Starting phenix.real_space_refine on Wed Sep 17 08:16:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kqi_62505/09_2025/9kqi_62505.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kqi_62505/09_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_62505/09_2025/9kqi_62505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kqi_62505/09_2025/9kqi_62505.map" model { file = "/net/cci-nas-00/data/ceres_data/9kqi_62505/09_2025/9kqi_62505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kqi_62505/09_2025/9kqi_62505.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.04, per 1000 atoms: 0.29 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: 0.78 Conformation dependent library (CDL) restraints added in 372.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.19 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: 1.13 Time building geometry restraints manager: 0.90 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: 0.01 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: 1.260 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.560 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.580 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG B 286 TYR 0.007 0.001 TYR B 139 PHE 0.013 0.001 PHE A 79 TRP 0.012 0.001 TRP A 321 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 7288) covalent geometry : angle 0.55716 ( 9796) hydrogen bonds : bond 0.21439 ( 393) hydrogen bonds : angle 8.01893 ( 1167) *********************** 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 : 0.241 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: 0.0964 time to fit residues: 11.8058 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 : 0.248 ------------------------------------------------------------------------------- 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 49 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.174879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.134664 restraints weight = 6757.674| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.75 r_work: 0.3369 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1054 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= 0.140 Angle : 0.550 7.600 9796 Z= 0.271 Chirality : 0.041 0.154 1004 Planarity : 0.004 0.038 1128 Dihedral : 26.011 167.286 1484 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.53 % Allowed : 18.68 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.30), residues: 746 helix: 0.71 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.57 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 184 TYR 0.012 0.001 TYR B 291 PHE 0.011 0.001 PHE A 79 TRP 0.014 0.001 TRP A 321 HIS 0.003 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7288) covalent geometry : angle 0.54990 ( 9796) hydrogen bonds : bond 0.04653 ( 393) hydrogen bonds : angle 4.82418 ( 1167) *********************** 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 113 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.244 Fit side-chains REVERT: A 22 ARG cc_start: 0.8007 (mtp-110) cc_final: 0.7743 (mtp85) REVERT: A 71 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6034 (mmp-170) REVERT: A 387 TRP cc_start: 0.5002 (OUTLIER) cc_final: 0.3813 (t60) REVERT: B 170 PHE cc_start: 0.6394 (OUTLIER) cc_final: 0.4663 (m-80) REVERT: B 244 THR cc_start: 0.7769 (p) cc_final: 0.7550 (m) REVERT: B 387 TRP cc_start: 0.4769 (OUTLIER) cc_final: 0.3709 (t60) REVERT: B 393 PHE cc_start: 0.7091 (m-10) cc_final: 0.6627 (m-10) outliers start: 24 outliers final: 10 residues processed: 103 average time/residue: 0.1044 time to fit residues: 13.9476 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 : 0.172 ------------------------------------------------------------------------------- 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 45 optimal weight: 2.9990 chunk 59 optimal weight: 0.0470 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 37 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 54 optimal weight: 0.0570 chunk 21 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.3974 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.183157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.144037 restraints weight = 6722.271| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.73 r_work: 0.3474 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1614 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= 0.096 Angle : 0.501 9.582 9796 Z= 0.239 Chirality : 0.038 0.149 1004 Planarity : 0.003 0.032 1128 Dihedral : 23.015 166.348 1482 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.79 % Allowed : 20.74 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.31), residues: 746 helix: 1.29 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.37 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 184 TYR 0.011 0.001 TYR B 291 PHE 0.010 0.001 PHE B 21 TRP 0.015 0.001 TRP A 321 HIS 0.002 0.000 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 7288) covalent geometry : angle 0.50134 ( 9796) hydrogen bonds : bond 0.03606 ( 393) hydrogen bonds : angle 4.26996 ( 1167) *********************** 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: 19 poor density : 95 time to evaluate : 0.239 Fit side-chains REVERT: A 22 ARG cc_start: 0.7916 (mtp-110) cc_final: 0.7667 (mtp85) REVERT: A 387 TRP cc_start: 0.5019 (OUTLIER) cc_final: 0.3761 (t60) REVERT: A 393 PHE cc_start: 0.7117 (m-10) cc_final: 0.6680 (m-10) REVERT: B 71 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6039 (mmp-170) REVERT: B 170 PHE cc_start: 0.6413 (OUTLIER) cc_final: 0.6104 (t80) REVERT: B 387 TRP cc_start: 0.4895 (OUTLIER) cc_final: 0.3851 (t60) REVERT: B 393 PHE cc_start: 0.7026 (m-10) cc_final: 0.6528 (m-10) outliers start: 19 outliers final: 8 residues processed: 106 average time/residue: 0.1184 time to fit residues: 15.8277 Evaluate side-chains 101 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 TRP 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 170 PHE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 ILE 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 66 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 42 optimal weight: 0.0570 chunk 20 optimal weight: 0.7980 chunk 54 optimal weight: 0.0970 chunk 31 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.0010 chunk 47 optimal weight: 2.9990 overall best weight: 0.3302 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.164164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.124343 restraints weight = 7033.829| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.68 r_work: 0.3173 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7288 Z= 0.092 Angle : 0.483 8.315 9796 Z= 0.231 Chirality : 0.038 0.177 1004 Planarity : 0.003 0.031 1128 Dihedral : 22.222 165.424 1482 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.82 % Allowed : 19.85 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.31), residues: 746 helix: 1.47 (0.23), residues: 550 sheet: None (None), residues: 0 loop : -0.31 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 238 TYR 0.008 0.001 TYR B 186 PHE 0.009 0.001 PHE A 79 TRP 0.016 0.001 TRP B 321 HIS 0.013 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 7288) covalent geometry : angle 0.48268 ( 9796) hydrogen bonds : bond 0.03362 ( 393) hydrogen bonds : angle 4.08940 ( 1167) *********************** 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: 26 poor density : 92 time to evaluate : 0.246 Fit side-chains REVERT: A 22 ARG cc_start: 0.7662 (mtp-110) cc_final: 0.7410 (mtp85) REVERT: A 71 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.5440 (mmp-170) REVERT: A 387 TRP cc_start: 0.4818 (OUTLIER) cc_final: 0.3643 (t60) REVERT: A 393 PHE cc_start: 0.6684 (m-10) cc_final: 0.6233 (m-10) REVERT: B 71 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.6374 (mmm-85) REVERT: B 170 PHE cc_start: 0.5961 (OUTLIER) cc_final: 0.4388 (m-80) REVERT: B 387 TRP cc_start: 0.4787 (OUTLIER) cc_final: 0.3765 (t60) REVERT: B 393 PHE cc_start: 0.6569 (m-10) cc_final: 0.6107 (m-10) outliers start: 26 outliers final: 13 residues processed: 108 average time/residue: 0.1184 time to fit residues: 16.1267 Evaluate side-chains 103 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 387 TRP 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 379 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 7 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 5 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.163079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.123208 restraints weight = 7047.740| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.67 r_work: 0.3240 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1840 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 : 0.479 7.271 9796 Z= 0.231 Chirality : 0.039 0.143 1004 Planarity : 0.003 0.030 1128 Dihedral : 21.791 164.936 1482 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.30), residues: 746 helix: 1.58 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.28 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 336 TYR 0.007 0.001 TYR B 186 PHE 0.009 0.001 PHE A 79 TRP 0.017 0.001 TRP B 321 HIS 0.002 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7288) covalent geometry : angle 0.47860 ( 9796) hydrogen bonds : bond 0.03419 ( 393) hydrogen bonds : angle 4.01878 ( 1167) *********************** 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 113 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.174 Fit side-chains REVERT: A 22 ARG cc_start: 0.7740 (mtp-110) cc_final: 0.7498 (mtp85) REVERT: A 71 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.5669 (mmp-170) REVERT: A 387 TRP cc_start: 0.4881 (OUTLIER) cc_final: 0.3702 (t60) REVERT: A 393 PHE cc_start: 0.6779 (m-10) cc_final: 0.6342 (m-10) REVERT: B 71 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.5620 (mmp-170) REVERT: B 170 PHE cc_start: 0.5990 (OUTLIER) cc_final: 0.4469 (m-80) REVERT: B 238 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.6434 (mtm-85) REVERT: B 387 TRP cc_start: 0.4837 (OUTLIER) cc_final: 0.3804 (t60) REVERT: B 393 PHE cc_start: 0.6662 (m-10) cc_final: 0.6214 (m-10) outliers start: 23 outliers final: 14 residues processed: 104 average time/residue: 0.1144 time to fit residues: 14.9268 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 : 0.227 ------------------------------------------------------------------------------- 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 182 LEU 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 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 192 ILE Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 379 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.0060 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.160963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.120809 restraints weight = 7103.015| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.69 r_work: 0.3201 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7288 Z= 0.136 Angle : 0.522 9.353 9796 Z= 0.248 Chirality : 0.041 0.174 1004 Planarity : 0.003 0.033 1128 Dihedral : 22.022 165.197 1482 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.26 % Allowed : 19.56 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.30), residues: 746 helix: 1.55 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.25 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 184 TYR 0.005 0.001 TYR B 245 PHE 0.010 0.001 PHE A 79 TRP 0.015 0.001 TRP B 321 HIS 0.003 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 7288) covalent geometry : angle 0.52238 ( 9796) hydrogen bonds : bond 0.03729 ( 393) hydrogen bonds : angle 4.08041 ( 1167) *********************** 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 119 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.218 Fit side-chains REVERT: A 71 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.5665 (mmp-170) REVERT: A 298 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7637 (mt0) REVERT: A 387 TRP cc_start: 0.4949 (OUTLIER) cc_final: 0.3681 (t60) REVERT: A 393 PHE cc_start: 0.6732 (m-10) cc_final: 0.6313 (m-10) REVERT: B 71 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.5637 (mmp-170) REVERT: B 88 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8404 (m-10) REVERT: B 170 PHE cc_start: 0.5976 (OUTLIER) cc_final: 0.4561 (m-10) REVERT: B 238 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.6440 (mtm-85) REVERT: B 387 TRP cc_start: 0.4930 (OUTLIER) cc_final: 0.3838 (t60) REVERT: B 393 PHE cc_start: 0.6700 (m-10) cc_final: 0.6252 (m-10) outliers start: 29 outliers final: 17 residues processed: 108 average time/residue: 0.1152 time to fit residues: 15.6788 Evaluate side-chains 114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 182 LEU 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 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 46 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 37 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 = 0.3757 r_free = 0.3757 target = 0.161593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121550 restraints weight = 7061.790| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.69 r_work: 0.3211 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1813 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= 0.121 Angle : 0.495 7.628 9796 Z= 0.237 Chirality : 0.040 0.144 1004 Planarity : 0.003 0.033 1128 Dihedral : 21.842 165.471 1482 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.68 % Allowed : 20.00 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.30), residues: 746 helix: 1.61 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.37 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 184 TYR 0.007 0.001 TYR B 186 PHE 0.010 0.001 PHE A 79 TRP 0.016 0.001 TRP B 321 HIS 0.003 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7288) covalent geometry : angle 0.49470 ( 9796) hydrogen bonds : bond 0.03585 ( 393) hydrogen bonds : angle 4.02631 ( 1167) *********************** 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 114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.239 Fit side-chains REVERT: A 71 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.5638 (mmp-170) REVERT: A 387 TRP cc_start: 0.4943 (OUTLIER) cc_final: 0.3769 (t60) REVERT: A 393 PHE cc_start: 0.6604 (m-10) cc_final: 0.6191 (m-10) REVERT: B 71 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.5630 (mmp-170) REVERT: B 88 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8424 (m-10) REVERT: B 170 PHE cc_start: 0.5988 (OUTLIER) cc_final: 0.4567 (m-10) REVERT: B 387 TRP cc_start: 0.4936 (OUTLIER) cc_final: 0.3831 (t60) REVERT: B 393 PHE cc_start: 0.6650 (m-10) cc_final: 0.6202 (m-10) outliers start: 25 outliers final: 16 residues processed: 105 average time/residue: 0.1204 time to fit residues: 15.8545 Evaluate side-chains 111 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 182 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 3 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 309 HIS B 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.160856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.120505 restraints weight = 7147.207| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.71 r_work: 0.3247 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1946 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= 0.118 Angle : 0.491 7.186 9796 Z= 0.237 Chirality : 0.040 0.145 1004 Planarity : 0.003 0.033 1128 Dihedral : 20.993 165.245 1482 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.12 % Allowed : 20.15 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.30), residues: 746 helix: 1.66 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.35 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 336 TYR 0.006 0.001 TYR B 186 PHE 0.010 0.001 PHE B 79 TRP 0.017 0.001 TRP B 321 HIS 0.002 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7288) covalent geometry : angle 0.49054 ( 9796) hydrogen bonds : bond 0.03544 ( 393) hydrogen bonds : angle 3.97801 ( 1167) *********************** 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 118 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.193 Fit side-chains REVERT: A 71 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.5849 (mmp-170) REVERT: A 170 PHE cc_start: 0.6125 (OUTLIER) cc_final: 0.4720 (m-10) REVERT: A 298 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7653 (mt0) REVERT: A 387 TRP cc_start: 0.5056 (OUTLIER) cc_final: 0.3764 (t60) REVERT: A 393 PHE cc_start: 0.6691 (m-10) cc_final: 0.6273 (m-10) REVERT: A 402 MET cc_start: 0.6430 (OUTLIER) cc_final: 0.6229 (ppp) REVERT: B 71 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.5819 (mmp-170) REVERT: B 88 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8420 (m-10) REVERT: B 170 PHE cc_start: 0.6149 (OUTLIER) cc_final: 0.4744 (m-10) REVERT: B 387 TRP cc_start: 0.4997 (OUTLIER) cc_final: 0.3867 (t60) REVERT: B 393 PHE cc_start: 0.6699 (m-10) cc_final: 0.6244 (m-10) outliers start: 28 outliers final: 16 residues processed: 107 average time/residue: 0.1108 time to fit residues: 14.9504 Evaluate side-chains 112 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 182 LEU 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 6 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 71 optimal weight: 0.0770 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.161591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120131 restraints weight = 7086.165| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.80 r_work: 0.3378 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1992 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= 0.109 Angle : 0.484 7.209 9796 Z= 0.233 Chirality : 0.039 0.141 1004 Planarity : 0.003 0.032 1128 Dihedral : 20.650 165.013 1482 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.68 % Allowed : 20.29 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.30), residues: 746 helix: 1.71 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.43 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 184 TYR 0.008 0.001 TYR B 186 PHE 0.010 0.001 PHE B 79 TRP 0.016 0.001 TRP B 321 HIS 0.003 0.000 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7288) covalent geometry : angle 0.48365 ( 9796) hydrogen bonds : bond 0.03445 ( 393) hydrogen bonds : angle 3.93649 ( 1167) *********************** 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 113 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.267 Fit side-chains REVERT: A 71 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.5823 (mmp-170) REVERT: A 170 PHE cc_start: 0.6064 (OUTLIER) cc_final: 0.4683 (m-10) REVERT: A 298 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7699 (mt0) REVERT: A 387 TRP cc_start: 0.5025 (OUTLIER) cc_final: 0.3757 (t60) REVERT: A 393 PHE cc_start: 0.6665 (m-10) cc_final: 0.6246 (m-10) REVERT: A 402 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.6230 (ppp) REVERT: B 71 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.5842 (mmp-170) REVERT: B 88 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8439 (m-10) REVERT: B 170 PHE cc_start: 0.6084 (OUTLIER) cc_final: 0.4690 (m-10) REVERT: B 387 TRP cc_start: 0.4985 (OUTLIER) cc_final: 0.3871 (t60) REVERT: B 393 PHE cc_start: 0.6715 (m-10) cc_final: 0.6268 (m-10) outliers start: 25 outliers final: 16 residues processed: 104 average time/residue: 0.1215 time to fit residues: 15.7346 Evaluate side-chains 109 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 182 LEU 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 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 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 54 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.0170 chunk 42 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.161955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.121721 restraints weight = 7044.171| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.70 r_work: 0.3336 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7288 Z= 0.105 Angle : 0.483 7.172 9796 Z= 0.234 Chirality : 0.039 0.140 1004 Planarity : 0.003 0.032 1128 Dihedral : 20.557 164.641 1482 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.53 % Allowed : 20.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.30), residues: 746 helix: 1.75 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 286 TYR 0.008 0.001 TYR B 186 PHE 0.010 0.001 PHE B 79 TRP 0.017 0.001 TRP B 321 HIS 0.002 0.000 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7288) covalent geometry : angle 0.48297 ( 9796) hydrogen bonds : bond 0.03385 ( 393) hydrogen bonds : angle 3.90895 ( 1167) ********************** 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 111 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.242 Fit side-chains REVERT: A 71 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.5851 (mmp-170) REVERT: A 170 PHE cc_start: 0.6072 (OUTLIER) cc_final: 0.4694 (m-10) REVERT: A 298 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7675 (mt0) REVERT: A 387 TRP cc_start: 0.5018 (OUTLIER) cc_final: 0.3765 (t60) REVERT: A 393 PHE cc_start: 0.6671 (m-10) cc_final: 0.6274 (m-10) REVERT: B 71 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.5896 (mmp-170) REVERT: B 88 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8441 (m-10) REVERT: B 170 PHE cc_start: 0.6104 (OUTLIER) cc_final: 0.4729 (m-10) REVERT: B 387 TRP cc_start: 0.4976 (OUTLIER) cc_final: 0.3861 (t60) REVERT: B 393 PHE cc_start: 0.6718 (m-10) cc_final: 0.6277 (m-10) outliers start: 24 outliers final: 14 residues processed: 102 average time/residue: 0.1160 time to fit residues: 14.8859 Evaluate side-chains 107 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 182 LEU 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 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 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 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.161164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.120744 restraints weight = 7047.150| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.71 r_work: 0.3379 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2002 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= 0.122 Angle : 0.501 7.107 9796 Z= 0.242 Chirality : 0.040 0.144 1004 Planarity : 0.003 0.033 1128 Dihedral : 20.644 164.685 1482 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.53 % Allowed : 20.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.30), residues: 746 helix: 1.72 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.39 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 336 TYR 0.007 0.001 TYR B 186 PHE 0.010 0.001 PHE A 79 TRP 0.016 0.001 TRP B 321 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7288) covalent geometry : angle 0.50124 ( 9796) hydrogen bonds : bond 0.03504 ( 393) hydrogen bonds : angle 3.93412 ( 1167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1993.81 seconds wall clock time: 34 minutes 50.42 seconds (2090.42 seconds total)