Starting phenix.real_space_refine on Tue May 13 20:25:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xyz_38784/05_2025/8xyz_38784.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xyz_38784/05_2025/8xyz_38784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xyz_38784/05_2025/8xyz_38784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xyz_38784/05_2025/8xyz_38784.map" model { file = "/net/cci-nas-00/data/ceres_data/8xyz_38784/05_2025/8xyz_38784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xyz_38784/05_2025/8xyz_38784.cif" } resolution = 2.96 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= 0.003 sd= 0.041 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 5732 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 37 5.16 5 C 4112 2.51 5 N 1067 2.21 5 O 1212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6429 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "A" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4885 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 29, 'TRANS': 566} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.83, per 1000 atoms: 0.60 Number of scatterers: 6429 At special positions: 0 Unit cell: (75.21, 86.25, 122.13, 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 37 16.00 O 1212 8.00 N 1067 7.00 C 4112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.43 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.63 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: 1.39 Conformation dependent library (CDL) restraints added in 807.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 57.4% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.535A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.291A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.211A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.574A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.163A pdb=" N GLU A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 104 through 108 removed outlier: 4.149A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 108' Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.528A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.567A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.869A pdb=" N ASP A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 4.142A pdb=" N ASP A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 283 removed outlier: 3.563A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Proline residue: A 280 - end of helix removed outlier: 4.010A pdb=" N VAL A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.761A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 397 through 413 removed outlier: 4.545A pdb=" N HIS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 466 removed outlier: 3.637A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.615A pdb=" N ALA A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.486A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.509A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 561 removed outlier: 3.754A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.580A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.599A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.667A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA5, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.600A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.736A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) 301 hydrogen bonds defined for protein. 876 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.66 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: 1661 1.33 - 1.45: 1413 1.45 - 1.57: 3481 1.57 - 1.69: 1 1.69 - 1.81: 58 Bond restraints: 6614 Sorted by residual: bond pdb=" C TYR A 215 " pdb=" N ASN A 216 " ideal model delta sigma weight residual 1.330 1.226 0.103 1.37e-02 5.33e+03 5.68e+01 bond pdb=" C ASN A 216 " pdb=" N TYR A 217 " ideal model delta sigma weight residual 1.331 1.254 0.077 1.30e-02 5.92e+03 3.53e+01 bond pdb=" C TYR A 83 " pdb=" N PRO A 84 " ideal model delta sigma weight residual 1.331 1.389 -0.058 1.27e-02 6.20e+03 2.08e+01 bond pdb=" CA LYS B 386 " pdb=" C LYS B 386 " ideal model delta sigma weight residual 1.526 1.577 -0.051 1.29e-02 6.01e+03 1.57e+01 bond pdb=" CA TYR A 83 " pdb=" C TYR A 83 " ideal model delta sigma weight residual 1.523 1.568 -0.045 1.19e-02 7.06e+03 1.42e+01 ... (remaining 6609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 8685 2.38 - 4.77: 226 4.77 - 7.15: 47 7.15 - 9.54: 25 9.54 - 11.92: 8 Bond angle restraints: 8991 Sorted by residual: angle pdb=" N TYR B 495 " pdb=" CA TYR B 495 " pdb=" C TYR B 495 " ideal model delta sigma weight residual 111.36 121.55 -10.19 1.09e+00 8.42e-01 8.75e+01 angle pdb=" N ALA B 520 " pdb=" CA ALA B 520 " pdb=" C ALA B 520 " ideal model delta sigma weight residual 108.25 97.62 10.63 1.16e+00 7.43e-01 8.39e+01 angle pdb=" N THR B 523 " pdb=" CA THR B 523 " pdb=" C THR B 523 " ideal model delta sigma weight residual 111.07 119.59 -8.52 1.07e+00 8.73e-01 6.33e+01 angle pdb=" N LEU A 591 " pdb=" CA LEU A 591 " pdb=" C LEU A 591 " ideal model delta sigma weight residual 111.36 103.01 8.35 1.09e+00 8.42e-01 5.86e+01 angle pdb=" N THR A 82 " pdb=" CA THR A 82 " pdb=" C THR A 82 " ideal model delta sigma weight residual 111.28 119.42 -8.14 1.09e+00 8.42e-01 5.57e+01 ... (remaining 8986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 3222 17.40 - 34.81: 468 34.81 - 52.21: 154 52.21 - 69.61: 36 69.61 - 87.02: 13 Dihedral angle restraints: 3893 sinusoidal: 1566 harmonic: 2327 Sorted by residual: dihedral pdb=" N CYS B 525 " pdb=" C CYS B 525 " pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " ideal model delta harmonic sigma weight residual 122.80 112.36 10.44 0 2.50e+00 1.60e-01 1.74e+01 dihedral pdb=" N ASP A 338 " pdb=" C ASP A 338 " pdb=" CA ASP A 338 " pdb=" CB ASP A 338 " ideal model delta harmonic sigma weight residual 122.80 133.06 -10.26 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" C GLU A 145 " pdb=" N GLU A 145 " pdb=" CA GLU A 145 " pdb=" CB GLU A 145 " ideal model delta harmonic sigma weight residual -122.60 -132.52 9.92 0 2.50e+00 1.60e-01 1.57e+01 ... (remaining 3890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 829 0.094 - 0.188: 74 0.188 - 0.283: 20 0.283 - 0.377: 7 0.377 - 0.471: 3 Chirality restraints: 933 Sorted by residual: chirality pdb=" CA GLU A 145 " pdb=" N GLU A 145 " pdb=" C GLU A 145 " pdb=" CB GLU A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" CA ASP A 338 " pdb=" N ASP A 338 " pdb=" C ASP A 338 " pdb=" CB ASP A 338 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA THR A 82 " pdb=" N THR A 82 " pdb=" C THR A 82 " pdb=" CB THR A 82 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.41 2.00e-01 2.50e+01 4.29e+00 ... (remaining 930 not shown) Planarity restraints: 1166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 524 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.00e+00 pdb=" C VAL B 524 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL B 524 " -0.016 2.00e-02 2.50e+03 pdb=" N CYS B 525 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 209 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" CD GLU A 209 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLU A 209 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU A 209 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 335 " 0.039 5.00e-02 4.00e+02 5.74e-02 5.28e+00 pdb=" N PRO A 336 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 336 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 336 " 0.032 5.00e-02 4.00e+02 ... (remaining 1163 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 93 2.62 - 3.19: 5637 3.19 - 3.76: 9504 3.76 - 4.33: 12327 4.33 - 4.90: 20435 Nonbonded interactions: 47996 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.056 2.230 nonbonded pdb=" OD1 ASP A 303 " pdb=" N ALA A 304 " model vdw 2.147 3.120 nonbonded pdb=" O ASN A 194 " pdb=" OD1 ASN A 194 " model vdw 2.201 3.040 nonbonded pdb=" OG SER A 109 " pdb=" OD1 ASP A 111 " model vdw 2.235 3.040 nonbonded pdb=" ND2 ASN B 334 " pdb=" O ASN B 360 " model vdw 2.292 3.120 ... (remaining 47991 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.650 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 : 0.011 0.599 6618 Z= 0.554 Angle : 1.093 26.879 8995 Z= 0.679 Chirality : 0.069 0.471 933 Planarity : 0.006 0.083 1166 Dihedral : 19.008 87.018 2395 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 1.91 % Favored : 97.84 % Rotamer: Outliers : 1.86 % Allowed : 40.11 % Favored : 58.02 % Cbeta Deviations : 0.27 % 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: 0.97 (0.29), residues: 787 helix: 1.73 (0.26), residues: 397 sheet: 2.02 (0.82), residues: 31 loop : -0.75 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 353 HIS 0.005 0.001 HIS A 374 PHE 0.026 0.002 PHE A 314 TYR 0.026 0.002 TYR A 521 ARG 0.018 0.001 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.17893 ( 301) hydrogen bonds : angle 5.71856 ( 876) metal coordination : bond 0.17321 ( 2) SS BOND : bond 0.50701 ( 2) SS BOND : angle 18.48355 ( 4) covalent geometry : bond 0.00554 ( 6614) covalent geometry : angle 1.02092 ( 8991) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 211 time to evaluate : 0.656 Fit side-chains REVERT: A 194 ASN cc_start: 0.7989 (t0) cc_final: 0.7747 (t0) outliers start: 13 outliers final: 7 residues processed: 218 average time/residue: 0.9602 time to fit residues: 221.4120 Evaluate side-chains 207 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 200 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 365 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 4.9990 chunk 59 optimal weight: 0.0030 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN B 409 GLN B 414 GLN B 422 ASN B 501 ASN A 33 ASN A 60 GLN A 96 GLN A 101 GLN A 117 ASN A 134 ASN A 300 GLN A 442 GLN A 508 ASN A 535 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.129025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.108143 restraints weight = 10311.110| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.34 r_work: 0.3309 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6618 Z= 0.182 Angle : 0.623 9.234 8995 Z= 0.325 Chirality : 0.044 0.147 933 Planarity : 0.005 0.044 1166 Dihedral : 5.479 51.066 876 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.03 % Favored : 97.84 % Rotamer: Outliers : 5.59 % Allowed : 31.81 % Favored : 62.61 % 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: 1.14 (0.29), residues: 787 helix: 1.91 (0.26), residues: 408 sheet: 1.97 (0.86), residues: 31 loop : -0.78 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.004 0.001 HIS A 228 PHE 0.022 0.002 PHE B 497 TYR 0.015 0.002 TYR A 521 ARG 0.003 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.07539 ( 301) hydrogen bonds : angle 4.47185 ( 876) metal coordination : bond 0.00189 ( 2) SS BOND : bond 0.00261 ( 2) SS BOND : angle 1.06566 ( 4) covalent geometry : bond 0.00399 ( 6614) covalent geometry : angle 0.62251 ( 8991) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: B 495 TYR cc_start: 0.8728 (m-80) cc_final: 0.8412 (m-80) REVERT: A 114 GLN cc_start: 0.8451 (tt0) cc_final: 0.8199 (tt0) REVERT: A 115 ARG cc_start: 0.8482 (tpm-80) cc_final: 0.8085 (tpt90) REVERT: A 131 LYS cc_start: 0.8731 (mmtm) cc_final: 0.8482 (mmtm) REVERT: A 162 LEU cc_start: 0.8785 (tm) cc_final: 0.8523 (tt) REVERT: A 181 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8063 (mm-30) REVERT: A 194 ASN cc_start: 0.8751 (t0) cc_final: 0.8262 (t0) REVERT: A 288 LYS cc_start: 0.8550 (mtpp) cc_final: 0.8270 (mmtp) REVERT: A 297 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8147 (mtp) REVERT: A 435 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7418 (mm-30) REVERT: A 531 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8382 (tm-30) REVERT: A 532 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8817 (mm) REVERT: A 595 LEU cc_start: 0.8609 (mp) cc_final: 0.8392 (mt) outliers start: 39 outliers final: 10 residues processed: 211 average time/residue: 1.0283 time to fit residues: 228.7127 Evaluate side-chains 196 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 545 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 0.0370 chunk 35 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN A 33 ASN A 101 GLN A 300 GLN A 442 GLN A 508 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.131427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.110508 restraints weight = 10365.949| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.38 r_work: 0.3362 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6618 Z= 0.130 Angle : 0.555 7.522 8995 Z= 0.286 Chirality : 0.041 0.155 933 Planarity : 0.004 0.041 1166 Dihedral : 4.613 35.953 869 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.30 % Allowed : 32.81 % Favored : 62.89 % 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: 1.27 (0.30), residues: 787 helix: 2.07 (0.26), residues: 404 sheet: 2.18 (0.86), residues: 29 loop : -0.77 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.008 0.001 PHE B 374 TYR 0.017 0.001 TYR A 50 ARG 0.004 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.06013 ( 301) hydrogen bonds : angle 4.14346 ( 876) metal coordination : bond 0.00089 ( 2) SS BOND : bond 0.00060 ( 2) SS BOND : angle 0.52948 ( 4) covalent geometry : bond 0.00275 ( 6614) covalent geometry : angle 0.55456 ( 8991) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: B 495 TYR cc_start: 0.8653 (m-80) cc_final: 0.8367 (m-80) REVERT: A 115 ARG cc_start: 0.8404 (tpm-80) cc_final: 0.8181 (tpm-80) REVERT: A 162 LEU cc_start: 0.8755 (tm) cc_final: 0.8493 (tt) REVERT: A 181 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7979 (mm-30) REVERT: A 194 ASN cc_start: 0.8717 (t0) cc_final: 0.8151 (t0) REVERT: A 288 LYS cc_start: 0.8498 (mtpp) cc_final: 0.8256 (mmtp) REVERT: A 331 SER cc_start: 0.8716 (p) cc_final: 0.8482 (p) REVERT: A 385 TYR cc_start: 0.8414 (p90) cc_final: 0.8173 (p90) REVERT: A 435 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7417 (mm-30) REVERT: A 531 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8301 (tm-30) REVERT: A 532 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8696 (mm) outliers start: 30 outliers final: 12 residues processed: 203 average time/residue: 1.0151 time to fit residues: 217.2475 Evaluate side-chains 200 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 532 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 49 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 0.0040 chunk 52 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 439 ASN A 53 ASN A 58 ASN A 101 GLN A 232 GLN A 300 GLN A 442 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.129323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108604 restraints weight = 10526.132| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.37 r_work: 0.3340 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6618 Z= 0.141 Angle : 0.552 7.401 8995 Z= 0.287 Chirality : 0.041 0.138 933 Planarity : 0.004 0.039 1166 Dihedral : 4.226 16.208 865 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.87 % Allowed : 33.38 % Favored : 61.75 % 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: 1.30 (0.30), residues: 787 helix: 2.14 (0.27), residues: 404 sheet: 1.86 (0.85), residues: 29 loop : -0.78 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 PHE 0.031 0.001 PHE B 497 TYR 0.016 0.001 TYR A 385 ARG 0.003 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.06273 ( 301) hydrogen bonds : angle 4.06931 ( 876) metal coordination : bond 0.00081 ( 2) SS BOND : bond 0.00076 ( 2) SS BOND : angle 0.45319 ( 4) covalent geometry : bond 0.00307 ( 6614) covalent geometry : angle 0.55232 ( 8991) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: B 495 TYR cc_start: 0.8654 (m-80) cc_final: 0.8315 (m-80) REVERT: A 115 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8148 (tpm-80) REVERT: A 162 LEU cc_start: 0.8776 (tm) cc_final: 0.8511 (tt) REVERT: A 181 GLU cc_start: 0.8260 (mm-30) cc_final: 0.8054 (mm-30) REVERT: A 288 LYS cc_start: 0.8487 (mtpp) cc_final: 0.8250 (mmtp) REVERT: A 297 MET cc_start: 0.8361 (mtt) cc_final: 0.8056 (mtp) REVERT: A 331 SER cc_start: 0.8741 (p) cc_final: 0.8502 (p) REVERT: A 385 TYR cc_start: 0.8450 (p90) cc_final: 0.8165 (p90) REVERT: A 435 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7469 (mm-30) REVERT: A 470 LYS cc_start: 0.8945 (ttmm) cc_final: 0.8566 (ttmt) REVERT: A 531 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8294 (tm-30) outliers start: 34 outliers final: 13 residues processed: 208 average time/residue: 0.9808 time to fit residues: 215.1998 Evaluate side-chains 196 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 430 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 439 ASN A 101 GLN A 194 ASN A 300 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.109312 restraints weight = 10323.484| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.36 r_work: 0.3336 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6618 Z= 0.148 Angle : 0.560 7.750 8995 Z= 0.292 Chirality : 0.042 0.135 933 Planarity : 0.004 0.037 1166 Dihedral : 4.214 16.352 865 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.87 % Allowed : 33.81 % Favored : 61.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.31 (0.30), residues: 787 helix: 2.13 (0.27), residues: 404 sheet: 2.06 (0.85), residues: 29 loop : -0.76 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 PHE 0.032 0.001 PHE B 497 TYR 0.017 0.001 TYR A 385 ARG 0.003 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.06427 ( 301) hydrogen bonds : angle 4.06382 ( 876) metal coordination : bond 0.00115 ( 2) SS BOND : bond 0.00114 ( 2) SS BOND : angle 0.44688 ( 4) covalent geometry : bond 0.00325 ( 6614) covalent geometry : angle 0.56032 ( 8991) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: B 493 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: B 495 TYR cc_start: 0.8619 (m-80) cc_final: 0.8351 (m-80) REVERT: A 115 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8133 (tpm-80) REVERT: A 162 LEU cc_start: 0.8775 (tm) cc_final: 0.8510 (tt) REVERT: A 181 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7880 (mt-10) REVERT: A 288 LYS cc_start: 0.8500 (mtpp) cc_final: 0.8263 (mmtp) REVERT: A 331 SER cc_start: 0.8737 (p) cc_final: 0.8486 (p) REVERT: A 385 TYR cc_start: 0.8456 (p90) cc_final: 0.8145 (p90) REVERT: A 435 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7427 (mm-30) REVERT: A 470 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8538 (ttmt) REVERT: A 531 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8293 (tm-30) outliers start: 34 outliers final: 12 residues processed: 205 average time/residue: 1.0301 time to fit residues: 222.6588 Evaluate side-chains 195 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 427 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 71 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 73 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 439 ASN A 101 GLN A 194 ASN A 300 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.129557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.108712 restraints weight = 10238.948| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.36 r_work: 0.3325 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6618 Z= 0.157 Angle : 0.573 8.837 8995 Z= 0.297 Chirality : 0.042 0.141 933 Planarity : 0.004 0.037 1166 Dihedral : 4.231 16.672 865 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.58 % Allowed : 34.81 % Favored : 60.60 % 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: 1.26 (0.30), residues: 787 helix: 2.10 (0.27), residues: 404 sheet: 2.07 (0.85), residues: 29 loop : -0.80 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 349 HIS 0.005 0.001 HIS A 374 PHE 0.030 0.001 PHE B 497 TYR 0.018 0.001 TYR A 385 ARG 0.002 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.06620 ( 301) hydrogen bonds : angle 4.06943 ( 876) metal coordination : bond 0.00096 ( 2) SS BOND : bond 0.00111 ( 2) SS BOND : angle 0.43717 ( 4) covalent geometry : bond 0.00348 ( 6614) covalent geometry : angle 0.57334 ( 8991) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: B 493 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: A 115 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8135 (tpm-80) REVERT: A 162 LEU cc_start: 0.8784 (tm) cc_final: 0.8523 (tt) REVERT: A 181 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7962 (mt-10) REVERT: A 189 GLU cc_start: 0.8605 (tp30) cc_final: 0.8255 (tp30) REVERT: A 331 SER cc_start: 0.8729 (p) cc_final: 0.8482 (p) REVERT: A 385 TYR cc_start: 0.8455 (p90) cc_final: 0.8156 (p90) REVERT: A 435 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7429 (mm-30) REVERT: A 470 LYS cc_start: 0.8946 (ttmm) cc_final: 0.8532 (ttmt) REVERT: A 531 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8297 (tm-30) REVERT: A 580 ASP cc_start: 0.8047 (t0) cc_final: 0.7811 (t0) outliers start: 32 outliers final: 16 residues processed: 203 average time/residue: 1.0416 time to fit residues: 222.6903 Evaluate side-chains 199 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 427 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 40 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 439 ASN A 101 GLN A 117 ASN A 194 ASN A 300 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.132262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.111491 restraints weight = 10294.538| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.36 r_work: 0.3366 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6618 Z= 0.123 Angle : 0.551 8.963 8995 Z= 0.283 Chirality : 0.040 0.143 933 Planarity : 0.004 0.034 1166 Dihedral : 4.131 21.718 865 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.72 % Allowed : 36.10 % Favored : 60.17 % 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: 1.42 (0.30), residues: 787 helix: 2.24 (0.27), residues: 396 sheet: 2.06 (0.86), residues: 29 loop : -0.67 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 PHE 0.028 0.001 PHE B 497 TYR 0.016 0.001 TYR A 385 ARG 0.002 0.000 ARG A 518 Details of bonding type rmsd hydrogen bonds : bond 0.05359 ( 301) hydrogen bonds : angle 3.91612 ( 876) metal coordination : bond 0.00091 ( 2) SS BOND : bond 0.00074 ( 2) SS BOND : angle 0.28701 ( 4) covalent geometry : bond 0.00265 ( 6614) covalent geometry : angle 0.55132 ( 8991) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: B 493 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: B 495 TYR cc_start: 0.8670 (m-80) cc_final: 0.8305 (m-80) REVERT: A 115 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8063 (tpm-80) REVERT: A 162 LEU cc_start: 0.8732 (tm) cc_final: 0.8482 (tt) REVERT: A 181 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7922 (mt-10) REVERT: A 189 GLU cc_start: 0.8580 (tp30) cc_final: 0.8227 (tp30) REVERT: A 209 GLU cc_start: 0.7308 (pm20) cc_final: 0.7052 (pm20) REVERT: A 364 VAL cc_start: 0.8501 (t) cc_final: 0.8048 (t) REVERT: A 435 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7428 (mm-30) REVERT: A 470 LYS cc_start: 0.8960 (ttmm) cc_final: 0.8552 (ttmt) REVERT: A 531 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8254 (tm-30) outliers start: 26 outliers final: 15 residues processed: 200 average time/residue: 1.0617 time to fit residues: 223.6798 Evaluate side-chains 199 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 607 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 71 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 439 ASN A 101 GLN A 194 ASN A 213 ASN A 300 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.130584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.109762 restraints weight = 10263.760| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.38 r_work: 0.3341 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6618 Z= 0.146 Angle : 0.589 9.318 8995 Z= 0.302 Chirality : 0.041 0.136 933 Planarity : 0.004 0.034 1166 Dihedral : 4.160 20.296 865 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.01 % Allowed : 36.10 % Favored : 60.89 % 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: 1.39 (0.30), residues: 787 helix: 2.23 (0.27), residues: 396 sheet: 2.06 (0.87), residues: 29 loop : -0.70 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 PHE 0.036 0.001 PHE B 497 TYR 0.018 0.001 TYR A 385 ARG 0.002 0.000 ARG A 518 Details of bonding type rmsd hydrogen bonds : bond 0.06132 ( 301) hydrogen bonds : angle 3.97883 ( 876) metal coordination : bond 0.00107 ( 2) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.39053 ( 4) covalent geometry : bond 0.00325 ( 6614) covalent geometry : angle 0.58871 ( 8991) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: B 493 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: B 495 TYR cc_start: 0.8636 (m-80) cc_final: 0.8326 (m-80) REVERT: A 115 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8212 (tpt90) REVERT: A 162 LEU cc_start: 0.8744 (tm) cc_final: 0.8501 (tt) REVERT: A 189 GLU cc_start: 0.8552 (tp30) cc_final: 0.8165 (tp30) REVERT: A 209 GLU cc_start: 0.7354 (pm20) cc_final: 0.7085 (pm20) REVERT: A 213 ASN cc_start: 0.8479 (t0) cc_final: 0.8272 (t0) REVERT: A 435 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7455 (mm-30) REVERT: A 470 LYS cc_start: 0.8943 (ttmm) cc_final: 0.8648 (ttmt) REVERT: A 531 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8291 (tm-30) REVERT: A 595 LEU cc_start: 0.8591 (mp) cc_final: 0.8384 (mt) outliers start: 21 outliers final: 12 residues processed: 200 average time/residue: 0.9750 time to fit residues: 205.9307 Evaluate side-chains 193 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 607 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 26 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 0.0570 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 439 ASN A 101 GLN A 117 ASN A 194 ASN A 300 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.112398 restraints weight = 10356.970| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.42 r_work: 0.3381 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6618 Z= 0.120 Angle : 0.563 7.958 8995 Z= 0.290 Chirality : 0.040 0.133 933 Planarity : 0.004 0.034 1166 Dihedral : 4.030 20.304 865 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.44 % Allowed : 35.96 % Favored : 61.60 % 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: 1.41 (0.30), residues: 787 helix: 2.18 (0.27), residues: 396 sheet: 2.10 (0.87), residues: 29 loop : -0.59 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 PHE 0.032 0.001 PHE B 497 TYR 0.016 0.001 TYR A 385 ARG 0.002 0.000 ARG A 518 Details of bonding type rmsd hydrogen bonds : bond 0.04985 ( 301) hydrogen bonds : angle 3.85729 ( 876) metal coordination : bond 0.00060 ( 2) SS BOND : bond 0.00090 ( 2) SS BOND : angle 0.45860 ( 4) covalent geometry : bond 0.00262 ( 6614) covalent geometry : angle 0.56270 ( 8991) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: B 493 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: B 495 TYR cc_start: 0.8619 (m-80) cc_final: 0.8268 (m-80) REVERT: A 115 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8066 (tpm-80) REVERT: A 162 LEU cc_start: 0.8693 (tm) cc_final: 0.8457 (tt) REVERT: A 189 GLU cc_start: 0.8520 (tp30) cc_final: 0.8178 (tp30) REVERT: A 194 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8125 (t0) REVERT: A 209 GLU cc_start: 0.7393 (pm20) cc_final: 0.7132 (pm20) REVERT: A 213 ASN cc_start: 0.8429 (t0) cc_final: 0.8189 (t0) REVERT: A 435 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7480 (mm-30) REVERT: A 475 LYS cc_start: 0.8799 (ttpp) cc_final: 0.8473 (ttmm) REVERT: A 531 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8254 (tm-30) REVERT: A 582 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7918 (mpp80) REVERT: A 595 LEU cc_start: 0.8584 (mp) cc_final: 0.8370 (mt) outliers start: 17 outliers final: 9 residues processed: 197 average time/residue: 1.0114 time to fit residues: 210.0452 Evaluate side-chains 189 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 607 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.0060 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 71 optimal weight: 0.0030 chunk 11 optimal weight: 5.9990 overall best weight: 0.6210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 439 ASN A 101 GLN A 300 GLN A 586 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.132378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.111523 restraints weight = 10398.442| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.42 r_work: 0.3371 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6618 Z= 0.127 Angle : 0.591 9.712 8995 Z= 0.301 Chirality : 0.040 0.140 933 Planarity : 0.004 0.033 1166 Dihedral : 4.014 19.161 865 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.58 % Allowed : 37.82 % Favored : 60.60 % 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 (0.30), residues: 787 helix: 2.08 (0.27), residues: 403 sheet: 2.05 (0.87), residues: 29 loop : -0.52 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 PHE 0.035 0.001 PHE B 497 TYR 0.017 0.001 TYR A 385 ARG 0.003 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.05209 ( 301) hydrogen bonds : angle 3.87401 ( 876) metal coordination : bond 0.00142 ( 2) SS BOND : bond 0.00111 ( 2) SS BOND : angle 0.29055 ( 4) covalent geometry : bond 0.00284 ( 6614) covalent geometry : angle 0.59118 ( 8991) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: B 493 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: B 495 TYR cc_start: 0.8568 (m-80) cc_final: 0.8342 (m-80) REVERT: A 115 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8055 (tpm-80) REVERT: A 162 LEU cc_start: 0.8728 (tm) cc_final: 0.8495 (tt) REVERT: A 189 GLU cc_start: 0.8530 (tp30) cc_final: 0.8204 (tp30) REVERT: A 209 GLU cc_start: 0.7402 (pm20) cc_final: 0.7153 (pm20) REVERT: A 213 ASN cc_start: 0.8441 (t0) cc_final: 0.8219 (t0) REVERT: A 435 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7435 (mm-30) REVERT: A 475 LYS cc_start: 0.8781 (ttpp) cc_final: 0.8456 (ttmm) REVERT: A 531 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8268 (tm-30) REVERT: A 582 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7902 (mpp80) REVERT: A 595 LEU cc_start: 0.8576 (mp) cc_final: 0.8361 (mt) outliers start: 11 outliers final: 7 residues processed: 187 average time/residue: 1.0330 time to fit residues: 203.9340 Evaluate side-chains 187 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 582 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN A 101 GLN A 194 ASN A 300 GLN A 586 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.132032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.111003 restraints weight = 10481.491| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.44 r_work: 0.3361 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6618 Z= 0.133 Angle : 0.596 9.578 8995 Z= 0.306 Chirality : 0.040 0.139 933 Planarity : 0.004 0.034 1166 Dihedral : 4.042 21.796 865 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.86 % Allowed : 37.39 % Favored : 60.74 % 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: 1.38 (0.30), residues: 787 helix: 2.15 (0.27), residues: 396 sheet: 2.08 (0.86), residues: 29 loop : -0.60 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.036 0.001 PHE B 497 TYR 0.017 0.001 TYR A 385 ARG 0.005 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.05453 ( 301) hydrogen bonds : angle 3.87889 ( 876) metal coordination : bond 0.00140 ( 2) SS BOND : bond 0.00118 ( 2) SS BOND : angle 0.26187 ( 4) covalent geometry : bond 0.00298 ( 6614) covalent geometry : angle 0.59648 ( 8991) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5738.27 seconds wall clock time: 99 minutes 4.24 seconds (5944.24 seconds total)