Starting phenix.real_space_refine on Thu Jul 2 05:56:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kqi_62505/07_2026/9kqi_62505.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kqi_62505/07_2026/9kqi_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_62505/07_2026/9kqi_62505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kqi_62505/07_2026/9kqi_62505.map" model { file = "/net/cci-nas-00/data/ceres_data/9kqi_62505/07_2026/9kqi_62505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kqi_62505/07_2026/9kqi_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 369 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'C14': 1, 'D12': 1, 'LBN': 5, 'PSF': 2, 'T7X': 1} Inner-chain residues flagged as termini: ['pdbres="SER A 511 "'] Classifications: {'peptide': 1, 'undetermined': 10} Modifications used: {'COO': 1} Link IDs: {None: 9} Chain breaks: 1 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, 369 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'C14': 1, 'D12': 1, 'LBN': 5, 'PSF': 2, 'T7X': 1} Classifications: {'peptide': 1, 'undetermined': 10} Modifications used: {'COO': 1} Link IDs: {None: 9} Chain breaks: 1 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: 1.67, per 1000 atoms: 0.24 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: 0.68 Conformation dependent library (CDL) restraints added in 404.4 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: 0.17 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: 1.00 Time building geometry restraints manager: 0.89 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: 3962 33.92 - 67.83: 230 67.83 - 101.75: 41 101.75 - 135.66: 15 135.66 - 169.58: 12 Dihedral angle restraints: 4260 sinusoidal: 2038 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=" O5 LBN B 505 " pdb=" C2 LBN B 505 " pdb=" C3 LBN B 505 " pdb=" O7 LBN B 505 " ideal model delta sinusoidal sigma weight residual 62.67 -102.17 164.84 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 4257 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: 0.02 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.490 Find NCS groups from input model: 0.120 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 : 24.255 169.578 2820 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 are 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/Z covalent geometry : bond 0.00488 / 0.19 ( 7288) covalent geometry : angle 0.55716 / 0.27 ( 9796) hydrogen bonds : bond 0.21439 / 14.29 ( 393) hydrogen bonds : angle 8.01893 / 5.91 ( 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 : 0.235 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: 0.0879 time to fit residues: 10.8047 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 : 0.231 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.175010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134795 restraints weight = 6750.272| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.75 r_work: 0.3373 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7288 Z= 0.138 Angle : 0.548 7.628 9796 Z= 0.270 Chirality : 0.040 0.154 1004 Planarity : 0.004 0.038 1128 Dihedral : 24.800 167.451 1410 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.53 % Allowed : 18.38 % Favored : 78.09 % 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 are not related in a simple way. whole: 0.48 (0.30), residues: 746 helix: 0.72 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.56 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 238 TYR 0.011 0.001 TYR B 291 PHE 0.011 0.001 PHE A 79 TRP 0.015 0.001 TRP A 321 HIS 0.003 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 7288) covalent geometry : angle 0.54801 / 0.27 ( 9796) hydrogen bonds : bond 0.04613 / 3.07 ( 393) hydrogen bonds : angle 4.81279 / 3.47 ( 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 : 0.156 Fit side-chains REVERT: A 22 ARG cc_start: 0.8017 (mtp-110) cc_final: 0.7752 (mtp85) REVERT: A 71 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6045 (mmp-170) REVERT: A 387 TRP cc_start: 0.5013 (OUTLIER) cc_final: 0.3822 (t60) REVERT: B 170 PHE cc_start: 0.6421 (OUTLIER) cc_final: 0.4689 (m-80) REVERT: B 244 THR cc_start: 0.7763 (p) cc_final: 0.7542 (m) REVERT: B 387 TRP cc_start: 0.4773 (OUTLIER) cc_final: 0.3716 (t60) REVERT: B 393 PHE cc_start: 0.7103 (m-10) cc_final: 0.6633 (m-10) outliers start: 24 outliers final: 10 residues processed: 103 average time/residue: 0.0874 time to fit residues: 11.8897 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 : 0.250 ------------------------------------------------------------------------------- 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: 1.9990 chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.174099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134590 restraints weight = 6915.413| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.73 r_work: 0.3442 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1416 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 : 0.518 9.290 9796 Z= 0.248 Chirality : 0.040 0.151 1004 Planarity : 0.003 0.035 1128 Dihedral : 22.617 166.410 1408 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.24 % Allowed : 20.59 % 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 are not related in a simple way. whole: 1.10 (0.31), residues: 746 helix: 1.20 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.43 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 336 TYR 0.010 0.001 TYR B 291 PHE 0.010 0.001 PHE A 79 TRP 0.015 0.001 TRP B 321 HIS 0.003 0.000 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 7288) covalent geometry : angle 0.51767 / 0.25 ( 9796) hydrogen bonds : bond 0.03963 / 2.64 ( 393) hydrogen bonds : angle 4.38322 / 3.13 ( 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: 22 poor density : 92 time to evaluate : 0.248 Fit side-chains REVERT: A 22 ARG cc_start: 0.7932 (mtp-110) cc_final: 0.7668 (mtp85) REVERT: A 387 TRP cc_start: 0.5054 (OUTLIER) cc_final: 0.3699 (t60) REVERT: A 393 PHE cc_start: 0.7049 (m-10) cc_final: 0.6613 (m-10) REVERT: B 19 MET cc_start: 0.7697 (ttt) cc_final: 0.7491 (ttt) REVERT: B 71 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.5987 (mmp-170) REVERT: B 170 PHE cc_start: 0.6476 (OUTLIER) cc_final: 0.6189 (t80) REVERT: B 387 TRP cc_start: 0.4960 (OUTLIER) cc_final: 0.3767 (t60) REVERT: B 393 PHE cc_start: 0.7055 (m-10) cc_final: 0.6563 (m-10) outliers start: 22 outliers final: 13 residues processed: 104 average time/residue: 0.0947 time to fit residues: 12.7848 Evaluate side-chains 104 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 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 394 THR 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: 2.9990 chunk 64 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.0470 chunk 47 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.161341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.121159 restraints weight = 7045.863| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.69 r_work: 0.3140 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7288 Z= 0.111 Angle : 0.508 7.812 9796 Z= 0.243 Chirality : 0.040 0.211 1004 Planarity : 0.003 0.033 1128 Dihedral : 22.122 166.365 1408 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.31), residues: 746 helix: 1.33 (0.23), residues: 550 sheet: None (None), residues: 0 loop : -0.32 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 60 TYR 0.008 0.001 TYR B 186 PHE 0.010 0.001 PHE A 79 TRP 0.016 0.001 TRP B 321 HIS 0.007 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 7288) covalent geometry : angle 0.50800 / 0.24 ( 9796) hydrogen bonds : bond 0.03687 / 2.45 ( 393) hydrogen bonds : angle 4.22269 / 3.01 ( 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 114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.232 Fit side-chains REVERT: A 22 ARG cc_start: 0.7796 (mtp-110) cc_final: 0.7552 (mtp85) REVERT: A 71 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.5627 (mmp-170) REVERT: A 387 TRP cc_start: 0.4959 (OUTLIER) cc_final: 0.3628 (t60) REVERT: A 393 PHE cc_start: 0.6794 (m-10) cc_final: 0.6348 (m-10) REVERT: B 71 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.5529 (mmp-170) REVERT: B 170 PHE cc_start: 0.6112 (OUTLIER) cc_final: 0.5810 (t80) REVERT: B 387 TRP cc_start: 0.4896 (OUTLIER) cc_final: 0.3752 (t60) REVERT: B 393 PHE cc_start: 0.6783 (m-10) cc_final: 0.6316 (m-10) outliers start: 25 outliers final: 14 residues processed: 103 average time/residue: 0.1036 time to fit residues: 13.5567 Evaluate side-chains 104 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 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 172 HIS 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 7 optimal weight: 0.0670 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 1 optimal weight: 0.0000 chunk 61 optimal weight: 1.9990 overall best weight: 0.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 ASN B 309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.163615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.123961 restraints weight = 7019.519| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.66 r_work: 0.3177 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7288 Z= 0.092 Angle : 0.473 8.444 9796 Z= 0.228 Chirality : 0.038 0.143 1004 Planarity : 0.003 0.031 1128 Dihedral : 21.334 165.731 1408 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.58 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 are not related in a simple way. whole: 1.58 (0.31), residues: 746 helix: 1.56 (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 0.003 0.000 ARG B 184 TYR 0.008 0.001 TYR B 291 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/Z covalent geometry : bond 0.00210 / 0.09 ( 7288) covalent geometry : angle 0.47301 / 0.23 ( 9796) hydrogen bonds : bond 0.03322 / 2.21 ( 393) hydrogen bonds : angle 4.02298 / 2.86 ( 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 117 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.233 Fit side-chains REVERT: A 22 ARG cc_start: 0.7731 (mtp-110) cc_final: 0.7484 (mtp85) REVERT: A 71 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.5632 (mmp-170) REVERT: A 387 TRP cc_start: 0.4911 (OUTLIER) cc_final: 0.3676 (t60) REVERT: A 393 PHE cc_start: 0.6682 (m-10) cc_final: 0.6254 (m-10) REVERT: B 71 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.5586 (mmp-170) REVERT: B 170 PHE cc_start: 0.6052 (OUTLIER) cc_final: 0.4478 (m-80) REVERT: B 238 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6457 (mtm-85) REVERT: B 387 TRP cc_start: 0.4841 (OUTLIER) cc_final: 0.3778 (t60) REVERT: B 393 PHE cc_start: 0.6613 (m-10) cc_final: 0.6142 (m-10) outliers start: 25 outliers final: 14 residues processed: 108 average time/residue: 0.1052 time to fit residues: 14.3230 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 : 0.234 ------------------------------------------------------------------------------- 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 394 THR 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 309 HIS 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 24 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.159863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.119266 restraints weight = 7091.406| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.72 r_work: 0.3097 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7288 Z= 0.165 Angle : 0.552 8.422 9796 Z= 0.262 Chirality : 0.042 0.227 1004 Planarity : 0.003 0.036 1128 Dihedral : 21.741 165.715 1408 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.30), residues: 746 helix: 1.46 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.23 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.007 0.001 TYR B 186 PHE 0.011 0.001 PHE A 79 TRP 0.016 0.001 TRP B 321 HIS 0.004 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.16 ( 7288) covalent geometry : angle 0.55160 / 0.26 ( 9796) hydrogen bonds : bond 0.03937 / 2.61 ( 393) hydrogen bonds : angle 4.18424 / 2.99 ( 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 114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.160 Fit side-chains REVERT: A 71 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.5475 (mmp-170) REVERT: A 298 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7607 (mt0) REVERT: A 387 TRP cc_start: 0.5081 (OUTLIER) cc_final: 0.3676 (t60) REVERT: A 393 PHE cc_start: 0.6709 (m-10) cc_final: 0.6322 (m-10) REVERT: B 71 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.5465 (mmp-170) REVERT: B 170 PHE cc_start: 0.5871 (OUTLIER) cc_final: 0.4357 (m-80) REVERT: B 238 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.6417 (mtm-85) REVERT: B 387 TRP cc_start: 0.4940 (OUTLIER) cc_final: 0.3734 (t60) REVERT: B 393 PHE cc_start: 0.6632 (m-10) cc_final: 0.6194 (m-10) outliers start: 24 outliers final: 14 residues processed: 105 average time/residue: 0.0938 time to fit residues: 12.6308 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 : 0.219 ------------------------------------------------------------------------------- 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 298 GLN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 46 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.161537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.121479 restraints weight = 7019.062| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.69 r_work: 0.3212 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1782 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= 0.116 Angle : 0.496 6.279 9796 Z= 0.238 Chirality : 0.040 0.144 1004 Planarity : 0.003 0.033 1128 Dihedral : 21.133 166.210 1408 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.82 % Allowed : 20.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.30), residues: 746 helix: 1.58 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.34 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 184 TYR 0.007 0.001 TYR B 186 PHE 0.011 0.001 PHE B 79 TRP 0.016 0.001 TRP B 321 HIS 0.002 0.000 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 7288) covalent geometry : angle 0.49603 / 0.24 ( 9796) hydrogen bonds : bond 0.03559 / 2.36 ( 393) hydrogen bonds : angle 4.05741 / 2.89 ( 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 113 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.236 Fit side-chains REVERT: A 71 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.5674 (mmp-170) REVERT: A 170 PHE cc_start: 0.5963 (OUTLIER) cc_final: 0.4549 (m-10) REVERT: A 298 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7579 (mt0) REVERT: A 387 TRP cc_start: 0.5036 (OUTLIER) cc_final: 0.3711 (t60) REVERT: A 393 PHE cc_start: 0.6652 (m-10) cc_final: 0.6262 (m-10) REVERT: B 71 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.5651 (mmp-170) REVERT: B 88 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8465 (m-10) REVERT: B 170 PHE cc_start: 0.6029 (OUTLIER) cc_final: 0.4617 (m-10) REVERT: B 238 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.6488 (mtm-85) REVERT: B 387 TRP cc_start: 0.4927 (OUTLIER) cc_final: 0.3767 (t60) REVERT: B 393 PHE cc_start: 0.6661 (m-10) cc_final: 0.6200 (m-10) outliers start: 26 outliers final: 14 residues processed: 105 average time/residue: 0.1046 time to fit residues: 13.7907 Evaluate side-chains 109 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 54 MET Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 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 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 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 3 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.162921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122597 restraints weight = 7105.127| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.73 r_work: 0.3131 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 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 0.042 7288 Z= 0.112 Angle : 0.490 6.214 9796 Z= 0.235 Chirality : 0.040 0.146 1004 Planarity : 0.003 0.033 1128 Dihedral : 19.988 165.809 1408 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.24 % Allowed : 21.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.30), residues: 746 helix: 1.66 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.33 (0.40), 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 B 79 TRP 0.017 0.001 TRP B 321 HIS 0.002 0.000 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 ( 7288) covalent geometry : angle 0.48993 / 0.24 ( 9796) hydrogen bonds : bond 0.03472 / 2.30 ( 393) hydrogen bonds : angle 3.99142 / 2.84 ( 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 110 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.221 Fit side-chains REVERT: A 71 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.5469 (mmp-170) REVERT: A 170 PHE cc_start: 0.5770 (OUTLIER) cc_final: 0.4397 (m-10) REVERT: A 298 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7583 (mt0) REVERT: A 387 TRP cc_start: 0.4952 (OUTLIER) cc_final: 0.3612 (t60) REVERT: A 393 PHE cc_start: 0.6493 (m-10) cc_final: 0.6110 (m-10) REVERT: B 71 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.5436 (mmp-170) REVERT: B 88 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8374 (m-10) REVERT: B 170 PHE cc_start: 0.5890 (OUTLIER) cc_final: 0.4512 (m-10) REVERT: B 387 TRP cc_start: 0.4898 (OUTLIER) cc_final: 0.3775 (t60) REVERT: B 393 PHE cc_start: 0.6524 (m-10) cc_final: 0.6062 (m-10) outliers start: 22 outliers final: 12 residues processed: 104 average time/residue: 0.0970 time to fit residues: 12.8678 Evaluate side-chains 103 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 71 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 402 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 6 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 7 optimal weight: 0.0270 chunk 71 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.162223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.121862 restraints weight = 7027.224| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.70 r_work: 0.3212 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1972 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= 0.109 Angle : 0.481 6.174 9796 Z= 0.232 Chirality : 0.039 0.143 1004 Planarity : 0.003 0.033 1128 Dihedral : 19.765 164.818 1408 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.09 % Allowed : 21.18 % 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 are not related in a simple way. whole: 1.73 (0.30), residues: 746 helix: 1.70 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 60 TYR 0.007 0.001 TYR B 186 PHE 0.010 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/Z covalent geometry : bond 0.00263 / 0.11 ( 7288) covalent geometry : angle 0.48144 / 0.23 ( 9796) hydrogen bonds : bond 0.03428 / 2.26 ( 393) hydrogen bonds : angle 3.95543 / 2.82 ( 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 105 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.241 Fit side-chains REVERT: A 71 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.5678 (mmp-170) REVERT: A 170 PHE cc_start: 0.6024 (OUTLIER) cc_final: 0.4656 (m-10) REVERT: A 298 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7587 (mt0) REVERT: A 387 TRP cc_start: 0.5036 (OUTLIER) cc_final: 0.3737 (t60) REVERT: A 393 PHE cc_start: 0.6641 (m-10) cc_final: 0.6258 (m-10) REVERT: B 71 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.5664 (mmp-170) REVERT: B 88 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8419 (m-10) REVERT: B 170 PHE cc_start: 0.6027 (OUTLIER) cc_final: 0.4663 (m-10) REVERT: B 387 TRP cc_start: 0.4914 (OUTLIER) cc_final: 0.3777 (t60) REVERT: B 393 PHE cc_start: 0.6654 (m-10) cc_final: 0.6198 (m-10) REVERT: B 402 MET cc_start: 0.6424 (OUTLIER) cc_final: 0.6214 (ppp) outliers start: 21 outliers final: 11 residues processed: 99 average time/residue: 0.1058 time to fit residues: 13.4540 Evaluate side-chains 104 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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 379 THR 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 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: 4.9990 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 0.0870 chunk 45 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 0.0060 chunk 42 optimal weight: 4.9990 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.164236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123406 restraints weight = 7000.421| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.76 r_work: 0.3404 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2165 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= 0.090 Angle : 0.458 6.018 9796 Z= 0.223 Chirality : 0.038 0.138 1004 Planarity : 0.003 0.031 1128 Dihedral : 19.285 163.821 1408 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.94 % Allowed : 21.03 % 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 are not related in a simple way. whole: 1.86 (0.30), residues: 746 helix: 1.84 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.41 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 184 TYR 0.008 0.001 TYR B 186 PHE 0.010 0.001 PHE A 79 TRP 0.018 0.001 TRP B 321 HIS 0.002 0.000 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 ( 7288) covalent geometry : angle 0.45835 / 0.22 ( 9796) hydrogen bonds : bond 0.03168 / 2.10 ( 393) hydrogen bonds : angle 3.84039 / 2.73 ( 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 101 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.182 Fit side-chains REVERT: A 22 ARG cc_start: 0.7755 (mtp-110) cc_final: 0.7526 (mtp85) REVERT: A 71 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.5804 (mmp-170) REVERT: A 170 PHE cc_start: 0.6018 (OUTLIER) cc_final: 0.4647 (m-10) REVERT: A 298 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7738 (mt0) REVERT: A 387 TRP cc_start: 0.4955 (OUTLIER) cc_final: 0.3714 (t60) REVERT: A 393 PHE cc_start: 0.6669 (m-10) cc_final: 0.6292 (m-10) REVERT: B 71 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.5845 (mmp-170) REVERT: B 88 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8517 (m-10) REVERT: B 170 PHE cc_start: 0.6028 (OUTLIER) cc_final: 0.4668 (m-10) REVERT: B 387 TRP cc_start: 0.4935 (OUTLIER) cc_final: 0.3907 (t60) outliers start: 20 outliers final: 12 residues processed: 96 average time/residue: 0.1031 time to fit residues: 12.6408 Evaluate side-chains 101 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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 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 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: 2.9990 chunk 43 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 47 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.163261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.122027 restraints weight = 7006.588| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.78 r_work: 0.3351 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7288 Z= 0.117 Angle : 0.485 6.271 9796 Z= 0.235 Chirality : 0.040 0.144 1004 Planarity : 0.003 0.033 1128 Dihedral : 19.513 163.449 1408 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.09 % Allowed : 20.88 % 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 are not related in a simple way. whole: 1.86 (0.30), residues: 746 helix: 1.80 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.31 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 184 TYR 0.007 0.001 TYR B 186 PHE 0.010 0.001 PHE A 79 TRP 0.016 0.001 TRP A 321 HIS 0.003 0.000 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 7288) covalent geometry : angle 0.48536 / 0.23 ( 9796) hydrogen bonds : bond 0.03449 / 2.28 ( 393) hydrogen bonds : angle 3.91321 / 2.79 ( 1167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1812.71 seconds wall clock time: 31 minutes 39.68 seconds (1899.68 seconds total)