Starting phenix.real_space_refine on Sat May 10 23:14:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kqi_62505/05_2025/9kqi_62505.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kqi_62505/05_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_62505/05_2025/9kqi_62505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kqi_62505/05_2025/9kqi_62505.map" model { file = "/net/cci-nas-00/data/ceres_data/9kqi_62505/05_2025/9kqi_62505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kqi_62505/05_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-5687/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: 4.70, per 1000 atoms: 0.66 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: 2.00 Conformation dependent library (CDL) restraints added in 659.8 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: 0.53 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: 1.73 Time building geometry restraints manager: 2.31 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.830 Find NCS groups from input model: 0.280 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.130 ------------------------------------------------------------------------------- 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 : 0.631 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: 0.2019 time to fit residues: 24.5508 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 : 0.614 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.132014 restraints weight = 6731.365| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.74 r_work: 0.3331 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 : 0.703 Fit side-chains REVERT: A 22 ARG cc_start: 0.7994 (mtp-110) cc_final: 0.7725 (mtp85) REVERT: A 71 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6032 (mmp-170) REVERT: A 387 TRP cc_start: 0.5012 (OUTLIER) cc_final: 0.3835 (t60) REVERT: B 170 PHE cc_start: 0.6376 (OUTLIER) cc_final: 0.4648 (m-80) REVERT: B 244 THR cc_start: 0.7725 (p) cc_final: 0.7522 (m) REVERT: B 387 TRP cc_start: 0.4827 (OUTLIER) cc_final: 0.3783 (t60) outliers start: 23 outliers final: 10 residues processed: 102 average time/residue: 0.2238 time to fit residues: 29.6800 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 : 0.698 ------------------------------------------------------------------------------- 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: 0.8980 chunk 19 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.174159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.134413 restraints weight = 7011.870| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.74 r_work: 0.3433 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7288 Z= 0.118 Angle : 0.510 9.235 9796 Z= 0.247 Chirality : 0.039 0.150 1004 Planarity : 0.003 0.035 1128 Dihedral : 23.531 166.497 1482 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.24 % Allowed : 21.18 % Favored : 75.59 % 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: 1.07 (0.31), residues: 746 helix: 1.20 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.49 (0.42), residues: 200 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 A 79 TYR 0.010 0.001 TYR B 291 ARG 0.001 0.000 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 393) hydrogen bonds : angle 4.40551 ( 1167) covalent geometry : bond 0.00282 ( 7288) covalent geometry : angle 0.51007 ( 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 114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.726 Fit side-chains REVERT: A 22 ARG cc_start: 0.7971 (mtp-110) cc_final: 0.7710 (mtp85) REVERT: A 387 TRP cc_start: 0.5053 (OUTLIER) cc_final: 0.3711 (t60) REVERT: B 19 MET cc_start: 0.7740 (ttt) cc_final: 0.7540 (ttt) REVERT: B 71 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6057 (mmp-170) REVERT: B 170 PHE cc_start: 0.6522 (OUTLIER) cc_final: 0.6232 (t80) REVERT: B 387 TRP cc_start: 0.4982 (OUTLIER) cc_final: 0.3809 (t60) REVERT: B 393 PHE cc_start: 0.7041 (m-10) cc_final: 0.6578 (m-10) outliers start: 22 outliers final: 13 residues processed: 104 average time/residue: 0.2337 time to fit residues: 31.3159 Evaluate side-chains 105 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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: 0.1980 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.162477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.122328 restraints weight = 7121.031| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.70 r_work: 0.3146 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7288 Z= 0.102 Angle : 0.498 7.747 9796 Z= 0.239 Chirality : 0.039 0.209 1004 Planarity : 0.003 0.032 1128 Dihedral : 22.718 166.319 1482 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.68 % Allowed : 21.18 % Favored : 75.15 % 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: 1.32 (0.31), residues: 746 helix: 1.37 (0.23), residues: 550 sheet: None (None), residues: 0 loop : -0.39 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 321 HIS 0.011 0.001 HIS B 309 PHE 0.010 0.001 PHE B 79 TYR 0.008 0.001 TYR B 186 ARG 0.001 0.000 ARG B 238 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 393) hydrogen bonds : angle 4.20684 ( 1167) covalent geometry : bond 0.00236 ( 7288) covalent geometry : angle 0.49807 ( 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 117 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.713 Fit side-chains REVERT: A 22 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.7513 (mtp85) REVERT: A 71 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.5612 (mmp-170) REVERT: A 387 TRP cc_start: 0.4931 (OUTLIER) cc_final: 0.3636 (t60) REVERT: A 393 PHE cc_start: 0.6778 (m-10) cc_final: 0.6323 (m-10) REVERT: B 71 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.5504 (mmp-170) REVERT: B 170 PHE cc_start: 0.6103 (OUTLIER) cc_final: 0.5802 (t80) REVERT: B 387 TRP cc_start: 0.4848 (OUTLIER) cc_final: 0.3759 (t60) REVERT: B 393 PHE cc_start: 0.6641 (m-10) cc_final: 0.6200 (m-10) outliers start: 25 outliers final: 14 residues processed: 106 average time/residue: 0.2547 time to fit residues: 33.9897 Evaluate side-chains 107 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 23 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.158667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118351 restraints weight = 6987.598| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.68 r_work: 0.3095 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7288 Z= 0.162 Angle : 0.548 8.153 9796 Z= 0.261 Chirality : 0.041 0.158 1004 Planarity : 0.003 0.037 1128 Dihedral : 22.830 166.634 1482 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.41 % Allowed : 20.29 % Favored : 75.29 % 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: 1.25 (0.31), residues: 746 helix: 1.32 (0.23), residues: 548 sheet: None (None), residues: 0 loop : -0.42 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 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 139 ARG 0.002 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 393) hydrogen bonds : angle 4.28416 ( 1167) covalent geometry : bond 0.00401 ( 7288) covalent geometry : angle 0.54776 ( 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 121 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.662 Fit side-chains REVERT: A 71 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.5497 (mmp-170) REVERT: A 298 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7567 (mt0) REVERT: A 387 TRP cc_start: 0.5051 (OUTLIER) cc_final: 0.3636 (t60) REVERT: A 393 PHE cc_start: 0.6647 (m-10) cc_final: 0.6218 (m-10) REVERT: B 71 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.5438 (mmp-170) REVERT: B 170 PHE cc_start: 0.6012 (OUTLIER) cc_final: 0.5688 (t80) REVERT: B 238 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6543 (mtm-85) REVERT: B 387 TRP cc_start: 0.4987 (OUTLIER) cc_final: 0.3739 (t60) REVERT: B 393 PHE cc_start: 0.6631 (m-10) cc_final: 0.6218 (m-10) outliers start: 30 outliers final: 15 residues processed: 108 average time/residue: 0.2242 time to fit residues: 31.3665 Evaluate side-chains 109 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 70 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 25 optimal weight: 0.0770 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.162641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122951 restraints weight = 7069.204| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.67 r_work: 0.3254 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7288 Z= 0.100 Angle : 0.494 9.589 9796 Z= 0.236 Chirality : 0.039 0.180 1004 Planarity : 0.003 0.034 1128 Dihedral : 22.001 167.014 1482 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.61 % Favored : 98.26 % Rotamer: Outliers : 3.53 % Allowed : 21.03 % Favored : 75.44 % 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: 1.53 (0.30), residues: 746 helix: 1.56 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.45 (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 A 21 TYR 0.008 0.001 TYR B 291 ARG 0.001 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 393) hydrogen bonds : angle 4.06311 ( 1167) covalent geometry : bond 0.00230 ( 7288) covalent geometry : angle 0.49436 ( 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 118 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.672 Fit side-chains REVERT: A 71 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.5648 (mmp-170) REVERT: A 387 TRP cc_start: 0.4881 (OUTLIER) cc_final: 0.3674 (t60) REVERT: A 393 PHE cc_start: 0.6660 (m-10) cc_final: 0.6225 (m-10) REVERT: B 71 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.5620 (mmp-170) REVERT: B 170 PHE cc_start: 0.5988 (OUTLIER) cc_final: 0.4461 (m-80) REVERT: B 238 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6555 (mtm-85) REVERT: B 387 TRP cc_start: 0.4836 (OUTLIER) cc_final: 0.3743 (t60) REVERT: B 393 PHE cc_start: 0.6613 (m-10) cc_final: 0.6198 (m-10) outliers start: 24 outliers final: 15 residues processed: 110 average time/residue: 0.2855 time to fit residues: 39.1964 Evaluate side-chains 112 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 384 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 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: 0.2980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.162337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.122685 restraints weight = 6928.601| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.66 r_work: 0.3143 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7288 Z= 0.108 Angle : 0.489 7.194 9796 Z= 0.235 Chirality : 0.039 0.146 1004 Planarity : 0.003 0.033 1128 Dihedral : 21.197 166.259 1482 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.68 % Allowed : 20.88 % Favored : 75.44 % 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: 1.64 (0.30), residues: 746 helix: 1.64 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.42 (0.40), residues: 196 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 0.011 0.001 PHE A 88 TYR 0.006 0.001 TYR B 186 ARG 0.001 0.000 ARG B 60 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 393) hydrogen bonds : angle 4.01743 ( 1167) covalent geometry : bond 0.00255 ( 7288) covalent geometry : angle 0.48902 ( 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 118 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.791 Fit side-chains REVERT: A 71 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.5454 (mmp-170) REVERT: A 170 PHE cc_start: 0.5785 (OUTLIER) cc_final: 0.4384 (m-10) REVERT: A 298 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: A 387 TRP cc_start: 0.4923 (OUTLIER) cc_final: 0.3656 (t60) REVERT: A 393 PHE cc_start: 0.6508 (m-10) cc_final: 0.6087 (m-10) REVERT: B 71 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.5444 (mmp-170) REVERT: B 170 PHE cc_start: 0.5802 (OUTLIER) cc_final: 0.4427 (m-10) REVERT: B 238 ARG cc_start: 0.6624 (OUTLIER) cc_final: 0.6394 (mtm-85) REVERT: B 387 TRP cc_start: 0.4838 (OUTLIER) cc_final: 0.3720 (t60) REVERT: B 393 PHE cc_start: 0.6593 (m-10) cc_final: 0.6174 (m-10) outliers start: 25 outliers final: 15 residues processed: 110 average time/residue: 0.2552 time to fit residues: 35.2378 Evaluate side-chains 114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 309 HIS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 VAL 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 182 LEU Chi-restraints excluded: chain B residue 192 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 65 optimal weight: 0.0470 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.162799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.121860 restraints weight = 7033.196| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.76 r_work: 0.3247 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7288 Z= 0.102 Angle : 0.477 7.001 9796 Z= 0.230 Chirality : 0.039 0.141 1004 Planarity : 0.003 0.032 1128 Dihedral : 20.551 165.684 1482 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.38 % Allowed : 21.03 % Favored : 75.59 % 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: 1.72 (0.30), residues: 746 helix: 1.71 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 196 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 0.010 0.001 PHE A 79 TYR 0.007 0.001 TYR B 186 ARG 0.001 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 393) hydrogen bonds : angle 3.95573 ( 1167) covalent geometry : bond 0.00239 ( 7288) covalent geometry : angle 0.47710 ( 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 111 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.760 Fit side-chains REVERT: A 22 ARG cc_start: 0.7794 (mtp-110) cc_final: 0.7560 (mtp85) REVERT: A 71 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.5776 (mmp-170) REVERT: A 170 PHE cc_start: 0.5958 (OUTLIER) cc_final: 0.4545 (m-10) REVERT: A 298 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7638 (mt0) REVERT: A 387 TRP cc_start: 0.4936 (OUTLIER) cc_final: 0.3707 (t60) REVERT: A 393 PHE cc_start: 0.6639 (m-10) cc_final: 0.6222 (m-10) REVERT: B 71 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.5798 (mmp-170) REVERT: B 170 PHE cc_start: 0.6062 (OUTLIER) cc_final: 0.4668 (m-10) REVERT: B 238 ARG cc_start: 0.6746 (OUTLIER) cc_final: 0.6527 (mtm-85) REVERT: B 387 TRP cc_start: 0.4898 (OUTLIER) cc_final: 0.3780 (t60) REVERT: B 393 PHE cc_start: 0.6794 (m-10) cc_final: 0.6374 (m-10) outliers start: 23 outliers final: 13 residues processed: 105 average time/residue: 0.2963 time to fit residues: 38.9989 Evaluate side-chains 107 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 384 VAL 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 182 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 384 VAL 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: 1.9990 chunk 17 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.160241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120176 restraints weight = 7095.415| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.68 r_work: 0.3237 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7288 Z= 0.124 Angle : 0.497 6.916 9796 Z= 0.239 Chirality : 0.040 0.149 1004 Planarity : 0.003 0.033 1128 Dihedral : 20.691 165.004 1482 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.09 % Allowed : 21.62 % Favored : 75.29 % 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: 1.69 (0.30), residues: 746 helix: 1.68 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.38 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 321 HIS 0.003 0.000 HIS A 309 PHE 0.013 0.001 PHE B 88 TYR 0.007 0.001 TYR B 186 ARG 0.001 0.000 ARG B 60 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 393) hydrogen bonds : angle 4.00376 ( 1167) covalent geometry : bond 0.00302 ( 7288) covalent geometry : angle 0.49739 ( 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 108 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.700 Fit side-chains REVERT: A 71 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.5730 (mmp-170) REVERT: A 170 PHE cc_start: 0.6023 (OUTLIER) cc_final: 0.4626 (m-10) REVERT: A 298 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: A 387 TRP cc_start: 0.5031 (OUTLIER) cc_final: 0.3744 (t60) REVERT: A 393 PHE cc_start: 0.6628 (m-10) cc_final: 0.6223 (m-10) REVERT: A 402 MET cc_start: 0.6416 (OUTLIER) cc_final: 0.6201 (ppp) REVERT: B 71 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.5694 (mmp-170) REVERT: B 170 PHE cc_start: 0.6047 (OUTLIER) cc_final: 0.4657 (m-10) REVERT: B 387 TRP cc_start: 0.4926 (OUTLIER) cc_final: 0.3764 (t60) REVERT: B 393 PHE cc_start: 0.6794 (m-10) cc_final: 0.6392 (m-10) outliers start: 21 outliers final: 12 residues processed: 101 average time/residue: 0.2710 time to fit residues: 34.5349 Evaluate side-chains 107 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 384 VAL 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 182 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 384 VAL 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: 0.7980 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.159646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.119419 restraints weight = 7170.435| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.71 r_work: 0.3327 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1903 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= 0.131 Angle : 0.502 6.829 9796 Z= 0.242 Chirality : 0.040 0.149 1004 Planarity : 0.003 0.034 1128 Dihedral : 20.818 165.243 1482 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.94 % Allowed : 21.47 % Favored : 75.59 % 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: 1.62 (0.30), residues: 746 helix: 1.65 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.47 (0.40), 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 0.011 0.001 PHE B 88 TYR 0.006 0.001 TYR B 186 ARG 0.001 0.000 ARG B 60 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 393) hydrogen bonds : angle 4.03880 ( 1167) covalent geometry : bond 0.00323 ( 7288) covalent geometry : angle 0.50219 ( 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 106 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.728 Fit side-chains REVERT: A 71 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.5851 (mmp-170) REVERT: A 170 PHE cc_start: 0.6106 (OUTLIER) cc_final: 0.4707 (m-10) REVERT: A 298 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7667 (mt0) REVERT: A 387 TRP cc_start: 0.5145 (OUTLIER) cc_final: 0.3781 (t60) REVERT: A 393 PHE cc_start: 0.6727 (m-10) cc_final: 0.6315 (m-10) REVERT: A 402 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.6190 (ppp) REVERT: B 71 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.5854 (mmp-170) REVERT: B 170 PHE cc_start: 0.6119 (OUTLIER) cc_final: 0.4741 (m-10) REVERT: B 387 TRP cc_start: 0.5030 (OUTLIER) cc_final: 0.3805 (t60) REVERT: B 393 PHE cc_start: 0.6908 (m-10) cc_final: 0.6504 (m-10) REVERT: B 402 MET cc_start: 0.6342 (OUTLIER) cc_final: 0.6076 (ppp) outliers start: 20 outliers final: 11 residues processed: 99 average time/residue: 0.2569 time to fit residues: 32.3241 Evaluate side-chains 106 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 384 VAL 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 182 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 384 VAL 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: 0.7980 chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.171840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.130228 restraints weight = 6877.712| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.84 r_work: 0.3278 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7288 Z= 0.119 Angle : 0.488 6.818 9796 Z= 0.236 Chirality : 0.040 0.145 1004 Planarity : 0.003 0.033 1128 Dihedral : 20.744 172.039 1482 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.94 % Allowed : 21.47 % Favored : 75.59 % 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: 1.67 (0.30), residues: 746 helix: 1.67 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.42 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 321 HIS 0.003 0.000 HIS A 309 PHE 0.012 0.001 PHE B 88 TYR 0.007 0.001 TYR B 186 ARG 0.001 0.000 ARG B 286 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 393) hydrogen bonds : angle 3.98834 ( 1167) covalent geometry : bond 0.00290 ( 7288) covalent geometry : angle 0.48776 ( 9796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4015.33 seconds wall clock time: 70 minutes 35.81 seconds (4235.81 seconds total)