Starting phenix.real_space_refine on Sat Dec 28 00:57:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d85_46630/12_2024/9d85_46630_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d85_46630/12_2024/9d85_46630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d85_46630/12_2024/9d85_46630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d85_46630/12_2024/9d85_46630.map" model { file = "/net/cci-nas-00/data/ceres_data/9d85_46630/12_2024/9d85_46630_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d85_46630/12_2024/9d85_46630_neut.cif" } resolution = 3.59 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= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 65 5.49 5 S 27 5.16 5 C 4342 2.51 5 N 1229 2.21 5 O 1538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7201 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1585 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 188} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1114 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "K" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2502 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 310} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "P" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 615 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "T" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1385 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 11, 'rna3p_pur': 28, 'rna3p_pyr': 23} Link IDs: {'rna2p': 14, 'rna3p': 50} Chain breaks: 3 Time building chain proxies: 4.51, per 1000 atoms: 0.63 Number of scatterers: 7201 At special positions: 0 Unit cell: (70.04, 89.61, 130.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 65 15.00 O 1538 8.00 N 1229 7.00 C 4342 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 Atom "ATOM 5823 O4' G T 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 858.9 milliseconds 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1380 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 53.5% alpha, 14.7% beta 13 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'B' and resid 369 through 391 Processing helix chain 'B' and resid 392 through 395 Processing helix chain 'B' and resid 421 through 426 removed outlier: 4.443A pdb=" N GLU B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 445 removed outlier: 3.817A pdb=" N TYR B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS B 441 " --> pdb=" O GLU B 437 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 496 removed outlier: 3.771A pdb=" N LYS B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 514 Processing helix chain 'B' and resid 516 through 529 removed outlier: 3.964A pdb=" N ILE B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 removed outlier: 4.125A pdb=" N ASN C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 51 Processing helix chain 'C' and resid 57 through 68 removed outlier: 4.094A pdb=" N LEU C 63 " --> pdb=" O TRP C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 80 removed outlier: 3.598A pdb=" N ALA C 75 " --> pdb=" O GLN C 71 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS C 77 " --> pdb=" O HIS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 104 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 115 through 124 Processing helix chain 'C' and resid 133 through 144 Processing helix chain 'K' and resid 45 through 63 Proline residue: K 53 - end of helix Processing helix chain 'K' and resid 79 through 98 Processing helix chain 'K' and resid 106 through 118 removed outlier: 3.747A pdb=" N ILE K 111 " --> pdb=" O CYS K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 166 Processing helix chain 'K' and resid 170 through 179 removed outlier: 4.339A pdb=" N TYR K 174 " --> pdb=" O PRO K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 212 Processing helix chain 'K' and resid 215 through 243 Processing helix chain 'K' and resid 251 through 255 Processing helix chain 'K' and resid 256 through 270 removed outlier: 3.961A pdb=" N ARG K 260 " --> pdb=" O ASN K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 278 through 283 removed outlier: 3.623A pdb=" N GLY K 283 " --> pdb=" O LYS K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 299 removed outlier: 4.250A pdb=" N ILE K 289 " --> pdb=" O ASN K 285 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN K 299 " --> pdb=" O LEU K 295 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 308 Processing helix chain 'K' and resid 315 through 319 removed outlier: 3.571A pdb=" N VAL K 319 " --> pdb=" O THR K 316 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 32 removed outlier: 4.095A pdb=" N TYR P 29 " --> pdb=" O GLU P 25 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU P 30 " --> pdb=" O ALA P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 80 removed outlier: 3.833A pdb=" N ILE P 80 " --> pdb=" O ALA P 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 346 through 351 Processing sheet with id=AA2, first strand: chain 'B' and resid 419 through 420 Processing sheet with id=AA3, first strand: chain 'B' and resid 447 through 449 Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AA5, first strand: chain 'K' and resid 23 through 31 removed outlier: 3.525A pdb=" N GLU K 23 " --> pdb=" O THR K 19 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE K 17 " --> pdb=" O LEU K 25 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASN K 27 " --> pdb=" O VAL K 15 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL K 15 " --> pdb=" O ASN K 27 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR K 29 " --> pdb=" O THR K 13 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR K 13 " --> pdb=" O THR K 29 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE K 71 " --> pdb=" O ILE K 102 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL K 104 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE K 73 " --> pdb=" O VAL K 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 143 through 148 removed outlier: 6.527A pdb=" N VAL K 135 " --> pdb=" O PHE K 146 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU K 148 " --> pdb=" O THR K 133 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N THR K 133 " --> pdb=" O GLU K 148 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU K 124 " --> pdb=" O MET K 248 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL K 250 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU K 126 " --> pdb=" O VAL K 250 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL K 247 " --> pdb=" O ASP K 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 192 through 193 removed outlier: 3.669A pdb=" N LYS K 193 " --> pdb=" O ASP K 196 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 7 through 13 324 hydrogen bonds defined for protein. 918 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1430 1.33 - 1.45: 1919 1.45 - 1.57: 3937 1.57 - 1.69: 126 1.69 - 1.81: 46 Bond restraints: 7458 Sorted by residual: bond pdb=" CA PRO K 34 " pdb=" C PRO K 34 " ideal model delta sigma weight residual 1.517 1.549 -0.032 9.30e-03 1.16e+04 1.21e+01 bond pdb=" N GLN K 37 " pdb=" CA GLN K 37 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.27e-02 6.20e+03 1.03e+01 bond pdb=" C LYS K 33 " pdb=" N PRO K 34 " ideal model delta sigma weight residual 1.329 1.365 -0.036 1.18e-02 7.18e+03 9.17e+00 bond pdb=" N LYS K 33 " pdb=" CA LYS K 33 " ideal model delta sigma weight residual 1.457 1.498 -0.042 1.41e-02 5.03e+03 8.70e+00 bond pdb=" O5' U T 44 " pdb=" C5' U T 44 " ideal model delta sigma weight residual 1.420 1.464 -0.044 1.50e-02 4.44e+03 8.63e+00 ... (remaining 7453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.23: 10335 6.23 - 12.46: 34 12.46 - 18.69: 8 18.69 - 24.92: 3 24.92 - 31.15: 3 Bond angle restraints: 10383 Sorted by residual: angle pdb=" N TYR K 32 " pdb=" CA TYR K 32 " pdb=" C TYR K 32 " ideal model delta sigma weight residual 109.96 78.81 31.15 1.50e+00 4.44e-01 4.31e+02 angle pdb=" C ARG B 529 " pdb=" CA ARG B 529 " pdb=" CB ARG B 529 " ideal model delta sigma weight residual 110.94 81.56 29.38 1.65e+00 3.67e-01 3.17e+02 angle pdb=" N LYS K 33 " pdb=" CA LYS K 33 " pdb=" CB LYS K 33 " ideal model delta sigma weight residual 110.37 83.48 26.89 1.78e+00 3.16e-01 2.28e+02 angle pdb=" N ARG B 529 " pdb=" CA ARG B 529 " pdb=" C ARG B 529 " ideal model delta sigma weight residual 112.72 128.78 -16.06 1.14e+00 7.69e-01 1.98e+02 angle pdb=" N GLU K 43 " pdb=" CA GLU K 43 " pdb=" C GLU K 43 " ideal model delta sigma weight residual 110.33 93.31 17.02 1.29e+00 6.01e-01 1.74e+02 ... (remaining 10378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.86: 4306 33.86 - 67.71: 277 67.71 - 101.57: 40 101.57 - 135.43: 3 135.43 - 169.28: 3 Dihedral angle restraints: 4629 sinusoidal: 2487 harmonic: 2142 Sorted by residual: dihedral pdb=" C ARG B 529 " pdb=" N ARG B 529 " pdb=" CA ARG B 529 " pdb=" CB ARG B 529 " ideal model delta harmonic sigma weight residual -122.60 -94.98 -27.62 0 2.50e+00 1.60e-01 1.22e+02 dihedral pdb=" N LYS K 33 " pdb=" C LYS K 33 " pdb=" CA LYS K 33 " pdb=" CB LYS K 33 " ideal model delta harmonic sigma weight residual 122.80 96.34 26.46 0 2.50e+00 1.60e-01 1.12e+02 dihedral pdb=" C TYR K 32 " pdb=" N TYR K 32 " pdb=" CA TYR K 32 " pdb=" CB TYR K 32 " ideal model delta harmonic sigma weight residual -122.60 -97.19 -25.41 0 2.50e+00 1.60e-01 1.03e+02 ... (remaining 4626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1168 0.125 - 0.249: 45 0.249 - 0.374: 2 0.374 - 0.499: 14 0.499 - 0.623: 9 Chirality restraints: 1238 Sorted by residual: chirality pdb=" CA TYR K 32 " pdb=" N TYR K 32 " pdb=" C TYR K 32 " pdb=" CB TYR K 32 " both_signs ideal model delta sigma weight residual False 2.51 3.13 -0.62 2.00e-01 2.50e+01 9.72e+00 chirality pdb=" P U T 44 " pdb=" OP1 U T 44 " pdb=" OP2 U T 44 " pdb=" O5' U T 44 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" P C T 40 " pdb=" OP1 C T 40 " pdb=" OP2 C T 40 " pdb=" O5' C T 40 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.00e+00 ... (remaining 1235 not shown) Planarity restraints: 1083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 532 " -1.008 9.50e-02 1.11e+02 4.52e-01 1.23e+02 pdb=" NE ARG B 532 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG B 532 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG B 532 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 532 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 163 " -0.809 9.50e-02 1.11e+02 3.63e-01 8.01e+01 pdb=" NE ARG K 163 " 0.051 2.00e-02 2.50e+03 pdb=" CZ ARG K 163 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG K 163 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG K 163 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 526 " 0.016 2.00e-02 2.50e+03 3.10e-02 9.64e+00 pdb=" C ASP B 526 " -0.054 2.00e-02 2.50e+03 pdb=" O ASP B 526 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL B 527 " 0.018 2.00e-02 2.50e+03 ... (remaining 1080 not shown) Histogram of nonbonded interaction distances: 0.99 - 1.77: 7 1.77 - 2.56: 162 2.56 - 3.34: 10118 3.34 - 4.12: 19580 4.12 - 4.90: 32785 Warning: very small nonbonded interaction distances. Nonbonded interactions: 62652 Sorted by model distance: nonbonded pdb=" CE1 HIS C 73 " pdb=" O4' G T 1 " model vdw 0.994 3.260 nonbonded pdb=" CE1 PHE C 21 " pdb=" N7 A T 76 " model vdw 1.188 3.420 nonbonded pdb=" CZ PHE C 21 " pdb=" C5 A T 76 " model vdw 1.329 3.560 nonbonded pdb=" CE1 PHE C 21 " pdb=" C5 A T 76 " model vdw 1.449 3.560 nonbonded pdb=" CD1 PHE C 21 " pdb=" N7 A T 76 " model vdw 1.565 3.420 ... (remaining 62647 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.020 Find NCS groups from input model: 0.060 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4417 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 : 0.005 0.050 7458 Z= 0.321 Angle : 1.213 31.151 10383 Z= 0.765 Chirality : 0.083 0.623 1238 Planarity : 0.018 0.452 1083 Dihedral : 21.010 169.283 3249 Min Nonbonded Distance : 0.994 Molprobity Statistics. All-atom Clashscore : 27.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.43 % Favored : 93.43 % Rotamer: Outliers : 0.33 % Allowed : 0.33 % Favored : 99.35 % Cbeta Deviations : 0.87 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.31), residues: 731 helix: 0.13 (0.27), residues: 348 sheet: -0.51 (0.57), residues: 95 loop : -1.83 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP P 72 HIS 0.002 0.001 HIS K 106 PHE 0.011 0.001 PHE B 506 TYR 0.019 0.002 TYR K 226 ARG 0.007 0.001 ARG K 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 MET cc_start: 0.4362 (mtm) cc_final: 0.3609 (mtm) REVERT: B 470 LEU cc_start: 0.6470 (mp) cc_final: 0.5907 (tt) REVERT: C 60 MET cc_start: 0.5579 (tmm) cc_final: 0.4348 (mtt) REVERT: C 70 ARG cc_start: 0.5801 (mtt-85) cc_final: 0.5425 (tpt170) REVERT: C 115 ASN cc_start: 0.8670 (p0) cc_final: 0.8457 (p0) REVERT: K 204 THR cc_start: 0.8004 (m) cc_final: 0.7645 (p) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.2718 time to fit residues: 56.2705 Evaluate side-chains 101 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.3980 chunk 59 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 0.0670 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN C 22 ASN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS K 160 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4815 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7458 Z= 0.268 Angle : 0.807 7.730 10383 Z= 0.420 Chirality : 0.048 0.201 1238 Planarity : 0.006 0.082 1083 Dihedral : 22.986 168.451 1841 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.60 % Allowed : 14.63 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.30), residues: 731 helix: 0.09 (0.26), residues: 352 sheet: -0.87 (0.52), residues: 99 loop : -1.48 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 291 HIS 0.009 0.003 HIS K 106 PHE 0.028 0.003 PHE B 457 TYR 0.022 0.003 TYR B 510 ARG 0.005 0.001 ARG B 368 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 461 LYS cc_start: 0.4951 (tptp) cc_final: 0.4212 (tptp) REVERT: B 470 LEU cc_start: 0.6809 (mp) cc_final: 0.6146 (tt) REVERT: B 473 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6473 (mm) REVERT: C 115 ASN cc_start: 0.8659 (p0) cc_final: 0.8130 (p0) REVERT: C 124 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7277 (pm20) REVERT: K 1 MET cc_start: -0.0126 (mmm) cc_final: -0.0732 (tpp) outliers start: 16 outliers final: 8 residues processed: 129 average time/residue: 0.2450 time to fit residues: 41.7016 Evaluate side-chains 102 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 108 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 417 ASN ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 HIS ** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5024 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7458 Z= 0.266 Angle : 0.747 11.450 10383 Z= 0.378 Chirality : 0.044 0.213 1238 Planarity : 0.005 0.045 1083 Dihedral : 22.583 166.773 1841 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.88 % Allowed : 19.35 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.30), residues: 731 helix: 0.04 (0.26), residues: 355 sheet: -0.87 (0.54), residues: 94 loop : -1.43 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP K 291 HIS 0.008 0.002 HIS K 106 PHE 0.017 0.003 PHE C 21 TYR 0.020 0.002 TYR K 190 ARG 0.008 0.001 ARG K 260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 461 LYS cc_start: 0.5160 (tptp) cc_final: 0.4557 (tptm) REVERT: C 115 ASN cc_start: 0.8575 (p0) cc_final: 0.8038 (p0) REVERT: K 97 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7611 (tp) REVERT: K 195 MET cc_start: 0.5865 (mmm) cc_final: 0.5587 (mmm) REVERT: K 204 THR cc_start: 0.7396 (m) cc_final: 0.7001 (p) REVERT: K 228 PHE cc_start: 0.4172 (m-10) cc_final: 0.3863 (m-10) REVERT: K 266 MET cc_start: 0.0724 (tmm) cc_final: -0.1619 (ttt) REVERT: K 289 ILE cc_start: 0.4481 (mt) cc_final: 0.2794 (mt) REVERT: K 298 LYS cc_start: 0.5087 (tttt) cc_final: 0.4528 (tttt) outliers start: 30 outliers final: 15 residues processed: 140 average time/residue: 0.2011 time to fit residues: 37.1346 Evaluate side-chains 114 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain K residue 154 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 417 ASN B 495 HIS ** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5103 moved from start: 0.6324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7458 Z= 0.221 Angle : 0.708 13.665 10383 Z= 0.358 Chirality : 0.044 0.175 1238 Planarity : 0.004 0.036 1083 Dihedral : 22.259 167.610 1841 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.55 % Allowed : 23.25 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.30), residues: 731 helix: 0.12 (0.26), residues: 354 sheet: -0.94 (0.54), residues: 93 loop : -1.39 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 291 HIS 0.011 0.002 HIS K 106 PHE 0.024 0.003 PHE P 14 TYR 0.017 0.002 TYR K 190 ARG 0.006 0.001 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 461 LYS cc_start: 0.5522 (tptp) cc_final: 0.5075 (tptm) REVERT: B 470 LEU cc_start: 0.6892 (mp) cc_final: 0.5977 (tt) REVERT: C 115 ASN cc_start: 0.8728 (p0) cc_final: 0.8239 (p0) REVERT: C 117 ASP cc_start: 0.8146 (m-30) cc_final: 0.7504 (m-30) REVERT: C 119 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7401 (mm-30) REVERT: C 124 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7026 (pm20) REVERT: K 248 MET cc_start: 0.4634 (tpt) cc_final: 0.3236 (tpp) REVERT: K 266 MET cc_start: 0.0998 (tmm) cc_final: -0.1015 (ttt) REVERT: K 289 ILE cc_start: 0.3409 (mt) cc_final: 0.3085 (mt) REVERT: K 296 MET cc_start: 0.0757 (ttm) cc_final: 0.0528 (ttm) outliers start: 28 outliers final: 16 residues processed: 129 average time/residue: 0.1997 time to fit residues: 35.2283 Evaluate side-chains 111 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 261 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 495 HIS ** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5162 moved from start: 0.7098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7458 Z= 0.211 Angle : 0.704 12.495 10383 Z= 0.352 Chirality : 0.043 0.159 1238 Planarity : 0.004 0.044 1083 Dihedral : 22.045 168.937 1841 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.23 % Allowed : 26.18 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.82 (0.30), residues: 731 helix: 0.25 (0.27), residues: 353 sheet: -0.98 (0.49), residues: 111 loop : -1.29 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP K 291 HIS 0.007 0.001 HIS K 110 PHE 0.015 0.002 PHE P 14 TYR 0.024 0.002 TYR B 415 ARG 0.005 0.001 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 MET cc_start: 0.5504 (OUTLIER) cc_final: 0.4951 (ptm) REVERT: B 461 LYS cc_start: 0.5731 (tptp) cc_final: 0.5417 (tptp) REVERT: C 115 ASN cc_start: 0.8764 (p0) cc_final: 0.8287 (p0) REVERT: C 117 ASP cc_start: 0.8093 (m-30) cc_final: 0.7527 (m-30) REVERT: C 124 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7062 (pm20) REVERT: K 1 MET cc_start: 0.0115 (tpp) cc_final: -0.0285 (tpp) REVERT: K 97 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7542 (tp) REVERT: K 248 MET cc_start: 0.4736 (tpt) cc_final: 0.3719 (tpp) REVERT: K 266 MET cc_start: 0.1125 (tmm) cc_final: -0.0731 (ttt) REVERT: K 288 MET cc_start: 0.4653 (ppp) cc_final: 0.4416 (ppp) outliers start: 26 outliers final: 17 residues processed: 121 average time/residue: 0.1727 time to fit residues: 29.5564 Evaluate side-chains 112 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 276 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 495 HIS ** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5173 moved from start: 0.7639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7458 Z= 0.185 Angle : 0.681 11.359 10383 Z= 0.335 Chirality : 0.042 0.161 1238 Planarity : 0.004 0.033 1083 Dihedral : 21.855 169.590 1841 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.09 % Allowed : 28.46 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.70 (0.30), residues: 731 helix: 0.31 (0.27), residues: 352 sheet: -0.66 (0.50), residues: 104 loop : -1.30 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP K 291 HIS 0.005 0.001 HIS B 495 PHE 0.021 0.002 PHE K 281 TYR 0.013 0.001 TYR K 190 ARG 0.004 0.000 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 MET cc_start: 0.4988 (mtm) cc_final: 0.4453 (ptm) REVERT: B 461 LYS cc_start: 0.5802 (tptp) cc_final: 0.5490 (tttp) REVERT: C 115 ASN cc_start: 0.8763 (p0) cc_final: 0.8314 (p0) REVERT: C 116 GLU cc_start: 0.8095 (pm20) cc_final: 0.7860 (pm20) REVERT: C 117 ASP cc_start: 0.8114 (m-30) cc_final: 0.7451 (m-30) REVERT: C 119 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7500 (mm-30) REVERT: C 121 LEU cc_start: 0.7846 (mm) cc_final: 0.7514 (tp) REVERT: C 124 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6986 (pm20) REVERT: K 97 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7505 (tp) REVERT: K 248 MET cc_start: 0.4975 (tpt) cc_final: 0.4107 (tpp) REVERT: K 266 MET cc_start: 0.1433 (tmm) cc_final: -0.0266 (ttt) REVERT: K 288 MET cc_start: 0.4386 (ppp) cc_final: 0.3454 (ppp) outliers start: 19 outliers final: 12 residues processed: 113 average time/residue: 0.1718 time to fit residues: 27.3488 Evaluate side-chains 103 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 250 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5289 moved from start: 0.8375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7458 Z= 0.213 Angle : 0.694 12.781 10383 Z= 0.347 Chirality : 0.042 0.255 1238 Planarity : 0.004 0.033 1083 Dihedral : 21.760 169.680 1841 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.55 % Allowed : 27.97 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.64 (0.31), residues: 731 helix: 0.36 (0.27), residues: 351 sheet: -0.75 (0.49), residues: 111 loop : -1.20 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP K 291 HIS 0.007 0.002 HIS B 495 PHE 0.016 0.002 PHE K 281 TYR 0.018 0.002 TYR K 190 ARG 0.004 0.001 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 461 LYS cc_start: 0.5881 (tptp) cc_final: 0.5677 (tttp) REVERT: C 27 PHE cc_start: 0.7104 (p90) cc_final: 0.6861 (p90) REVERT: C 115 ASN cc_start: 0.8781 (p0) cc_final: 0.8201 (p0) REVERT: C 119 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7402 (mm-30) REVERT: C 124 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7067 (pm20) REVERT: K 210 TYR cc_start: 0.3579 (OUTLIER) cc_final: 0.3165 (m-10) REVERT: K 248 MET cc_start: 0.5429 (tpt) cc_final: 0.4741 (tpp) REVERT: K 261 GLU cc_start: 0.7607 (mt-10) cc_final: 0.6730 (mm-30) REVERT: K 266 MET cc_start: 0.1586 (tmm) cc_final: -0.0042 (ttt) REVERT: K 281 PHE cc_start: 0.5977 (m-80) cc_final: 0.5713 (t80) REVERT: K 288 MET cc_start: 0.4283 (ppp) cc_final: 0.3951 (ppp) outliers start: 28 outliers final: 20 residues processed: 124 average time/residue: 0.1804 time to fit residues: 31.1387 Evaluate side-chains 113 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 210 TYR Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 311 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5306 moved from start: 0.8908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7458 Z= 0.214 Angle : 0.704 12.649 10383 Z= 0.352 Chirality : 0.043 0.246 1238 Planarity : 0.004 0.035 1083 Dihedral : 21.703 169.941 1841 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.90 % Allowed : 29.43 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.63 (0.31), residues: 731 helix: 0.32 (0.27), residues: 352 sheet: -0.60 (0.49), residues: 110 loop : -1.19 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP K 291 HIS 0.007 0.002 HIS B 449 PHE 0.012 0.002 PHE P 43 TYR 0.016 0.002 TYR K 190 ARG 0.005 0.001 ARG B 516 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 MET cc_start: 0.4897 (mtm) cc_final: 0.4544 (ptt) REVERT: B 423 ASP cc_start: 0.7619 (m-30) cc_final: 0.7407 (m-30) REVERT: C 27 PHE cc_start: 0.6987 (p90) cc_final: 0.6693 (p90) REVERT: C 115 ASN cc_start: 0.8727 (p0) cc_final: 0.8195 (p0) REVERT: C 119 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7351 (mm-30) REVERT: C 121 LEU cc_start: 0.7851 (mm) cc_final: 0.7509 (tp) REVERT: C 123 ARG cc_start: 0.6603 (mtp85) cc_final: 0.4722 (mmp-170) REVERT: C 124 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7155 (pm20) REVERT: K 1 MET cc_start: 0.0660 (tpp) cc_final: -0.0329 (tpp) REVERT: K 248 MET cc_start: 0.5296 (tpt) cc_final: 0.4921 (tpp) REVERT: K 261 GLU cc_start: 0.7649 (mt-10) cc_final: 0.6870 (mm-30) REVERT: K 266 MET cc_start: 0.1752 (tmm) cc_final: 0.0201 (ttt) REVERT: K 281 PHE cc_start: 0.6234 (m-80) cc_final: 0.5823 (t80) REVERT: K 298 LYS cc_start: 0.6395 (tttt) cc_final: 0.5786 (tptt) outliers start: 24 outliers final: 20 residues processed: 119 average time/residue: 0.1687 time to fit residues: 27.8646 Evaluate side-chains 111 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 276 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 HIS B 495 HIS ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 ASN K 160 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5553 moved from start: 1.0130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7458 Z= 0.295 Angle : 0.805 13.130 10383 Z= 0.407 Chirality : 0.045 0.235 1238 Planarity : 0.005 0.039 1083 Dihedral : 21.874 169.239 1841 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.39 % Allowed : 29.76 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.30), residues: 731 helix: -0.10 (0.26), residues: 352 sheet: -0.72 (0.49), residues: 104 loop : -1.44 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP K 291 HIS 0.008 0.002 HIS C 43 PHE 0.019 0.002 PHE K 52 TYR 0.027 0.002 TYR K 190 ARG 0.006 0.001 ARG K 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 MET cc_start: 0.5065 (mtm) cc_final: 0.4378 (ptp) REVERT: B 452 LEU cc_start: 0.6712 (mm) cc_final: 0.6443 (mm) REVERT: C 115 ASN cc_start: 0.8667 (p0) cc_final: 0.8130 (p0) REVERT: C 119 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7270 (mm-30) REVERT: C 124 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: K 1 MET cc_start: 0.2153 (tpp) cc_final: 0.1418 (tpp) REVERT: K 261 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7283 (mm-30) REVERT: K 266 MET cc_start: 0.3180 (tmm) cc_final: 0.2560 (ttt) REVERT: K 298 LYS cc_start: 0.6805 (tttt) cc_final: 0.6253 (tptt) outliers start: 27 outliers final: 18 residues processed: 124 average time/residue: 0.1739 time to fit residues: 29.9761 Evaluate side-chains 113 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 0.0870 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 0.0470 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 GLN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5482 moved from start: 1.0385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7458 Z= 0.216 Angle : 0.764 12.902 10383 Z= 0.380 Chirality : 0.045 0.267 1238 Planarity : 0.004 0.034 1083 Dihedral : 21.774 169.818 1841 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.41 % Allowed : 31.06 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.30), residues: 731 helix: -0.23 (0.26), residues: 354 sheet: -0.59 (0.48), residues: 111 loop : -1.40 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP K 291 HIS 0.011 0.002 HIS K 106 PHE 0.014 0.002 PHE K 52 TYR 0.016 0.002 TYR K 190 ARG 0.005 0.001 ARG B 516 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 MET cc_start: 0.5010 (mtm) cc_final: 0.4332 (ptp) REVERT: C 115 ASN cc_start: 0.8636 (p0) cc_final: 0.8131 (p0) REVERT: C 119 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7424 (mm-30) REVERT: C 121 LEU cc_start: 0.7883 (mm) cc_final: 0.7533 (tp) REVERT: C 123 ARG cc_start: 0.6894 (mtp85) cc_final: 0.5392 (mpt180) REVERT: C 124 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6794 (pm20) REVERT: C 138 VAL cc_start: 0.7204 (t) cc_final: 0.6996 (p) REVERT: K 1 MET cc_start: 0.1736 (tpp) cc_final: 0.1401 (tpt) REVERT: K 261 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7333 (mm-30) REVERT: K 266 MET cc_start: 0.3141 (tmm) cc_final: 0.2628 (ttt) REVERT: K 298 LYS cc_start: 0.6945 (tttt) cc_final: 0.6654 (tptt) outliers start: 21 outliers final: 17 residues processed: 124 average time/residue: 0.1837 time to fit residues: 31.9868 Evaluate side-chains 115 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 495 HIS ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5037 r_free = 0.5037 target = 0.169716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.143580 restraints weight = 21137.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.147721 restraints weight = 12083.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.150430 restraints weight = 8357.168| |-----------------------------------------------------------------------------| r_work (final): 0.4753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4752 r_free = 0.4752 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4752 r_free = 0.4752 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5838 moved from start: 1.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7458 Z= 0.223 Angle : 0.764 12.678 10383 Z= 0.381 Chirality : 0.045 0.242 1238 Planarity : 0.004 0.036 1083 Dihedral : 21.703 169.862 1841 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.93 % Allowed : 32.20 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.30), residues: 731 helix: -0.34 (0.26), residues: 362 sheet: -0.61 (0.47), residues: 119 loop : -1.51 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP K 291 HIS 0.013 0.002 HIS B 443 PHE 0.015 0.002 PHE C 27 TYR 0.017 0.002 TYR K 190 ARG 0.006 0.001 ARG B 516 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1735.18 seconds wall clock time: 33 minutes 15.63 seconds (1995.63 seconds total)