Starting phenix.real_space_refine on Thu Jul 31 07:46:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8je2_36183/07_2025/8je2_36183.cif Found real_map, /net/cci-nas-00/data/ceres_data/8je2_36183/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8je2_36183/07_2025/8je2_36183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8je2_36183/07_2025/8je2_36183.map" model { file = "/net/cci-nas-00/data/ceres_data/8je2_36183/07_2025/8je2_36183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8je2_36183/07_2025/8je2_36183.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.52, per 1000 atoms: 1.03 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: 2.46 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.87 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: 2.60 Time building geometry restraints manager: 2.91 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: 11.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 30.540 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.350 ------------------------------------------------------------------------------- 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 : 13.17 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (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 TRP 0.027 0.003 TRP D 367 HIS 0.005 0.001 HIS D 627 PHE 0.018 0.001 PHE D 447 TYR 0.020 0.001 TYR A 90 ARG 0.006 0.000 ARG D 387 Details of bonding type rmsd hydrogen bonds : bond 0.14266 ( 572) hydrogen bonds : angle 5.57778 ( 1704) metal coordination : bond 0.26023 ( 3) covalent geometry : bond 0.00398 ( 9443) covalent geometry : angle 0.71088 (12748) *********************** 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 : 1.006 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: 0.8164 (mmp) REVERT: A 297 MET cc_start: 0.9152 (mmm) cc_final: 0.8737 (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: 0.2002 time to fit residues: 24.2336 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 : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 H 581 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.050547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.036332 restraints weight = 145531.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.037872 restraints weight = 57863.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.038843 restraints weight = 33071.122| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9446 Z= 0.154 Angle : 0.580 7.283 12748 Z= 0.310 Chirality : 0.040 0.143 1435 Planarity : 0.004 0.050 1639 Dihedral : 4.326 17.986 1247 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.40 % Favored : 97.51 % Rotamer: Outliers : 0.49 % Allowed : 5.16 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.25), residues: 1128 helix: 1.54 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -0.26 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 367 HIS 0.004 0.001 HIS A 279 PHE 0.021 0.002 PHE D 388 TYR 0.013 0.001 TYR A 219 ARG 0.005 0.001 ARG H 576 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 572) hydrogen bonds : angle 4.70126 ( 1704) metal coordination : bond 0.00361 ( 3) covalent geometry : bond 0.00318 ( 9443) covalent geometry : angle 0.58006 (12748) *********************** 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 78 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8912 (mtp) cc_final: 0.8573 (mtp) REVERT: A 101 MET cc_start: 0.8359 (ppp) cc_final: 0.8089 (tmm) REVERT: A 294 MET cc_start: 0.8770 (mmp) cc_final: 0.8219 (mmm) REVERT: A 297 MET cc_start: 0.9072 (mmm) cc_final: 0.8696 (tpp) REVERT: A 406 MET cc_start: 0.8324 (tpt) cc_final: 0.8007 (tpt) REVERT: A 422 PHE cc_start: 0.9391 (t80) cc_final: 0.9015 (t80) REVERT: A 457 MET cc_start: 0.8955 (ppp) cc_final: 0.8601 (ppp) REVERT: H 575 ILE cc_start: 0.9049 (mm) cc_final: 0.8796 (mm) outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 0.1817 time to fit residues: 21.3705 Evaluate side-chains 66 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 233 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.049649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.035077 restraints weight = 184077.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.036737 restraints weight = 65060.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.037767 restraints weight = 35611.873| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9446 Z= 0.166 Angle : 0.581 9.440 12748 Z= 0.306 Chirality : 0.040 0.159 1435 Planarity : 0.004 0.048 1639 Dihedral : 4.352 18.145 1247 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 1.07 % Allowed : 6.52 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1128 helix: 1.54 (0.18), residues: 781 sheet: -0.80 (0.92), residues: 26 loop : -0.32 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 35 HIS 0.004 0.001 HIS D 218 PHE 0.015 0.001 PHE A 64 TYR 0.019 0.001 TYR A 194 ARG 0.004 0.000 ARG D 387 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 572) hydrogen bonds : angle 4.57361 ( 1704) metal coordination : bond 0.00188 ( 3) covalent geometry : bond 0.00353 ( 9443) covalent geometry : angle 0.58134 (12748) *********************** 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: 11 poor density : 65 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8908 (mtp) cc_final: 0.8638 (mtp) REVERT: A 86 MET cc_start: 0.9362 (tpp) cc_final: 0.8982 (mmm) REVERT: A 101 MET cc_start: 0.8298 (ppp) cc_final: 0.8056 (tmm) REVERT: A 137 MET cc_start: 0.8571 (ppp) cc_final: 0.8336 (ppp) REVERT: A 294 MET cc_start: 0.8882 (mmp) cc_final: 0.8325 (mmm) REVERT: A 406 MET cc_start: 0.8422 (tpt) cc_final: 0.8099 (tpt) REVERT: A 422 PHE cc_start: 0.9425 (t80) cc_final: 0.9043 (t80) REVERT: B 29 ARG cc_start: 0.9338 (mmm-85) cc_final: 0.9093 (mmm-85) REVERT: D 233 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8896 (p0) REVERT: D 326 MET cc_start: 0.7266 (tpt) cc_final: 0.6558 (tpt) REVERT: H 575 ILE cc_start: 0.9051 (mm) cc_final: 0.8809 (mm) outliers start: 11 outliers final: 6 residues processed: 74 average time/residue: 0.2029 time to fit residues: 22.2486 Evaluate side-chains 72 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 B residue 77 LEU Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 233 ASP 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 39 optimal weight: 20.0000 chunk 61 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.049517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.035109 restraints weight = 163758.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.036681 restraints weight = 61047.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.037690 restraints weight = 34000.821| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9446 Z= 0.141 Angle : 0.550 8.360 12748 Z= 0.287 Chirality : 0.039 0.134 1435 Planarity : 0.003 0.045 1639 Dihedral : 4.265 19.978 1247 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 1.07 % Allowed : 7.10 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.25), residues: 1128 helix: 1.64 (0.19), residues: 781 sheet: -0.92 (0.90), residues: 26 loop : -0.30 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 35 HIS 0.004 0.001 HIS A 279 PHE 0.014 0.001 PHE A 64 TYR 0.015 0.001 TYR A 219 ARG 0.005 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 572) hydrogen bonds : angle 4.45136 ( 1704) metal coordination : bond 0.00098 ( 3) covalent geometry : bond 0.00300 ( 9443) covalent geometry : angle 0.55014 (12748) *********************** 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 77 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8898 (mtp) cc_final: 0.8626 (mtp) REVERT: A 86 MET cc_start: 0.9337 (tpp) cc_final: 0.8931 (mmm) REVERT: A 101 MET cc_start: 0.8309 (ppp) cc_final: 0.7976 (tmm) REVERT: A 137 MET cc_start: 0.8431 (ppp) cc_final: 0.8163 (ppp) REVERT: A 236 MET cc_start: 0.8377 (mtp) cc_final: 0.7723 (mtp) REVERT: A 294 MET cc_start: 0.8944 (mmp) cc_final: 0.8417 (mmm) REVERT: A 297 MET cc_start: 0.9241 (mmm) cc_final: 0.8791 (tpp) REVERT: A 406 MET cc_start: 0.8508 (tpt) cc_final: 0.8193 (tpt) REVERT: A 422 PHE cc_start: 0.9441 (t80) cc_final: 0.9052 (t80) REVERT: D 395 MET cc_start: 0.9708 (ppp) cc_final: 0.9456 (ppp) REVERT: H 575 ILE cc_start: 0.9052 (mm) cc_final: 0.8790 (mm) outliers start: 11 outliers final: 6 residues processed: 74 average time/residue: 0.2236 time to fit residues: 24.5474 Evaluate side-chains 70 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 B residue 77 LEU Chi-restraints excluded: chain D residue 146 ASN 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 52 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 104 optimal weight: 0.0270 chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.049721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.035522 restraints weight = 139260.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.037012 restraints weight = 55795.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.037962 restraints weight = 32003.325| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9446 Z= 0.125 Angle : 0.553 8.342 12748 Z= 0.284 Chirality : 0.038 0.144 1435 Planarity : 0.003 0.044 1639 Dihedral : 4.214 18.861 1247 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 0.97 % Allowed : 8.66 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.25), residues: 1128 helix: 1.65 (0.19), residues: 781 sheet: -0.91 (0.91), residues: 26 loop : -0.26 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 35 HIS 0.003 0.001 HIS A 279 PHE 0.015 0.001 PHE A 64 TYR 0.014 0.001 TYR A 219 ARG 0.003 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 572) hydrogen bonds : angle 4.40686 ( 1704) metal coordination : bond 0.00358 ( 3) covalent geometry : bond 0.00269 ( 9443) covalent geometry : angle 0.55269 (12748) *********************** 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 75 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9321 (tpp) cc_final: 0.8903 (mmm) REVERT: A 101 MET cc_start: 0.8260 (ppp) cc_final: 0.7907 (tmm) REVERT: A 137 MET cc_start: 0.8486 (ppp) cc_final: 0.8183 (ppp) REVERT: A 236 MET cc_start: 0.8436 (mtp) cc_final: 0.7704 (mtp) REVERT: A 294 MET cc_start: 0.8951 (mmp) cc_final: 0.8398 (mmm) REVERT: A 297 MET cc_start: 0.9237 (mmm) cc_final: 0.8745 (tpp) REVERT: A 406 MET cc_start: 0.8547 (tpt) cc_final: 0.8234 (tpt) REVERT: A 422 PHE cc_start: 0.9439 (t80) cc_final: 0.9047 (t80) REVERT: D 280 MET cc_start: 0.2489 (ttm) cc_final: 0.1745 (tpp) REVERT: D 395 MET cc_start: 0.9703 (ppp) cc_final: 0.9374 (ppp) REVERT: H 575 ILE cc_start: 0.9002 (mm) cc_final: 0.8735 (mm) outliers start: 10 outliers final: 5 residues processed: 71 average time/residue: 0.2037 time to fit residues: 21.7820 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 : 1.146 ------------------------------------------------------------------------------- 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 241 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 chunk 39 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.049682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.035579 restraints weight = 128906.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.037046 restraints weight = 53460.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.037969 restraints weight = 31059.689| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9446 Z= 0.124 Angle : 0.547 9.018 12748 Z= 0.283 Chirality : 0.038 0.137 1435 Planarity : 0.003 0.042 1639 Dihedral : 4.186 19.068 1247 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 1.07 % Allowed : 8.85 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.25), residues: 1128 helix: 1.58 (0.19), residues: 783 sheet: 0.39 (1.24), residues: 16 loop : -0.09 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP D 367 HIS 0.003 0.001 HIS A 279 PHE 0.013 0.001 PHE A 64 TYR 0.013 0.001 TYR A 219 ARG 0.018 0.000 ARG D 387 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 572) hydrogen bonds : angle 4.39588 ( 1704) metal coordination : bond 0.00126 ( 3) covalent geometry : bond 0.00268 ( 9443) covalent geometry : angle 0.54739 (12748) *********************** 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 74 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9308 (tpp) cc_final: 0.8901 (mmm) REVERT: A 137 MET cc_start: 0.8592 (ppp) cc_final: 0.8259 (ppp) REVERT: A 236 MET cc_start: 0.8398 (mtp) cc_final: 0.7711 (mtp) REVERT: A 294 MET cc_start: 0.8967 (mmp) cc_final: 0.8451 (mmm) REVERT: A 297 MET cc_start: 0.9229 (mmm) cc_final: 0.8727 (tpp) REVERT: A 406 MET cc_start: 0.8594 (tpt) cc_final: 0.8299 (tpt) REVERT: A 422 PHE cc_start: 0.9454 (t80) cc_final: 0.9063 (t80) REVERT: D 280 MET cc_start: 0.2509 (ttm) cc_final: 0.1775 (tpp) REVERT: H 575 ILE cc_start: 0.9023 (mm) cc_final: 0.8746 (mm) outliers start: 11 outliers final: 5 residues processed: 71 average time/residue: 0.1948 time to fit residues: 20.9993 Evaluate side-chains 66 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 241 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 0.4980 chunk 96 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 83 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.049880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.035216 restraints weight = 179951.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.036871 restraints weight = 64273.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.037901 restraints weight = 35249.221| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9446 Z= 0.119 Angle : 0.570 9.978 12748 Z= 0.292 Chirality : 0.038 0.147 1435 Planarity : 0.003 0.041 1639 Dihedral : 4.168 19.429 1247 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 0.78 % Allowed : 10.02 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.25), residues: 1128 helix: 1.62 (0.18), residues: 782 sheet: None (None), residues: 0 loop : -0.12 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 367 HIS 0.003 0.001 HIS A 279 PHE 0.014 0.001 PHE A 198 TYR 0.013 0.001 TYR A 219 ARG 0.004 0.000 ARG D 387 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 572) hydrogen bonds : angle 4.39075 ( 1704) metal coordination : bond 0.00117 ( 3) covalent geometry : bond 0.00255 ( 9443) covalent geometry : angle 0.57019 (12748) *********************** 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 72 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9317 (tpp) cc_final: 0.8908 (mmm) REVERT: A 137 MET cc_start: 0.8637 (ppp) cc_final: 0.8273 (ppp) REVERT: A 236 MET cc_start: 0.8370 (mtp) cc_final: 0.7737 (mtp) REVERT: A 294 MET cc_start: 0.9000 (mmp) cc_final: 0.8472 (mmm) REVERT: A 297 MET cc_start: 0.9215 (mmm) cc_final: 0.8740 (tpp) REVERT: A 422 PHE cc_start: 0.9469 (t80) cc_final: 0.9086 (t80) REVERT: D 280 MET cc_start: 0.2723 (ttm) cc_final: 0.2244 (tpp) REVERT: H 575 ILE cc_start: 0.9011 (mm) cc_final: 0.8732 (mm) outliers start: 8 outliers final: 4 residues processed: 71 average time/residue: 0.1926 time to fit residues: 20.9331 Evaluate side-chains 65 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 241 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 0 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 34 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 A 320 HIS ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.049794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.035150 restraints weight = 181090.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.036805 restraints weight = 64931.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.037857 restraints weight = 35663.138| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9446 Z= 0.116 Angle : 0.563 11.267 12748 Z= 0.287 Chirality : 0.038 0.145 1435 Planarity : 0.003 0.039 1639 Dihedral : 4.137 19.625 1247 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 0.68 % Allowed : 10.21 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.26), residues: 1128 helix: 1.73 (0.19), residues: 777 sheet: None (None), residues: 0 loop : -0.08 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 367 HIS 0.003 0.001 HIS A 279 PHE 0.014 0.001 PHE A 198 TYR 0.012 0.001 TYR A 219 ARG 0.006 0.000 ARG D 387 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 572) hydrogen bonds : angle 4.35065 ( 1704) metal coordination : bond 0.00113 ( 3) covalent geometry : bond 0.00248 ( 9443) covalent geometry : angle 0.56336 (12748) *********************** 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 70 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9319 (tpp) cc_final: 0.8914 (mmm) REVERT: A 137 MET cc_start: 0.8642 (ppp) cc_final: 0.8256 (ppp) REVERT: A 236 MET cc_start: 0.8370 (mtp) cc_final: 0.7739 (mtp) REVERT: A 294 MET cc_start: 0.9001 (mmp) cc_final: 0.8491 (mmm) REVERT: A 297 MET cc_start: 0.9216 (mmm) cc_final: 0.8731 (tpp) REVERT: A 422 PHE cc_start: 0.9485 (t80) cc_final: 0.9116 (t80) REVERT: D 280 MET cc_start: 0.2789 (ttm) cc_final: 0.2312 (tpp) REVERT: H 575 ILE cc_start: 0.8955 (mm) cc_final: 0.8668 (mm) outliers start: 7 outliers final: 5 residues processed: 68 average time/residue: 0.2070 time to fit residues: 21.4864 Evaluate side-chains 66 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 241 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 0.9980 chunk 78 optimal weight: 0.0870 chunk 57 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 16 optimal weight: 0.0870 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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 199 HIS 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 = 0.049854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.035810 restraints weight = 116341.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.037247 restraints weight = 50636.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.038140 restraints weight = 30045.464| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9446 Z= 0.112 Angle : 0.557 11.148 12748 Z= 0.284 Chirality : 0.038 0.140 1435 Planarity : 0.003 0.039 1639 Dihedral : 4.104 19.986 1247 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 0.68 % Allowed : 10.31 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.25), residues: 1128 helix: 1.79 (0.19), residues: 777 sheet: None (None), residues: 0 loop : -0.12 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 367 HIS 0.006 0.001 HIS A 190 PHE 0.013 0.001 PHE D 388 TYR 0.012 0.001 TYR A 219 ARG 0.005 0.000 ARG D 387 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 572) hydrogen bonds : angle 4.32812 ( 1704) metal coordination : bond 0.00130 ( 3) covalent geometry : bond 0.00237 ( 9443) covalent geometry : angle 0.55692 (12748) *********************** 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 74 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9306 (tpp) cc_final: 0.8897 (mmm) REVERT: A 137 MET cc_start: 0.8665 (ppp) cc_final: 0.8416 (ppp) REVERT: A 236 MET cc_start: 0.8426 (mtp) cc_final: 0.7802 (mtp) REVERT: A 294 MET cc_start: 0.9017 (mmp) cc_final: 0.8535 (mmm) REVERT: A 297 MET cc_start: 0.9217 (mmm) cc_final: 0.8720 (tpp) REVERT: A 406 MET cc_start: 0.7406 (tpt) cc_final: 0.7204 (tpt) REVERT: A 422 PHE cc_start: 0.9469 (t80) cc_final: 0.9103 (t80) REVERT: B 91 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7859 (tm-30) REVERT: D 280 MET cc_start: 0.2732 (ttm) cc_final: 0.2273 (tpp) REVERT: D 326 MET cc_start: 0.7499 (tpt) cc_final: 0.6781 (tpt) REVERT: H 575 ILE cc_start: 0.8965 (mm) cc_final: 0.8684 (mm) outliers start: 7 outliers final: 5 residues processed: 73 average time/residue: 0.2647 time to fit residues: 30.0485 Evaluate side-chains 67 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 146 ASN Chi-restraints excluded: chain D residue 241 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 0.0870 chunk 87 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 0.0040 chunk 77 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.4170 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.049960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.035983 restraints weight = 117445.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.037403 restraints weight = 51159.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.038309 restraints weight = 30299.791| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9446 Z= 0.108 Angle : 0.569 11.918 12748 Z= 0.286 Chirality : 0.038 0.225 1435 Planarity : 0.003 0.039 1639 Dihedral : 4.066 19.966 1247 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 0.58 % Allowed : 10.89 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.25), residues: 1128 helix: 1.82 (0.19), residues: 775 sheet: None (None), residues: 0 loop : -0.09 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 367 HIS 0.003 0.001 HIS A 279 PHE 0.014 0.001 PHE D 388 TYR 0.012 0.001 TYR A 219 ARG 0.005 0.000 ARG D 387 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 572) hydrogen bonds : angle 4.29178 ( 1704) metal coordination : bond 0.00257 ( 3) covalent geometry : bond 0.00229 ( 9443) covalent geometry : angle 0.56872 (12748) ********************** 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: 6 poor density : 67 time to evaluate : 1.136 Fit side-chains revert: symmetry clash REVERT: A 26 MET cc_start: 0.8865 (mtp) cc_final: 0.8610 (mtp) REVERT: A 86 MET cc_start: 0.9305 (tpp) cc_final: 0.8894 (mmm) REVERT: A 137 MET cc_start: 0.8691 (ppp) cc_final: 0.8427 (ppp) REVERT: A 236 MET cc_start: 0.8407 (mtp) cc_final: 0.7778 (mtp) REVERT: A 294 MET cc_start: 0.9024 (mmp) cc_final: 0.8558 (mmm) REVERT: A 297 MET cc_start: 0.9215 (mmm) cc_final: 0.8724 (tpp) REVERT: A 406 MET cc_start: 0.7354 (tpt) cc_final: 0.7092 (tpt) REVERT: A 422 PHE cc_start: 0.9459 (t80) cc_final: 0.9079 (t80) REVERT: B 46 LYS cc_start: 0.7934 (tmmt) cc_final: 0.7655 (tmmt) REVERT: B 91 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7879 (tm-30) REVERT: D 280 MET cc_start: 0.2739 (ttm) cc_final: 0.2271 (tpp) REVERT: H 575 ILE cc_start: 0.8967 (mm) cc_final: 0.8694 (mm) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.2149 time to fit residues: 23.2956 Evaluate side-chains 69 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 241 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 0.0870 chunk 77 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 110 optimal weight: 0.2980 chunk 57 optimal weight: 0.5980 chunk 83 optimal weight: 0.0970 chunk 89 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 72 optimal weight: 0.0770 chunk 37 optimal weight: 0.0010 overall best weight: 0.1120 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.050522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.036052 restraints weight = 155064.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.037647 restraints weight = 60424.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.038661 restraints weight = 34219.709| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3002 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= 0.107 Angle : 0.585 11.704 12748 Z= 0.290 Chirality : 0.038 0.206 1435 Planarity : 0.003 0.039 1639 Dihedral : 4.035 20.215 1247 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.73 % Favored : 96.18 % Rotamer: Outliers : 0.29 % Allowed : 11.67 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.25), residues: 1128 helix: 1.86 (0.19), residues: 775 sheet: None (None), residues: 0 loop : -0.09 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 367 HIS 0.003 0.001 HIS D 565 PHE 0.016 0.001 PHE D 388 TYR 0.011 0.001 TYR A 219 ARG 0.005 0.000 ARG D 387 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 572) hydrogen bonds : angle 4.28074 ( 1704) metal coordination : bond 0.00038 ( 3) covalent geometry : bond 0.00221 ( 9443) covalent geometry : angle 0.58501 (12748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5996.66 seconds wall clock time: 106 minutes 46.50 seconds (6406.50 seconds total)