 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 93 optimal weight: 0.4980 chunk 95 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 91 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.129985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.109450 restraints weight = 10176.321| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.16 r_work: 0.3085 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8577 Z= 0.163 Angle : 0.626 8.706 11626 Z= 0.307 Chirality : 0.040 0.300 1415 Planarity : 0.005 0.048 1434 Dihedral : 4.285 50.814 1176 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.13 % Allowed : 13.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.30 (0.23), residues: 1107 helix: 2.60 (0.15), residues: 958 sheet: None (None), residues: 0 loop : -0.76 (0.46), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 41 TYR 0.014 0.001 TYR a 11 PHE 0.011 0.001 PHE a 85 TRP 0.006 0.001 TRP a 231 HIS 0.006 0.001 HIS a 15 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8577) covalent geometry : angle 0.62597 (11626) hydrogen bonds : bond 0.05857 ( 813) hydrogen bonds : angle 4.09717 ( 2439) *********************** 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 150 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: I 6 MET cc_start: 0.4894 (mtm) cc_final: 0.3890 (ppp) REVERT: I 16 MET cc_start: 0.8298 (ttm) cc_final: 0.7990 (ttp) REVERT: I 57 MET cc_start: 0.8075 (tmm) cc_final: 0.7834 (ttp) REVERT: J 11 MET cc_start: 0.8097 (tpp) cc_final: 0.7790 (tpt) REVERT: J 41 ARG cc_start: 0.7245 (ttm-80) cc_final: 0.6776 (ttm-80) REVERT: O 42 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7119 (mm-40) REVERT: O 57 MET cc_start: 0.8567 (tmm) cc_final: 0.8315 (ttp) REVERT: P 6 MET cc_start: 0.4753 (ptt) cc_final: 0.4171 (mtp) REVERT: R 17 MET cc_start: 0.8504 (mmm) cc_final: 0.7996 (mmm) REVERT: R 57 MET cc_start: 0.8659 (ttp) cc_final: 0.8397 (ttt) REVERT: R 75 MET cc_start: 0.8910 (ttp) cc_final: 0.8506 (mtp) REVERT: X 1 MET cc_start: 0.5237 (mtt) cc_final: 0.4706 (ttm) REVERT: X 24 TYR cc_start: 0.8214 (m-10) cc_final: 0.7765 (m-10) REVERT: Y 18 VAL cc_start: 0.8040 (t) cc_final: 0.7763 (t) REVERT: a 6 MET cc_start: 0.7110 (mmt) cc_final: 0.6285 (tpt) REVERT: a 40 THR cc_start: 0.6989 (OUTLIER) cc_final: 0.6694 (p) REVERT: a 46 MET cc_start: 0.7213 (mmm) cc_final: 0.6843 (mtp) REVERT: a 116 ASN cc_start: 0.8692 (m-40) cc_final: 0.8196 (m110) outliers start: 18 outliers final: 16 residues processed: 144 average time/residue: 0.0890 time to fit residues: 18.0476 Evaluate side-chains 147 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 37 GLU 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 O residue 16 MET Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain a residue 40 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 81 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 55 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.111393 restraints weight = 10252.244| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.02 r_work: 0.3111 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3255 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= 0.160 Angle : 0.616 8.698 11626 Z= 0.304 Chirality : 0.039 0.301 1415 Planarity : 0.005 0.047 1434 Dihedral : 4.251 50.663 1176 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.39 (0.23), residues: 1107 helix: 2.67 (0.15), residues: 958 sheet: None (None), residues: 0 loop : -0.81 (0.45), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 41 TYR 0.013 0.001 TYR a 11 PHE 0.011 0.001 PHE a 85 TRP 0.006 0.001 TRP a 231 HIS 0.002 0.001 HIS a 15 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8577) covalent geometry : angle 0.61583 (11626) hydrogen bonds : bond 0.05734 ( 813) hydrogen bonds : angle 4.07308 ( 2439) ********************** 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 149 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: I 6 MET cc_start: 0.4958 (mtm) cc_final: 0.3986 (ppp) REVERT: I 16 MET cc_start: 0.8298 (ttm) cc_final: 0.7977 (ttp) REVERT: I 57 MET cc_start: 0.8099 (tmm) cc_final: 0.7842 (ttp) REVERT: J 11 MET cc_start: 0.8099 (tpp) cc_final: 0.7811 (tpt) REVERT: O 42 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7105 (mm-40) REVERT: O 57 MET cc_start: 0.8585 (tmm) cc_final: 0.8302 (ttp) REVERT: P 6 MET cc_start: 0.4725 (ptt) cc_final: 0.4207 (mtp) REVERT: R 17 MET cc_start: 0.8506 (mmm) cc_final: 0.7965 (mmm) REVERT: R 57 MET cc_start: 0.8663 (ttp) cc_final: 0.8280 (ttt) REVERT: R 75 MET cc_start: 0.8967 (ttp) cc_final: 0.8550 (mtp) REVERT: X 1 MET cc_start: 0.5315 (mtt) cc_final: 0.4792 (ttm) REVERT: X 24 TYR cc_start: 0.8192 (m-10) cc_final: 0.7759 (m-10) REVERT: Y 18 VAL cc_start: 0.8040 (t) cc_final: 0.7761 (t) REVERT: a 6 MET cc_start: 0.7180 (mmt) cc_final: 0.6227 (tpt) REVERT: a 40 THR cc_start: 0.7055 (OUTLIER) cc_final: 0.6770 (p) REVERT: a 46 MET cc_start: 0.7199 (mmm) cc_final: 0.6855 (mtp) REVERT: a 116 ASN cc_start: 0.8699 (m-40) cc_final: 0.8213 (m110) outliers start: 16 outliers final: 15 residues processed: 143 average time/residue: 0.0888 time to fit residues: 18.0855 Evaluate side-chains 144 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 37 GLU 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 X residue 22 MET Chi-restraints excluded: chain a residue 40 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 89 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.129647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.111115 restraints weight = 10203.807| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.02 r_work: 0.3101 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3276 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= 0.167 Angle : 0.619 8.336 11626 Z= 0.305 Chirality : 0.040 0.302 1415 Planarity : 0.005 0.049 1434 Dihedral : 4.255 50.815 1176 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.01 % Allowed : 13.93 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 are not related in a simple way. whole: 3.36 (0.23), residues: 1107 helix: 2.65 (0.15), residues: 958 sheet: None (None), residues: 0 loop : -0.79 (0.45), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 41 TYR 0.014 0.001 TYR a 11 PHE 0.011 0.001 PHE a 85 TRP 0.006 0.001 TRP a 241 HIS 0.003 0.001 HIS a 15 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8577) covalent geometry : angle 0.61888 (11626) hydrogen bonds : bond 0.05807 ( 813) hydrogen bonds : angle 4.07722 ( 2439) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2059.36 seconds wall clock time: 35 minutes 49.95 seconds (2149.95 seconds total)