Starting phenix.real_space_refine on Mon Apr 28 05:46:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kqi_62505/04_2025/9kqi_62505.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kqi_62505/04_2025/9kqi_62505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kqi_62505/04_2025/9kqi_62505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kqi_62505/04_2025/9kqi_62505.map" model { file = "/net/cci-nas-00/data/ceres_data/9kqi_62505/04_2025/9kqi_62505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kqi_62505/04_2025/9kqi_62505.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.105 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 16 5.49 5 S 40 5.16 5 C 4836 2.51 5 N 1018 2.21 5 O 1170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7082 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3171 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 364} Chain breaks: 1 Chain: "B" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3171 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 364} Chain breaks: 1 Chain: "A" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 370 Unusual residues: {' CA': 1, 'C14': 1, 'D12': 1, 'LBN': 5, 'PSF': 2, 'T7X': 1} Inner-chain residues flagged as termini: ['pdbres="SER A 511 "'] Classifications: {'peptide': 1, 'undetermined': 11} Modifications used: {'COO': 1} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'LBN:plan-3': 2} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 370 Unusual residues: {' CA': 1, 'C14': 1, 'D12': 1, 'LBN': 5, 'PSF': 2, 'T7X': 1} Classifications: {'peptide': 1, 'undetermined': 11} Modifications used: {'COO': 1} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'LBN:plan-3': 2} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 5.10, per 1000 atoms: 0.72 Number of scatterers: 7082 At special positions: 0 Unit cell: (91.785, 108.665, 71.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 40 16.00 P 16 15.00 O 1170 8.00 N 1018 7.00 C 4836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 782.8 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 0 sheets defined 76.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 14 through 23 removed outlier: 3.971A pdb=" N PHE A 21 " --> pdb=" O TYR A 17 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 22 " --> pdb=" O LYS A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 removed outlier: 3.783A pdb=" N PHE A 37 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG A 39 " --> pdb=" O PHE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 59 Processing helix chain 'A' and resid 64 through 88 removed outlier: 3.506A pdb=" N LEU A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 119 removed outlier: 3.652A pdb=" N VAL A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 135 through 140 removed outlier: 4.299A pdb=" N TYR A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 140' Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 166 through 184 Processing helix chain 'A' and resid 185 through 204 removed outlier: 3.554A pdb=" N CYS A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 224 through 242 Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 283 through 311 removed outlier: 3.591A pdb=" N GLU A 301 " --> pdb=" O TRP A 297 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 344 removed outlier: 4.042A pdb=" N ARG A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Proline residue: A 333 - end of helix removed outlier: 3.813A pdb=" N ARG A 336 " --> pdb=" O ALA A 332 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 372 removed outlier: 3.562A pdb=" N ALA A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 408 removed outlier: 3.576A pdb=" N THR A 394 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 406 " --> pdb=" O MET A 402 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 23 removed outlier: 3.995A pdb=" N PHE B 21 " --> pdb=" O TYR B 17 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG B 22 " --> pdb=" O LYS B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.782A pdb=" N PHE B 37 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG B 39 " --> pdb=" O PHE B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 59 removed outlier: 3.614A pdb=" N ILE B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 88 removed outlier: 3.616A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 69 " --> pdb=" O PRO B 65 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.522A pdb=" N VAL B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 134 Processing helix chain 'B' and resid 135 through 140 removed outlier: 4.265A pdb=" N TYR B 139 " --> pdb=" O PRO B 135 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 140' Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 166 through 184 removed outlier: 3.941A pdb=" N LEU B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 182 " --> pdb=" O MET B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 204 Processing helix chain 'B' and resid 213 through 219 removed outlier: 4.262A pdb=" N GLN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 242 Processing helix chain 'B' and resid 255 through 266 Processing helix chain 'B' and resid 283 through 311 removed outlier: 3.652A pdb=" N GLN B 298 " --> pdb=" O MET B 294 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 301 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B 304 " --> pdb=" O THR B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 344 removed outlier: 4.086A pdb=" N ARG B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Proline residue: B 333 - end of helix removed outlier: 3.796A pdb=" N ARG B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 372 removed outlier: 3.705A pdb=" N ALA B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 408 removed outlier: 3.575A pdb=" N THR B 394 " --> pdb=" O CYS B 390 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 406 " --> pdb=" O MET B 402 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1167 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: 1.65 Time building geometry restraints manager: 2.66 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: 975 1.32 - 1.44: 2259 1.44 - 1.56: 3960 1.56 - 1.69: 32 1.69 - 1.81: 62 Bond restraints: 7288 Sorted by residual: bond pdb=" CG1 ILE A 192 " pdb=" CD1 ILE A 192 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.94e+00 bond pdb=" CB CYS A 237 " pdb=" SG CYS A 237 " ideal model delta sigma weight residual 1.808 1.765 0.043 3.30e-02 9.18e+02 1.68e+00 bond pdb=" CG1 ILE B 192 " pdb=" CD1 ILE B 192 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.42e+00 bond pdb=" CB CYS B 237 " pdb=" SG CYS B 237 " ideal model delta sigma weight residual 1.808 1.771 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CB VAL A 359 " pdb=" CG2 VAL A 359 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.49e-01 ... (remaining 7283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 9518 1.34 - 2.69: 213 2.69 - 4.03: 46 4.03 - 5.38: 10 5.38 - 6.72: 9 Bond angle restraints: 9796 Sorted by residual: angle pdb=" C ALA A 87 " pdb=" N PHE A 88 " pdb=" CA PHE A 88 " ideal model delta sigma weight residual 122.38 116.09 6.29 2.90e+00 1.19e-01 4.71e+00 angle pdb=" C SER B 63 " pdb=" N VAL B 64 " pdb=" CA VAL B 64 " ideal model delta sigma weight residual 123.43 121.07 2.36 1.10e+00 8.26e-01 4.62e+00 angle pdb=" C ALA B 87 " pdb=" N PHE B 88 " pdb=" CA PHE B 88 " ideal model delta sigma weight residual 122.38 116.17 6.21 2.90e+00 1.19e-01 4.59e+00 angle pdb=" C VAL B 64 " pdb=" CA VAL B 64 " pdb=" CB VAL B 64 " ideal model delta sigma weight residual 110.37 112.64 -2.27 1.07e+00 8.73e-01 4.50e+00 angle pdb=" CB MET A 402 " pdb=" CG MET A 402 " pdb=" SD MET A 402 " ideal model delta sigma weight residual 112.70 118.98 -6.28 3.00e+00 1.11e-01 4.39e+00 ... (remaining 9791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.92: 4022 33.92 - 67.83: 238 67.83 - 101.75: 43 101.75 - 135.66: 15 135.66 - 169.58: 16 Dihedral angle restraints: 4334 sinusoidal: 2112 harmonic: 2222 Sorted by residual: dihedral pdb=" O5 LBN A 505 " pdb=" C2 LBN A 505 " pdb=" C3 LBN A 505 " pdb=" O7 LBN A 505 " ideal model delta sinusoidal sigma weight residual 62.67 -127.75 -169.58 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O5 LBN B 506 " pdb=" C2 LBN B 506 " pdb=" C3 LBN B 506 " pdb=" O7 LBN B 506 " ideal model delta sinusoidal sigma weight residual 62.67 -128.75 -168.58 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C7 T7X A 503 " pdb=" O13 T7X A 503 " pdb=" P1 T7X A 503 " pdb=" O11 T7X A 503 " ideal model delta sinusoidal sigma weight residual 318.06 149.69 168.37 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 4331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 602 0.033 - 0.066: 295 0.066 - 0.099: 83 0.099 - 0.133: 19 0.133 - 0.166: 5 Chirality restraints: 1004 Sorted by residual: chirality pdb=" CG LEU B 207 " pdb=" CB LEU B 207 " pdb=" CD1 LEU B 207 " pdb=" CD2 LEU B 207 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CB VAL A 359 " pdb=" CA VAL A 359 " pdb=" CG1 VAL A 359 " pdb=" CG2 VAL A 359 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" C2 LBN B 509 " pdb=" C1 LBN B 509 " pdb=" C3 LBN B 509 " pdb=" O7 LBN B 509 " both_signs ideal model delta sigma weight residual False -2.36 -2.22 -0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 1001 not shown) Planarity restraints: 1128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 332 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO B 333 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 333 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 333 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 332 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 333 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 64 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO B 65 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 65 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 65 " -0.020 5.00e-02 4.00e+02 ... (remaining 1125 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 849 2.74 - 3.28: 6641 3.28 - 3.82: 11702 3.82 - 4.36: 14768 4.36 - 4.90: 24919 Nonbonded interactions: 58879 Sorted by model distance: nonbonded pdb=" O PHE B 48 " pdb=" OG SER B 52 " model vdw 2.205 3.040 nonbonded pdb=" O LEU B 240 " pdb=" OH TYR B 245 " model vdw 2.216 3.040 nonbonded pdb=" OG1 THR B 44 " pdb=" O3 LBN B 501 " model vdw 2.247 3.040 nonbonded pdb=" O GLY B 187 " pdb=" OG1 THR B 191 " model vdw 2.248 3.040 nonbonded pdb=" OG1 THR A 44 " pdb=" O3 LBN A 512 " model vdw 2.261 3.040 ... (remaining 58874 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 408 or resid 502 or resid 505)) selection = (chain 'B' and (resid 14 through 408 or resid 502 or (resid 505 and (name C1 or \ name C12 or name C15 or name C18 or name C2 or name C25 or name C26 or name C27 \ or name C28 or name C29 or name C3 or name C30 or name C34 or name C35 or name C \ 36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C6 or nam \ e C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O5 or name O \ 6 or name O7 or name O8 or name P1 )))) } 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: 0.600 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.420 Find NCS groups from input model: 0.300 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 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 0.054 7288 Z= 0.194 Angle : 0.557 6.721 9796 Z= 0.269 Chirality : 0.042 0.166 1004 Planarity : 0.004 0.041 1128 Dihedral : 25.026 169.578 2894 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.44 % Allowed : 21.18 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.77 (0.29), residues: 746 helix: -0.38 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -0.42 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 321 HIS 0.003 0.001 HIS A 309 PHE 0.013 0.001 PHE A 79 TYR 0.007 0.001 TYR B 139 ARG 0.003 0.000 ARG B 286 Details of bonding type rmsd hydrogen bonds : bond 0.21439 ( 393) hydrogen bonds : angle 8.01893 ( 1167) covalent geometry : bond 0.00488 ( 7288) covalent geometry : angle 0.55716 ( 9796) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.674 Fit side-chains REVERT: B 67 ASP cc_start: 0.7266 (t70) cc_final: 0.6826 (m-30) outliers start: 3 outliers final: 1 residues processed: 92 average time/residue: 0.2065 time to fit residues: 25.1947 Evaluate side-chains 91 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 309 HIS B 125 GLN B 309 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.172764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.132031 restraints weight = 6731.365| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.75 r_work: 0.3330 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7288 Z= 0.142 Angle : 0.550 7.615 9796 Z= 0.271 Chirality : 0.041 0.155 1004 Planarity : 0.004 0.038 1128 Dihedral : 25.940 167.310 1484 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.38 % Allowed : 18.38 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.47 (0.30), residues: 746 helix: 0.72 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.57 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 321 HIS 0.003 0.001 HIS B 309 PHE 0.011 0.001 PHE A 79 TYR 0.011 0.001 TYR B 291 ARG 0.002 0.000 ARG B 323 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 393) hydrogen bonds : angle 4.81761 ( 1167) covalent geometry : bond 0.00342 ( 7288) covalent geometry : angle 0.55022 ( 9796) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.708 Fit side-chains REVERT: A 22 ARG cc_start: 0.7998 (mtp-110) cc_final: 0.7729 (mtp85) REVERT: A 71 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6037 (mmp-170) REVERT: A 387 TRP cc_start: 0.5017 (OUTLIER) cc_final: 0.3839 (t60) REVERT: B 170 PHE cc_start: 0.6382 (OUTLIER) cc_final: 0.4653 (m-80) REVERT: B 244 THR cc_start: 0.7726 (p) cc_final: 0.7523 (m) REVERT: B 387 TRP cc_start: 0.4833 (OUTLIER) cc_final: 0.3789 (t60) outliers start: 23 outliers final: 10 residues processed: 102 average time/residue: 0.2231 time to fit residues: 29.5542 Evaluate side-chains 105 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS B 309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.180643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.141333 restraints weight = 6975.465| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.75 r_work: 0.3458 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7288 Z= 0.108 Angle : 0.504 9.373 9796 Z= 0.243 Chirality : 0.039 0.148 1004 Planarity : 0.003 0.034 1128 Dihedral : 23.196 166.395 1482 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.38 % Allowed : 20.74 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.17 (0.31), residues: 746 helix: 1.25 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.40 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 321 HIS 0.003 0.000 HIS B 309 PHE 0.010 0.001 PHE B 79 TYR 0.011 0.001 TYR B 291 ARG 0.002 0.000 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 393) hydrogen bonds : angle 4.32971 ( 1167) covalent geometry : bond 0.00252 ( 7288) covalent geometry : angle 0.50408 ( 9796) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.665 Fit side-chains REVERT: A 22 ARG cc_start: 0.7942 (mtp-110) cc_final: 0.7690 (mtp85) REVERT: A 387 TRP cc_start: 0.5060 (OUTLIER) cc_final: 0.3741 (t60) REVERT: A 393 PHE cc_start: 0.7058 (m-10) cc_final: 0.6618 (m-10) REVERT: B 19 MET cc_start: 0.7709 (ttt) cc_final: 0.7505 (ttt) REVERT: B 71 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6001 (mmp-170) REVERT: B 170 PHE cc_start: 0.6440 (OUTLIER) cc_final: 0.6115 (t80) REVERT: B 387 TRP cc_start: 0.4984 (OUTLIER) cc_final: 0.3869 (t60) REVERT: B 393 PHE cc_start: 0.7043 (m-10) cc_final: 0.6593 (m-10) outliers start: 23 outliers final: 13 residues processed: 106 average time/residue: 0.2238 time to fit residues: 30.5912 Evaluate side-chains 104 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 309 HIS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 402 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.159754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.119422 restraints weight = 7159.042| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.70 r_work: 0.3109 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7288 Z= 0.150 Angle : 0.538 8.258 9796 Z= 0.256 Chirality : 0.041 0.224 1004 Planarity : 0.003 0.036 1128 Dihedral : 22.967 166.356 1482 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.12 % Allowed : 20.88 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.17 (0.31), residues: 746 helix: 1.25 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.42 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 321 HIS 0.008 0.001 HIS B 309 PHE 0.011 0.001 PHE A 79 TYR 0.007 0.001 TYR B 186 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 393) hydrogen bonds : angle 4.30572 ( 1167) covalent geometry : bond 0.00369 ( 7288) covalent geometry : angle 0.53811 ( 9796) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.766 Fit side-chains REVERT: A 71 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.5536 (mmp-170) REVERT: A 387 TRP cc_start: 0.5092 (OUTLIER) cc_final: 0.3741 (t60) REVERT: A 393 PHE cc_start: 0.6772 (m-10) cc_final: 0.6344 (m-10) REVERT: B 71 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.5443 (mmp-170) REVERT: B 170 PHE cc_start: 0.6047 (OUTLIER) cc_final: 0.5735 (t80) REVERT: B 387 TRP cc_start: 0.4944 (OUTLIER) cc_final: 0.3718 (t60) REVERT: B 393 PHE cc_start: 0.6664 (m-10) cc_final: 0.6259 (m-10) outliers start: 28 outliers final: 16 residues processed: 106 average time/residue: 0.2264 time to fit residues: 31.2339 Evaluate side-chains 108 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 402 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.157930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.117498 restraints weight = 7024.406| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.70 r_work: 0.3122 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7288 Z= 0.182 Angle : 0.565 8.150 9796 Z= 0.270 Chirality : 0.042 0.160 1004 Planarity : 0.003 0.039 1128 Dihedral : 22.808 167.323 1482 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.41 % Allowed : 20.59 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 746 helix: 1.19 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.58 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 321 HIS 0.003 0.001 HIS A 309 PHE 0.012 0.001 PHE B 79 TYR 0.007 0.001 TYR B 139 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 393) hydrogen bonds : angle 4.37863 ( 1167) covalent geometry : bond 0.00453 ( 7288) covalent geometry : angle 0.56460 ( 9796) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.633 Fit side-chains REVERT: A 71 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.5816 (mmp-170) REVERT: A 298 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7588 (mt0) REVERT: A 387 TRP cc_start: 0.5067 (OUTLIER) cc_final: 0.3667 (t60) REVERT: A 393 PHE cc_start: 0.6815 (m-10) cc_final: 0.6387 (m-10) REVERT: B 71 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.5747 (mmp-170) REVERT: B 170 PHE cc_start: 0.6177 (OUTLIER) cc_final: 0.5892 (t80) REVERT: B 238 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6714 (mtm-85) REVERT: B 387 TRP cc_start: 0.5202 (OUTLIER) cc_final: 0.3889 (t60) REVERT: B 393 PHE cc_start: 0.6736 (m-10) cc_final: 0.6329 (m-10) outliers start: 30 outliers final: 16 residues processed: 104 average time/residue: 0.2256 time to fit residues: 30.1266 Evaluate side-chains 109 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 402 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN B 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.160907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.119968 restraints weight = 7049.506| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.73 r_work: 0.3111 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7288 Z= 0.125 Angle : 0.523 9.472 9796 Z= 0.249 Chirality : 0.040 0.212 1004 Planarity : 0.003 0.036 1128 Dihedral : 21.773 168.240 1482 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.88 % Favored : 97.99 % Rotamer: Outliers : 3.82 % Allowed : 21.62 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.28 (0.30), residues: 746 helix: 1.37 (0.23), residues: 548 sheet: None (None), residues: 0 loop : -0.51 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 321 HIS 0.002 0.000 HIS A 309 PHE 0.010 0.001 PHE B 79 TYR 0.007 0.001 TYR B 186 ARG 0.002 0.000 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 393) hydrogen bonds : angle 4.19913 ( 1167) covalent geometry : bond 0.00302 ( 7288) covalent geometry : angle 0.52250 ( 9796) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.652 Fit side-chains REVERT: A 71 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.5480 (mmp-170) REVERT: A 170 PHE cc_start: 0.5830 (OUTLIER) cc_final: 0.4321 (m-80) REVERT: A 298 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7552 (mt0) REVERT: A 387 TRP cc_start: 0.4874 (OUTLIER) cc_final: 0.3568 (t60) REVERT: A 393 PHE cc_start: 0.6546 (m-10) cc_final: 0.6118 (m-10) REVERT: B 71 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.5406 (mmp-170) REVERT: B 170 PHE cc_start: 0.5867 (OUTLIER) cc_final: 0.4352 (m-80) REVERT: B 387 TRP cc_start: 0.4968 (OUTLIER) cc_final: 0.3765 (t60) REVERT: B 393 PHE cc_start: 0.6514 (m-10) cc_final: 0.6105 (m-10) outliers start: 26 outliers final: 17 residues processed: 106 average time/residue: 0.2332 time to fit residues: 31.5160 Evaluate side-chains 114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 402 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.158193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117867 restraints weight = 6967.592| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.68 r_work: 0.3086 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7288 Z= 0.170 Angle : 0.549 8.382 9796 Z= 0.263 Chirality : 0.042 0.158 1004 Planarity : 0.003 0.038 1128 Dihedral : 21.683 168.357 1482 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.26 % Allowed : 21.18 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.17 (0.30), residues: 746 helix: 1.30 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.57 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 321 HIS 0.003 0.001 HIS B 309 PHE 0.011 0.001 PHE B 79 TYR 0.006 0.001 TYR B 186 ARG 0.002 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 393) hydrogen bonds : angle 4.26576 ( 1167) covalent geometry : bond 0.00423 ( 7288) covalent geometry : angle 0.54930 ( 9796) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.640 Fit side-chains REVERT: A 22 ARG cc_start: 0.7816 (mtp-110) cc_final: 0.7588 (mtp85) REVERT: A 71 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.5495 (mmp-170) REVERT: A 88 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8589 (m-10) REVERT: A 170 PHE cc_start: 0.5883 (OUTLIER) cc_final: 0.4472 (m-10) REVERT: A 298 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7536 (mt0) REVERT: A 387 TRP cc_start: 0.4897 (OUTLIER) cc_final: 0.3471 (t60) REVERT: A 393 PHE cc_start: 0.6590 (m-10) cc_final: 0.6168 (m-10) REVERT: B 71 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.5435 (mmp-170) REVERT: B 170 PHE cc_start: 0.5878 (OUTLIER) cc_final: 0.4458 (m-10) REVERT: B 387 TRP cc_start: 0.5102 (OUTLIER) cc_final: 0.3793 (t60) REVERT: B 393 PHE cc_start: 0.6535 (m-10) cc_final: 0.6127 (m-10) outliers start: 29 outliers final: 19 residues processed: 103 average time/residue: 0.2281 time to fit residues: 30.3796 Evaluate side-chains 111 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 402 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 7 optimal weight: 0.0870 chunk 25 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.160532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120561 restraints weight = 7031.336| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.68 r_work: 0.3129 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7288 Z= 0.108 Angle : 0.487 8.032 9796 Z= 0.235 Chirality : 0.039 0.143 1004 Planarity : 0.003 0.034 1128 Dihedral : 21.128 168.658 1482 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.82 % Allowed : 21.62 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.44 (0.30), residues: 746 helix: 1.54 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.61 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 321 HIS 0.002 0.000 HIS B 309 PHE 0.011 0.001 PHE B 79 TYR 0.008 0.001 TYR B 291 ARG 0.001 0.000 ARG B 286 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 393) hydrogen bonds : angle 4.08926 ( 1167) covalent geometry : bond 0.00256 ( 7288) covalent geometry : angle 0.48686 ( 9796) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.675 Fit side-chains REVERT: A 71 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.5669 (mmp-170) REVERT: A 88 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8207 (m-10) REVERT: A 170 PHE cc_start: 0.5787 (OUTLIER) cc_final: 0.4388 (m-10) REVERT: A 298 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: A 387 TRP cc_start: 0.4850 (OUTLIER) cc_final: 0.3545 (t60) REVERT: A 393 PHE cc_start: 0.6485 (m-10) cc_final: 0.6072 (m-10) REVERT: B 71 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.5461 (mmp-170) REVERT: B 88 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8215 (m-10) REVERT: B 170 PHE cc_start: 0.5873 (OUTLIER) cc_final: 0.4448 (m-10) REVERT: B 387 TRP cc_start: 0.4912 (OUTLIER) cc_final: 0.3722 (t60) REVERT: B 393 PHE cc_start: 0.6616 (m-10) cc_final: 0.6207 (m-10) outliers start: 26 outliers final: 15 residues processed: 103 average time/residue: 0.2685 time to fit residues: 35.0039 Evaluate side-chains 108 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 402 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 48 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.159681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118312 restraints weight = 7074.517| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.79 r_work: 0.3297 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7288 Z= 0.124 Angle : 0.505 8.254 9796 Z= 0.242 Chirality : 0.040 0.150 1004 Planarity : 0.003 0.035 1128 Dihedral : 21.103 167.628 1482 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.53 % Allowed : 22.06 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.48 (0.30), residues: 746 helix: 1.57 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.61 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 321 HIS 0.003 0.000 HIS B 309 PHE 0.010 0.001 PHE A 79 TYR 0.007 0.001 TYR B 186 ARG 0.001 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 393) hydrogen bonds : angle 4.09710 ( 1167) covalent geometry : bond 0.00301 ( 7288) covalent geometry : angle 0.50536 ( 9796) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.751 Fit side-chains REVERT: A 22 ARG cc_start: 0.7818 (mtp-110) cc_final: 0.7555 (mtp85) REVERT: A 71 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.5829 (mmp-170) REVERT: A 88 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8242 (m-10) REVERT: A 170 PHE cc_start: 0.5979 (OUTLIER) cc_final: 0.4580 (m-10) REVERT: A 298 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7649 (mt0) REVERT: A 387 TRP cc_start: 0.4994 (OUTLIER) cc_final: 0.3680 (t60) REVERT: A 393 PHE cc_start: 0.6637 (m-10) cc_final: 0.6225 (m-10) REVERT: A 402 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.6172 (ppp) REVERT: B 71 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.5781 (mmp-170) REVERT: B 88 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8153 (m-10) REVERT: B 170 PHE cc_start: 0.6118 (OUTLIER) cc_final: 0.4700 (m-10) REVERT: B 387 TRP cc_start: 0.5090 (OUTLIER) cc_final: 0.3855 (t60) REVERT: B 393 PHE cc_start: 0.6845 (m-10) cc_final: 0.6426 (m-10) REVERT: B 402 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.6121 (ppp) outliers start: 24 outliers final: 12 residues processed: 102 average time/residue: 0.2574 time to fit residues: 33.3504 Evaluate side-chains 108 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 402 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 41 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.160742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.119263 restraints weight = 7155.955| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.79 r_work: 0.3373 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7288 Z= 0.114 Angle : 0.490 8.179 9796 Z= 0.236 Chirality : 0.040 0.147 1004 Planarity : 0.003 0.034 1128 Dihedral : 20.931 176.699 1482 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.38 % Allowed : 22.21 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.57 (0.30), residues: 746 helix: 1.65 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.61 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 321 HIS 0.002 0.000 HIS A 309 PHE 0.010 0.001 PHE A 79 TYR 0.007 0.001 TYR B 186 ARG 0.001 0.000 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 393) hydrogen bonds : angle 4.03833 ( 1167) covalent geometry : bond 0.00275 ( 7288) covalent geometry : angle 0.49030 ( 9796) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.725 Fit side-chains REVERT: A 22 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.7536 (mtp85) REVERT: A 71 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.5818 (mmp-170) REVERT: A 88 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8189 (m-10) REVERT: A 170 PHE cc_start: 0.6109 (OUTLIER) cc_final: 0.4716 (m-10) REVERT: A 298 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7661 (mt0) REVERT: A 387 TRP cc_start: 0.5132 (OUTLIER) cc_final: 0.3779 (t60) REVERT: A 393 PHE cc_start: 0.6676 (m-10) cc_final: 0.6260 (m-10) REVERT: A 402 MET cc_start: 0.6432 (OUTLIER) cc_final: 0.6210 (ppp) REVERT: B 71 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.5788 (mmp-170) REVERT: B 88 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8199 (m-10) REVERT: B 170 PHE cc_start: 0.6141 (OUTLIER) cc_final: 0.4761 (m-10) REVERT: B 387 TRP cc_start: 0.5004 (OUTLIER) cc_final: 0.3810 (t60) REVERT: B 393 PHE cc_start: 0.6846 (m-10) cc_final: 0.6426 (m-10) REVERT: B 402 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.6173 (ppp) outliers start: 23 outliers final: 12 residues processed: 99 average time/residue: 0.2687 time to fit residues: 33.4515 Evaluate side-chains 106 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 402 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.157804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.116990 restraints weight = 7105.689| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.76 r_work: 0.3275 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7288 Z= 0.195 Angle : 0.567 8.530 9796 Z= 0.271 Chirality : 0.043 0.157 1004 Planarity : 0.003 0.039 1128 Dihedral : 21.665 179.416 1482 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.82 % Allowed : 21.62 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.28 (0.30), residues: 746 helix: 1.40 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.61 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 321 HIS 0.004 0.001 HIS A 309 PHE 0.013 0.001 PHE B 79 TYR 0.006 0.001 TYR B 186 ARG 0.003 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 393) hydrogen bonds : angle 4.24704 ( 1167) covalent geometry : bond 0.00486 ( 7288) covalent geometry : angle 0.56728 ( 9796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3988.56 seconds wall clock time: 68 minutes 52.91 seconds (4132.91 seconds total)