Starting phenix.real_space_refine on Sat Aug 23 16:16:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8je2_36183/08_2025/8je2_36183.cif Found real_map, /net/cci-nas-00/data/ceres_data/8je2_36183/08_2025/8je2_36183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8je2_36183/08_2025/8je2_36183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8je2_36183/08_2025/8je2_36183.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8je2_36183/08_2025/8je2_36183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8je2_36183/08_2025/8je2_36183.map" } resolution = 3.63 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= -0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4937 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 67 5.16 5 C 5868 2.51 5 N 1606 2.21 5 O 1729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9271 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3757 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 13, 'TRANS': 440} Chain breaks: 1 Chain: "B" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain breaks: 3 Chain: "C" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 698 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain breaks: 1 Chain: "D" Number of atoms: 3930 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3919 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 480} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 494, 3919 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 480} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 3972 Chain: "H" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 188 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 2, 'TRANS': 20} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8853 SG CYS D 599 40.605 84.257 37.400 1.00126.88 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG D 177 " occ=0.43 ... (20 atoms not shown) pdb=" NH2BARG D 177 " occ=0.57 Time building chain proxies: 3.04, per 1000 atoms: 0.33 Number of scatterers: 9271 At special positions: 0 Unit cell: (117.86, 135.29, 141.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 67 16.00 O 1729 8.00 N 1606 7.00 C 5868 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: 0.73 Conformation dependent library (CDL) restraints added in 510.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" NE2 HIS D 627 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 599 " pdb="ZN ZN D 701 " - pdb=" NE2 HIS D 565 " 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2214 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 1 sheets defined 70.1% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 9 through 26 removed outlier: 3.535A pdb=" N ALA A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.694A pdb=" N SER A 40 " --> pdb=" O ASN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 79 Processing helix chain 'A' and resid 82 through 105 removed outlier: 3.895A pdb=" N CYS A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.567A pdb=" N ALA A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 155 through 173 Processing helix chain 'A' and resid 177 through 191 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 207 through 230 Processing helix chain 'A' and resid 231 through 253 Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 271 Processing helix chain 'A' and resid 274 through 288 removed outlier: 3.649A pdb=" N LEU A 278 " --> pdb=" O HIS A 274 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N HIS A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 Processing helix chain 'A' and resid 306 through 330 removed outlier: 4.320A pdb=" N HIS A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 358 removed outlier: 4.191A pdb=" N PHE A 339 " --> pdb=" O MET A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 375 Processing helix chain 'A' and resid 385 through 400 removed outlier: 4.018A pdb=" N GLU A 389 " --> pdb=" O CYS A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 4.003A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 446 Processing helix chain 'A' and resid 450 through 463 Processing helix chain 'B' and resid 23 through 36 Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 66 through 82 removed outlier: 3.526A pdb=" N THR C 78 " --> pdb=" O CYS C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 111 removed outlier: 4.622A pdb=" N LEU C 101 " --> pdb=" O PRO C 97 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLU C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 133 through 143 Processing helix chain 'D' and resid 156 through 165 Processing helix chain 'D' and resid 166 through 176 Processing helix chain 'D' and resid 189 through 197 Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 245 through 263 Processing helix chain 'D' and resid 268 through 284 Processing helix chain 'D' and resid 310 through 318 removed outlier: 3.532A pdb=" N LEU D 314 " --> pdb=" O ASN D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 338 removed outlier: 4.568A pdb=" N ALA D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 357 removed outlier: 4.072A pdb=" N ILE D 347 " --> pdb=" O VAL D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 378 Processing helix chain 'D' and resid 381 through 398 removed outlier: 4.004A pdb=" N PHE D 392 " --> pdb=" O PHE D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 429 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 433 through 457 Processing helix chain 'D' and resid 460 through 477 removed outlier: 4.084A pdb=" N LEU D 477 " --> pdb=" O ASN D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 485 removed outlier: 3.850A pdb=" N PHE D 485 " --> pdb=" O ARG D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 493 Processing helix chain 'D' and resid 511 through 521 removed outlier: 3.842A pdb=" N THR D 515 " --> pdb=" O ASN D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 541 removed outlier: 3.576A pdb=" N ILE D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 Processing helix chain 'D' and resid 575 through 580 Processing helix chain 'D' and resid 582 through 593 Processing helix chain 'D' and resid 596 through 609 Processing helix chain 'D' and resid 617 through 627 removed outlier: 3.810A pdb=" N GLU D 622 " --> pdb=" O ARG D 618 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE D 623 " --> pdb=" O THR D 619 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 49 through 50 removed outlier: 5.020A pdb=" N LYS C 32 " --> pdb=" O PHE B 15 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1704 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: 0.98 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2457 1.33 - 1.45: 1603 1.45 - 1.57: 5279 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 9443 Sorted by residual: bond pdb=" N ILE C 90 " pdb=" CA ILE C 90 " ideal model delta sigma weight residual 1.456 1.494 -0.038 8.70e-03 1.32e+04 1.87e+01 bond pdb=" N ARG C 82 " pdb=" CA ARG C 82 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.23e-02 6.61e+03 9.36e+00 bond pdb=" N TYR A 49 " pdb=" CA TYR A 49 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.04e-02 9.25e+03 9.30e+00 bond pdb=" N VAL D 528 " pdb=" CA VAL D 528 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.20e-02 6.94e+03 9.01e+00 bond pdb=" N VAL C 81 " pdb=" CA VAL C 81 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.88e+00 ... (remaining 9438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 12416 2.09 - 4.17: 290 4.17 - 6.26: 40 6.26 - 8.35: 1 8.35 - 10.43: 1 Bond angle restraints: 12748 Sorted by residual: angle pdb=" N PRO D 510 " pdb=" CA PRO D 510 " pdb=" CB PRO D 510 " ideal model delta sigma weight residual 103.25 111.19 -7.94 1.05e+00 9.07e-01 5.71e+01 angle pdb=" CA PHE C 93 " pdb=" C PHE C 93 " pdb=" N PRO C 94 " ideal model delta sigma weight residual 118.85 122.58 -3.73 9.50e-01 1.11e+00 1.54e+01 angle pdb=" N ILE A 185 " pdb=" CA ILE A 185 " pdb=" CB ILE A 185 " ideal model delta sigma weight residual 110.54 115.79 -5.25 1.36e+00 5.41e-01 1.49e+01 angle pdb=" CA THR C 84 " pdb=" C THR C 84 " pdb=" O THR C 84 " ideal model delta sigma weight residual 121.78 116.97 4.81 1.28e+00 6.10e-01 1.41e+01 angle pdb=" N GLU A 237 " pdb=" CA GLU A 237 " pdb=" CB GLU A 237 " ideal model delta sigma weight residual 110.28 116.05 -5.77 1.55e+00 4.16e-01 1.39e+01 ... (remaining 12743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 5268 16.89 - 33.79: 422 33.79 - 50.68: 75 50.68 - 67.57: 13 67.57 - 84.47: 5 Dihedral angle restraints: 5783 sinusoidal: 2385 harmonic: 3398 Sorted by residual: dihedral pdb=" C TYR A 49 " pdb=" N TYR A 49 " pdb=" CA TYR A 49 " pdb=" CB TYR A 49 " ideal model delta harmonic sigma weight residual -122.60 -133.13 10.53 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" CA GLU D 400 " pdb=" C GLU D 400 " pdb=" N THR D 401 " pdb=" CA THR D 401 " ideal model delta harmonic sigma weight residual 180.00 -160.59 -19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" N TYR A 49 " pdb=" C TYR A 49 " pdb=" CA TYR A 49 " pdb=" CB TYR A 49 " ideal model delta harmonic sigma weight residual 122.80 132.21 -9.41 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 5780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1283 0.071 - 0.141: 134 0.141 - 0.212: 13 0.212 - 0.283: 4 0.283 - 0.353: 1 Chirality restraints: 1435 Sorted by residual: chirality pdb=" CA TYR A 49 " pdb=" N TYR A 49 " pdb=" C TYR A 49 " pdb=" CB TYR A 49 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA PRO D 510 " pdb=" N PRO D 510 " pdb=" C PRO D 510 " pdb=" CB PRO D 510 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA LYS D 574 " pdb=" N LYS D 574 " pdb=" C LYS D 574 " pdb=" CB LYS D 574 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 1432 not shown) Planarity restraints: 1639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 233 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.33e+00 pdb=" C SER A 233 " -0.036 2.00e-02 2.50e+03 pdb=" O SER A 233 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN A 234 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 37 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO B 38 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 367 " -0.015 2.00e-02 2.50e+03 9.90e-03 2.45e+00 pdb=" CG TRP D 367 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP D 367 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP D 367 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 367 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 367 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 367 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 367 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 367 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 367 " 0.001 2.00e-02 2.50e+03 ... (remaining 1636 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1152 2.75 - 3.29: 9986 3.29 - 3.83: 15983 3.83 - 4.36: 18692 4.36 - 4.90: 30456 Nonbonded interactions: 76269 Sorted by model distance: nonbonded pdb=" NH1 ARG D 305 " pdb=" O THR D 306 " model vdw 2.215 3.120 nonbonded pdb=" OD1 ASP D 322 " pdb=" OH TYR D 354 " model vdw 2.225 3.040 nonbonded pdb=" NH2 ARG H 576 " pdb=" O CYS H 580 " model vdw 2.236 3.120 nonbonded pdb=" ND2 ASN D 155 " pdb=" O ASN H 579 " model vdw 2.258 3.120 nonbonded pdb=" NH1 ARG H 576 " pdb=" O CYS H 585 " model vdw 2.271 3.120 ... (remaining 76264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.850 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 0.006 0.367 9446 Z= 0.302 Angle : 0.711 10.434 12748 Z= 0.446 Chirality : 0.046 0.353 1435 Planarity : 0.004 0.052 1639 Dihedral : 12.657 84.467 3569 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.76 % Favored : 97.16 % Rotamer: Outliers : 0.39 % Allowed : 0.29 % Favored : 99.32 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % 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: 1.29 (0.25), residues: 1128 helix: 1.44 (0.19), residues: 770 sheet: None (None), residues: 0 loop : -0.33 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 387 TYR 0.020 0.001 TYR A 90 PHE 0.018 0.001 PHE D 447 TRP 0.027 0.003 TRP D 367 HIS 0.005 0.001 HIS D 627 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9443) covalent geometry : angle 0.71088 (12748) hydrogen bonds : bond 0.14266 ( 572) hydrogen bonds : angle 5.57778 ( 1704) metal coordination : bond 0.26023 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8890 (mtp) cc_final: 0.8597 (mtp) REVERT: A 294 MET cc_start: 0.8484 (mmp) cc_final: 0.8005 (mmm) REVERT: A 297 MET cc_start: 0.9152 (mmm) cc_final: 0.8742 (tpp) REVERT: A 406 MET cc_start: 0.8348 (tpt) cc_final: 0.8084 (tpt) REVERT: A 422 PHE cc_start: 0.9326 (t80) cc_final: 0.8951 (t80) REVERT: D 280 MET cc_start: 0.2391 (ttm) cc_final: 0.1758 (tpp) REVERT: D 395 MET cc_start: 0.9564 (ppp) cc_final: 0.9273 (ppp) REVERT: H 575 ILE cc_start: 0.9164 (mm) cc_final: 0.8713 (mm) outliers start: 4 outliers final: 0 residues processed: 83 average time/residue: 0.0860 time to fit residues: 10.4851 Evaluate side-chains 66 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.050376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.036611 restraints weight = 113906.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.037970 restraints weight = 50528.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.038837 restraints weight = 30261.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.039387 restraints weight = 21201.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.039753 restraints weight = 16545.167| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9446 Z= 0.163 Angle : 0.595 7.472 12748 Z= 0.317 Chirality : 0.040 0.148 1435 Planarity : 0.004 0.050 1639 Dihedral : 4.346 17.886 1247 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.49 % Favored : 97.42 % Rotamer: Outliers : 0.39 % Allowed : 5.35 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.40 (0.25), residues: 1128 helix: 1.51 (0.19), residues: 773 sheet: None (None), residues: 0 loop : -0.28 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 576 TYR 0.013 0.001 TYR A 219 PHE 0.019 0.002 PHE D 388 TRP 0.019 0.002 TRP D 367 HIS 0.004 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9443) covalent geometry : angle 0.59496 (12748) hydrogen bonds : bond 0.04606 ( 572) hydrogen bonds : angle 4.78638 ( 1704) metal coordination : bond 0.00678 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8873 (mtp) cc_final: 0.8544 (mtp) REVERT: A 101 MET cc_start: 0.8395 (ppp) cc_final: 0.8107 (tmm) REVERT: A 294 MET cc_start: 0.8734 (mmp) cc_final: 0.8180 (mmm) REVERT: A 297 MET cc_start: 0.9062 (mmm) cc_final: 0.8678 (tpp) REVERT: A 406 MET cc_start: 0.8329 (tpt) cc_final: 0.8044 (tpt) REVERT: A 422 PHE cc_start: 0.9364 (t80) cc_final: 0.8985 (t80) REVERT: A 457 MET cc_start: 0.8957 (ppp) cc_final: 0.8627 (ppp) REVERT: H 575 ILE cc_start: 0.9046 (mm) cc_final: 0.8789 (mm) outliers start: 4 outliers final: 2 residues processed: 75 average time/residue: 0.0868 time to fit residues: 9.9115 Evaluate side-chains 66 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain D residue 146 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 94 optimal weight: 0.2980 chunk 16 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 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 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.050207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.036327 restraints weight = 120870.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.037753 restraints weight = 51782.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.038656 restraints weight = 30381.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.039234 restraints weight = 21061.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.039612 restraints weight = 16322.471| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9446 Z= 0.136 Angle : 0.564 9.306 12748 Z= 0.295 Chirality : 0.040 0.189 1435 Planarity : 0.004 0.048 1639 Dihedral : 4.303 18.228 1247 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.93 % Favored : 96.98 % Rotamer: Outliers : 0.88 % Allowed : 6.03 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.42 (0.25), residues: 1128 helix: 1.57 (0.19), residues: 776 sheet: -2.42 (1.28), residues: 10 loop : -0.32 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 387 TYR 0.019 0.001 TYR A 194 PHE 0.014 0.001 PHE D 388 TRP 0.010 0.001 TRP A 35 HIS 0.003 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9443) covalent geometry : angle 0.56362 (12748) hydrogen bonds : bond 0.04131 ( 572) hydrogen bonds : angle 4.55426 ( 1704) metal coordination : bond 0.00300 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8869 (mtp) cc_final: 0.8553 (mtp) REVERT: A 86 MET cc_start: 0.9371 (tpp) cc_final: 0.9026 (mmm) REVERT: A 101 MET cc_start: 0.8360 (ppp) cc_final: 0.8072 (tmm) REVERT: A 137 MET cc_start: 0.8573 (ppp) cc_final: 0.8352 (ppp) REVERT: A 236 MET cc_start: 0.8305 (mtp) cc_final: 0.7868 (mtp) REVERT: A 294 MET cc_start: 0.8853 (mmp) cc_final: 0.8323 (mmm) REVERT: A 297 MET cc_start: 0.9184 (mmm) cc_final: 0.8735 (tpp) REVERT: A 311 MET cc_start: 0.9452 (tpp) cc_final: 0.9225 (tpp) REVERT: A 406 MET cc_start: 0.8457 (tpt) cc_final: 0.8163 (tpt) REVERT: A 422 PHE cc_start: 0.9390 (t80) cc_final: 0.9000 (t80) REVERT: H 575 ILE cc_start: 0.9019 (mm) cc_final: 0.8773 (mm) outliers start: 9 outliers final: 6 residues processed: 73 average time/residue: 0.0816 time to fit residues: 9.0371 Evaluate side-chains 68 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 241 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 37 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 108 optimal weight: 0.0770 chunk 79 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 581 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.050398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.036174 restraints weight = 147047.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.037735 restraints weight = 57408.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.038709 restraints weight = 32491.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.039341 restraints weight = 22010.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.039747 restraints weight = 16747.368| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9446 Z= 0.113 Angle : 0.535 8.648 12748 Z= 0.277 Chirality : 0.039 0.161 1435 Planarity : 0.003 0.047 1639 Dihedral : 4.183 18.987 1247 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.84 % Favored : 97.07 % Rotamer: Outliers : 0.97 % Allowed : 6.71 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.54 (0.25), residues: 1128 helix: 1.66 (0.19), residues: 781 sheet: -2.71 (1.14), residues: 10 loop : -0.29 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 29 TYR 0.014 0.001 TYR A 219 PHE 0.012 0.001 PHE A 64 TRP 0.011 0.001 TRP A 35 HIS 0.003 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 9443) covalent geometry : angle 0.53520 (12748) hydrogen bonds : bond 0.03770 ( 572) hydrogen bonds : angle 4.39781 ( 1704) metal coordination : bond 0.00285 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8864 (mtp) cc_final: 0.8541 (mtp) REVERT: A 86 MET cc_start: 0.9308 (tpp) cc_final: 0.8934 (mmm) REVERT: A 101 MET cc_start: 0.8304 (ppp) cc_final: 0.7988 (tmm) REVERT: A 137 MET cc_start: 0.8469 (ppp) cc_final: 0.8220 (ppp) REVERT: A 294 MET cc_start: 0.8855 (mmp) cc_final: 0.8362 (mmm) REVERT: A 406 MET cc_start: 0.8486 (tpt) cc_final: 0.8160 (tpt) REVERT: A 422 PHE cc_start: 0.9406 (t80) cc_final: 0.9015 (t80) REVERT: D 326 MET cc_start: 0.6980 (tpt) cc_final: 0.6279 (tpt) REVERT: H 575 ILE cc_start: 0.9047 (mm) cc_final: 0.8789 (mm) outliers start: 10 outliers final: 6 residues processed: 76 average time/residue: 0.0762 time to fit residues: 8.7811 Evaluate side-chains 71 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 241 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 0.0050 chunk 25 optimal weight: 0.2980 chunk 37 optimal weight: 0.0000 chunk 32 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 70 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.050547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.036486 restraints weight = 129076.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.037992 restraints weight = 53437.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.038931 restraints weight = 30944.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.039529 restraints weight = 21273.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.039926 restraints weight = 16414.173| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9446 Z= 0.114 Angle : 0.549 8.323 12748 Z= 0.282 Chirality : 0.039 0.232 1435 Planarity : 0.003 0.045 1639 Dihedral : 4.141 18.496 1247 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 0.88 % Allowed : 7.59 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.52 (0.25), residues: 1128 helix: 1.60 (0.19), residues: 783 sheet: -2.82 (1.07), residues: 10 loop : -0.19 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 387 TYR 0.012 0.001 TYR A 219 PHE 0.018 0.001 PHE D 388 TRP 0.042 0.003 TRP D 367 HIS 0.003 0.001 HIS D 565 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9443) covalent geometry : angle 0.54852 (12748) hydrogen bonds : bond 0.03660 ( 572) hydrogen bonds : angle 4.39633 ( 1704) metal coordination : bond 0.00107 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8863 (mtp) cc_final: 0.8544 (mtp) REVERT: A 86 MET cc_start: 0.9278 (tpp) cc_final: 0.8892 (mmm) REVERT: A 101 MET cc_start: 0.8235 (ppp) cc_final: 0.7908 (tmm) REVERT: A 137 MET cc_start: 0.8523 (ppp) cc_final: 0.8219 (ppp) REVERT: A 294 MET cc_start: 0.8902 (mmp) cc_final: 0.8378 (mmm) REVERT: A 311 MET cc_start: 0.9476 (tpp) cc_final: 0.9272 (tpp) REVERT: A 406 MET cc_start: 0.8566 (tpt) cc_final: 0.8277 (tpt) REVERT: A 422 PHE cc_start: 0.9420 (t80) cc_final: 0.9030 (t80) REVERT: D 326 MET cc_start: 0.7010 (tpt) cc_final: 0.6327 (tpt) REVERT: D 395 MET cc_start: 0.9686 (ppp) cc_final: 0.9440 (ppp) REVERT: D 513 LEU cc_start: 0.8985 (tp) cc_final: 0.8777 (tp) REVERT: H 575 ILE cc_start: 0.9056 (mm) cc_final: 0.8781 (mm) outliers start: 9 outliers final: 4 residues processed: 78 average time/residue: 0.0724 time to fit residues: 8.4974 Evaluate side-chains 68 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 159 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 HIS ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.050219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.035788 restraints weight = 157241.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.037388 restraints weight = 60553.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.038392 restraints weight = 34086.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.039029 restraints weight = 23069.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.039440 restraints weight = 17547.538| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9446 Z= 0.127 Angle : 0.553 9.414 12748 Z= 0.286 Chirality : 0.039 0.172 1435 Planarity : 0.003 0.044 1639 Dihedral : 4.126 19.562 1247 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 0.78 % Allowed : 8.46 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.51 (0.25), residues: 1128 helix: 1.59 (0.19), residues: 782 sheet: -3.00 (1.03), residues: 10 loop : -0.16 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 387 TYR 0.011 0.001 TYR A 219 PHE 0.025 0.001 PHE D 388 TRP 0.028 0.002 TRP D 367 HIS 0.003 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9443) covalent geometry : angle 0.55295 (12748) hydrogen bonds : bond 0.03605 ( 572) hydrogen bonds : angle 4.40245 ( 1704) metal coordination : bond 0.00106 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8859 (mtp) cc_final: 0.8587 (mtp) REVERT: A 86 MET cc_start: 0.9279 (tpp) cc_final: 0.8890 (mmm) REVERT: A 137 MET cc_start: 0.8562 (ppp) cc_final: 0.8216 (ppp) REVERT: A 236 MET cc_start: 0.8363 (mtp) cc_final: 0.7579 (mtp) REVERT: A 294 MET cc_start: 0.8960 (mmp) cc_final: 0.8425 (mmm) REVERT: A 297 MET cc_start: 0.9145 (mmm) cc_final: 0.8660 (tpp) REVERT: A 406 MET cc_start: 0.8558 (tpt) cc_final: 0.8257 (tpt) REVERT: A 422 PHE cc_start: 0.9446 (t80) cc_final: 0.9070 (t80) REVERT: D 280 MET cc_start: 0.2507 (ttm) cc_final: 0.1735 (tpp) REVERT: D 513 LEU cc_start: 0.9006 (tp) cc_final: 0.8785 (tp) REVERT: H 575 ILE cc_start: 0.9009 (mm) cc_final: 0.8733 (mm) outliers start: 8 outliers final: 6 residues processed: 70 average time/residue: 0.0962 time to fit residues: 9.9060 Evaluate side-chains 69 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 159 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 60 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 13 optimal weight: 0.0770 chunk 39 optimal weight: 10.0000 overall best weight: 0.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.050187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.035389 restraints weight = 199728.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.037117 restraints weight = 68212.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.038208 restraints weight = 36742.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.038899 restraints weight = 24170.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.039307 restraints weight = 18041.700| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9446 Z= 0.117 Angle : 0.569 11.787 12748 Z= 0.289 Chirality : 0.038 0.158 1435 Planarity : 0.003 0.044 1639 Dihedral : 4.102 19.676 1247 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.20 % Favored : 96.71 % Rotamer: Outliers : 0.97 % Allowed : 9.24 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.25), residues: 1128 helix: 1.69 (0.19), residues: 782 sheet: -3.04 (1.00), residues: 10 loop : -0.13 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 387 TYR 0.012 0.001 TYR A 219 PHE 0.021 0.001 PHE D 388 TRP 0.022 0.002 TRP D 367 HIS 0.003 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9443) covalent geometry : angle 0.56892 (12748) hydrogen bonds : bond 0.03513 ( 572) hydrogen bonds : angle 4.37590 ( 1704) metal coordination : bond 0.00130 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8878 (mtp) cc_final: 0.8603 (mtp) REVERT: A 86 MET cc_start: 0.9271 (tpp) cc_final: 0.8877 (mmm) REVERT: A 137 MET cc_start: 0.8586 (ppp) cc_final: 0.8222 (ppp) REVERT: A 294 MET cc_start: 0.8976 (mmp) cc_final: 0.8434 (mmm) REVERT: A 406 MET cc_start: 0.8592 (tpt) cc_final: 0.8297 (tpt) REVERT: A 422 PHE cc_start: 0.9446 (t80) cc_final: 0.9069 (t80) REVERT: D 280 MET cc_start: 0.2502 (ttm) cc_final: 0.1766 (tpp) REVERT: H 575 ILE cc_start: 0.8972 (mm) cc_final: 0.8691 (mm) outliers start: 10 outliers final: 7 residues processed: 71 average time/residue: 0.0676 time to fit residues: 7.3654 Evaluate side-chains 69 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 595 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 0.0980 chunk 5 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 96 optimal weight: 0.2980 chunk 83 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.050165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.035655 restraints weight = 165008.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.037291 restraints weight = 61849.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.038319 restraints weight = 34377.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.038969 restraints weight = 23044.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.039386 restraints weight = 17458.171| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9446 Z= 0.112 Angle : 0.581 12.742 12748 Z= 0.289 Chirality : 0.038 0.145 1435 Planarity : 0.003 0.042 1639 Dihedral : 4.071 20.080 1247 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 0.78 % Allowed : 9.53 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.72 (0.25), residues: 1128 helix: 1.76 (0.19), residues: 778 sheet: -2.79 (1.10), residues: 10 loop : -0.09 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 387 TYR 0.012 0.001 TYR A 219 PHE 0.021 0.001 PHE D 388 TRP 0.019 0.002 TRP D 367 HIS 0.003 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9443) covalent geometry : angle 0.58120 (12748) hydrogen bonds : bond 0.03464 ( 572) hydrogen bonds : angle 4.33658 ( 1704) metal coordination : bond 0.00101 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8860 (mtp) cc_final: 0.8594 (mtp) REVERT: A 86 MET cc_start: 0.9266 (tpp) cc_final: 0.8869 (mmm) REVERT: A 137 MET cc_start: 0.8604 (ppp) cc_final: 0.8215 (ppp) REVERT: A 294 MET cc_start: 0.8940 (mmp) cc_final: 0.8426 (mmm) REVERT: A 406 MET cc_start: 0.8598 (tpt) cc_final: 0.8317 (tpt) REVERT: A 422 PHE cc_start: 0.9438 (t80) cc_final: 0.9065 (t80) REVERT: D 280 MET cc_start: 0.2477 (ttm) cc_final: 0.2036 (tpp) REVERT: H 575 ILE cc_start: 0.8946 (mm) cc_final: 0.8665 (mm) outliers start: 8 outliers final: 5 residues processed: 70 average time/residue: 0.0745 time to fit residues: 7.8565 Evaluate side-chains 68 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain D residue 159 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 0.4980 chunk 41 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 0.0770 chunk 19 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.050219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.035449 restraints weight = 192579.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.037160 restraints weight = 66688.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.038240 restraints weight = 36195.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.038925 restraints weight = 23915.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.039370 restraints weight = 17891.524| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9446 Z= 0.111 Angle : 0.581 10.912 12748 Z= 0.290 Chirality : 0.038 0.143 1435 Planarity : 0.003 0.041 1639 Dihedral : 4.037 20.136 1247 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.47 % Favored : 96.44 % Rotamer: Outliers : 0.49 % Allowed : 9.53 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.79 (0.25), residues: 1128 helix: 1.76 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -0.03 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 387 TYR 0.012 0.001 TYR A 219 PHE 0.020 0.001 PHE D 388 TRP 0.018 0.002 TRP D 367 HIS 0.003 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9443) covalent geometry : angle 0.58070 (12748) hydrogen bonds : bond 0.03449 ( 572) hydrogen bonds : angle 4.32086 ( 1704) metal coordination : bond 0.00083 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8897 (mtp) cc_final: 0.8623 (mtp) REVERT: A 86 MET cc_start: 0.9275 (tpp) cc_final: 0.8878 (mmm) REVERT: A 137 MET cc_start: 0.8693 (ppp) cc_final: 0.8457 (ppp) REVERT: A 294 MET cc_start: 0.8935 (mmp) cc_final: 0.8673 (mmp) REVERT: A 406 MET cc_start: 0.8592 (tpt) cc_final: 0.8289 (tpt) REVERT: A 422 PHE cc_start: 0.9461 (t80) cc_final: 0.9091 (t80) REVERT: B 46 LYS cc_start: 0.7885 (tmmt) cc_final: 0.7638 (tmmt) REVERT: D 157 CYS cc_start: 0.8527 (m) cc_final: 0.7820 (t) REVERT: D 280 MET cc_start: 0.2490 (ttm) cc_final: 0.2020 (tpp) REVERT: H 575 ILE cc_start: 0.8950 (mm) cc_final: 0.8670 (mm) outliers start: 5 outliers final: 5 residues processed: 74 average time/residue: 0.0812 time to fit residues: 9.0485 Evaluate side-chains 70 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain D residue 159 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 4.9990 chunk 101 optimal weight: 0.0670 chunk 72 optimal weight: 0.9990 chunk 98 optimal weight: 0.0970 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.050026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.035773 restraints weight = 140005.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.037290 restraints weight = 56714.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.038260 restraints weight = 32660.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.038882 restraints weight = 22334.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.039290 restraints weight = 17150.312| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9446 Z= 0.120 Angle : 0.605 12.113 12748 Z= 0.299 Chirality : 0.039 0.213 1435 Planarity : 0.003 0.041 1639 Dihedral : 4.037 20.171 1247 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 0.68 % Allowed : 9.92 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.87 (0.25), residues: 1128 helix: 1.80 (0.19), residues: 776 sheet: 0.72 (1.25), residues: 16 loop : 0.05 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 387 TYR 0.012 0.001 TYR A 219 PHE 0.020 0.001 PHE D 388 TRP 0.016 0.002 TRP D 367 HIS 0.003 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9443) covalent geometry : angle 0.60522 (12748) hydrogen bonds : bond 0.03464 ( 572) hydrogen bonds : angle 4.33541 ( 1704) metal coordination : bond 0.00228 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8902 (mtp) cc_final: 0.8595 (mtp) REVERT: A 86 MET cc_start: 0.9281 (tpp) cc_final: 0.8878 (mmm) REVERT: A 137 MET cc_start: 0.8715 (ppp) cc_final: 0.8472 (ppp) REVERT: A 294 MET cc_start: 0.8929 (mmp) cc_final: 0.8678 (mmp) REVERT: A 297 MET cc_start: 0.9304 (mmm) cc_final: 0.8976 (mmm) REVERT: A 406 MET cc_start: 0.8586 (tpt) cc_final: 0.8280 (tpt) REVERT: A 422 PHE cc_start: 0.9445 (t80) cc_final: 0.9074 (t80) REVERT: B 46 LYS cc_start: 0.7913 (tmmt) cc_final: 0.7648 (tmmt) REVERT: B 91 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7831 (tm-30) REVERT: D 280 MET cc_start: 0.2537 (ttm) cc_final: 0.2252 (tpp) REVERT: H 575 ILE cc_start: 0.8959 (mm) cc_final: 0.8675 (mm) outliers start: 7 outliers final: 4 residues processed: 72 average time/residue: 0.0864 time to fit residues: 9.1127 Evaluate side-chains 67 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain D residue 159 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 84 optimal weight: 0.0980 chunk 45 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 48 optimal weight: 0.0060 chunk 59 optimal weight: 0.8980 chunk 94 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.050254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.035825 restraints weight = 156651.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.037419 restraints weight = 60427.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.038436 restraints weight = 34104.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.039085 restraints weight = 23030.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.039503 restraints weight = 17480.316| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9446 Z= 0.110 Angle : 0.603 11.224 12748 Z= 0.295 Chirality : 0.038 0.201 1435 Planarity : 0.003 0.041 1639 Dihedral : 4.021 20.186 1247 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 0.68 % Allowed : 10.02 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.91 (0.25), residues: 1128 helix: 1.84 (0.19), residues: 776 sheet: 0.70 (1.13), residues: 16 loop : 0.03 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 387 TYR 0.012 0.001 TYR A 219 PHE 0.021 0.001 PHE D 388 TRP 0.016 0.002 TRP D 367 HIS 0.003 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9443) covalent geometry : angle 0.60326 (12748) hydrogen bonds : bond 0.03442 ( 572) hydrogen bonds : angle 4.31068 ( 1704) metal coordination : bond 0.00059 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2447.03 seconds wall clock time: 42 minutes 45.56 seconds (2565.56 seconds total)