Starting phenix.real_space_refine on Mon Jun 9 20:40:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xyz_38784/06_2025/8xyz_38784.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xyz_38784/06_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_38784/06_2025/8xyz_38784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xyz_38784/06_2025/8xyz_38784.map" model { file = "/net/cci-nas-00/data/ceres_data/8xyz_38784/06_2025/8xyz_38784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xyz_38784/06_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-5710/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: 4.31, per 1000 atoms: 0.67 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: 1.60 Conformation dependent library (CDL) restraints added in 947.9 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: 0.72 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: 1.85 Time building geometry restraints manager: 1.92 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.470 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.390 ------------------------------------------------------------------------------- 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 : 0.676 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: 0.9572 time to fit residues: 220.8240 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 : 0.687 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.108138 restraints weight = 10311.111| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.34 r_work: 0.3309 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 1.06567 ( 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 : 0.672 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: 0.8447 (tt0) cc_final: 0.8196 (tt0) REVERT: A 115 ARG cc_start: 0.8481 (tpm-80) cc_final: 0.8084 (tpt90) REVERT: A 131 LYS cc_start: 0.8729 (mmtm) cc_final: 0.8481 (mmtm) REVERT: A 162 LEU cc_start: 0.8786 (tm) cc_final: 0.8524 (tt) REVERT: A 181 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8061 (mm-30) REVERT: A 194 ASN cc_start: 0.8749 (t0) cc_final: 0.8260 (t0) REVERT: A 288 LYS cc_start: 0.8550 (mtpp) cc_final: 0.8269 (mmtp) REVERT: A 297 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8147 (mtp) REVERT: A 435 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7417 (mm-30) REVERT: A 531 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8378 (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: 0.8391 (mt) outliers start: 39 outliers final: 10 residues processed: 211 average time/residue: 1.0045 time to fit residues: 223.9464 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 : 0.638 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.131348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110446 restraints weight = 10365.541| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.38 r_work: 0.3360 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1895 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 7.511 8995 Z= 0.286 Chirality : 0.041 0.138 933 Planarity : 0.004 0.041 1166 Dihedral : 4.603 35.581 869 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.73 % Allowed : 31.95 % Favored : 63.32 % 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: 1.27 (0.30), residues: 787 helix: 2.08 (0.26), residues: 404 sheet: 2.16 (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 0.05995 ( 301) hydrogen bonds : angle 4.13553 ( 876) metal coordination : bond 0.00077 ( 2) SS BOND : bond 0.00035 ( 2) SS BOND : angle 0.53338 ( 4) covalent geometry : bond 0.00278 ( 6614) covalent geometry : angle 0.55488 ( 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 233 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.665 Fit side-chains REVERT: B 495 TYR cc_start: 0.8653 (m-80) cc_final: 0.8370 (m-80) REVERT: A 115 ARG cc_start: 0.8403 (tpm-80) cc_final: 0.8173 (tpm-80) REVERT: A 162 LEU cc_start: 0.8758 (tm) cc_final: 0.8496 (tt) REVERT: A 194 ASN cc_start: 0.8717 (t0) cc_final: 0.8153 (t0) REVERT: A 288 LYS cc_start: 0.8498 (mtpp) cc_final: 0.8257 (mmtp) REVERT: A 331 SER cc_start: 0.8717 (p) cc_final: 0.8481 (p) REVERT: A 385 TYR cc_start: 0.8401 (p90) cc_final: 0.8139 (p90) REVERT: A 435 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7413 (mm-30) REVERT: A 531 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8289 (tm-30) REVERT: A 532 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8696 (mm) REVERT: A 597 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7863 (mm-30) outliers start: 33 outliers final: 13 residues processed: 214 average time/residue: 1.1062 time to fit residues: 248.7607 Evaluate side-chains 211 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 418 ILE 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 278 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 401 HIS 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: 3.9990 chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 49 optimal weight: 0.0570 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 chunk 52 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.127386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106507 restraints weight = 10480.498| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.38 r_work: 0.3310 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6618 Z= 0.177 Angle : 0.577 7.668 8995 Z= 0.304 Chirality : 0.043 0.138 933 Planarity : 0.004 0.039 1166 Dihedral : 4.345 16.484 865 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.16 % Allowed : 32.52 % Favored : 62.32 % 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: 1.24 (0.30), residues: 787 helix: 2.10 (0.27), residues: 404 sheet: 1.89 (0.85), residues: 29 loop : -0.84 (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 0.029 0.001 PHE B 497 TYR 0.018 0.002 TYR A 385 ARG 0.003 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.07278 ( 301) hydrogen bonds : angle 4.20811 ( 876) metal coordination : bond 0.00136 ( 2) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.49847 ( 4) covalent geometry : bond 0.00390 ( 6614) covalent geometry : angle 0.57706 ( 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 231 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.641 Fit side-chains REVERT: B 493 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: B 495 TYR cc_start: 0.8677 (m-80) cc_final: 0.8403 (m-80) REVERT: A 115 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8169 (tpm-80) REVERT: A 162 LEU cc_start: 0.8805 (tm) cc_final: 0.8541 (tt) REVERT: A 227 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7848 (mm-30) REVERT: A 288 LYS cc_start: 0.8506 (mtpp) cc_final: 0.8271 (mmtp) REVERT: A 385 TYR cc_start: 0.8560 (p90) cc_final: 0.8221 (p90) REVERT: A 435 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7432 (mm-30) REVERT: A 531 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8357 (tm-30) REVERT: A 597 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7857 (mm-30) outliers start: 36 outliers final: 16 residues processed: 213 average time/residue: 1.2101 time to fit residues: 271.1314 Evaluate side-chains 210 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 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 128 SER Chi-restraints excluded: chain A residue 201 ASP 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 332 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 427 SER 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: 5.9990 chunk 31 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 228 HIS A 300 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.128806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.107784 restraints weight = 10386.115| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.40 r_work: 0.3315 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 0.004 0.027 6618 Z= 0.168 Angle : 0.567 7.917 8995 Z= 0.299 Chirality : 0.042 0.137 933 Planarity : 0.004 0.038 1166 Dihedral : 4.339 16.757 865 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.16 % Allowed : 32.66 % Favored : 62.18 % 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: 1.22 (0.30), residues: 787 helix: 2.07 (0.27), residues: 404 sheet: 2.04 (0.84), residues: 29 loop : -0.83 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 349 HIS 0.004 0.001 HIS A 374 PHE 0.035 0.001 PHE B 497 TYR 0.018 0.001 TYR A 385 ARG 0.003 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.06928 ( 301) hydrogen bonds : angle 4.14684 ( 876) metal coordination : bond 0.00160 ( 2) SS BOND : bond 0.00085 ( 2) SS BOND : angle 0.44419 ( 4) covalent geometry : bond 0.00369 ( 6614) covalent geometry : angle 0.56712 ( 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 229 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.738 Fit side-chains REVERT: B 493 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: B 495 TYR cc_start: 0.8645 (m-80) cc_final: 0.8357 (m-80) REVERT: A 115 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8149 (tpm-80) REVERT: A 149 ASP cc_start: 0.8059 (m-30) cc_final: 0.7714 (m-30) REVERT: A 162 LEU cc_start: 0.8789 (tm) cc_final: 0.8532 (tt) REVERT: A 207 TYR cc_start: 0.8855 (m-80) cc_final: 0.8637 (m-80) REVERT: A 288 LYS cc_start: 0.8518 (mtpp) cc_final: 0.8288 (mmtp) REVERT: A 297 MET cc_start: 0.8419 (mtt) cc_final: 0.8121 (mtp) REVERT: A 385 TYR cc_start: 0.8505 (p90) cc_final: 0.8198 (p90) REVERT: A 435 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7397 (mm-30) REVERT: A 531 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8366 (tm-30) outliers start: 36 outliers final: 14 residues processed: 215 average time/residue: 1.1035 time to fit residues: 249.6346 Evaluate side-chains 205 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 201 ASP 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 Chi-restraints excluded: chain A residue 582 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 31 optimal weight: 0.0670 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.131045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110195 restraints weight = 10394.128| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.40 r_work: 0.3352 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6618 Z= 0.128 Angle : 0.564 10.240 8995 Z= 0.291 Chirality : 0.041 0.138 933 Planarity : 0.004 0.035 1166 Dihedral : 4.200 16.633 865 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.01 % Allowed : 34.96 % Favored : 61.03 % 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: 1.32 (0.30), residues: 787 helix: 2.03 (0.27), residues: 411 sheet: 2.07 (0.84), residues: 29 loop : -0.67 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 349 HIS 0.004 0.001 HIS A 374 PHE 0.029 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 0.05790 ( 301) hydrogen bonds : angle 3.98531 ( 876) metal coordination : bond 0.00105 ( 2) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.27920 ( 4) covalent geometry : bond 0.00277 ( 6614) covalent geometry : angle 0.56435 ( 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 230 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.843 Fit side-chains REVERT: B 493 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: B 495 TYR cc_start: 0.8653 (m-80) cc_final: 0.8353 (m-80) REVERT: A 115 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8162 (tpm-80) REVERT: A 162 LEU cc_start: 0.8749 (tm) cc_final: 0.8489 (tt) REVERT: A 207 TYR cc_start: 0.8810 (m-80) cc_final: 0.8569 (m-80) REVERT: A 288 LYS cc_start: 0.8483 (mtpp) cc_final: 0.8247 (mmtp) REVERT: A 364 VAL cc_start: 0.8460 (t) cc_final: 0.7951 (t) REVERT: A 385 TYR cc_start: 0.8298 (p90) cc_final: 0.8030 (p90) REVERT: A 420 ASN cc_start: 0.8571 (m-40) cc_final: 0.8359 (m-40) REVERT: A 435 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7399 (mm-30) REVERT: A 531 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8299 (tm-30) REVERT: A 580 ASP cc_start: 0.8057 (t0) cc_final: 0.7796 (t0) outliers start: 28 outliers final: 13 residues processed: 218 average time/residue: 1.1167 time to fit residues: 256.5844 Evaluate side-chains 208 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 30 GLU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 208 GLU 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 556 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 0.0270 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 213 ASN A 300 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.132194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111398 restraints weight = 10316.401| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.38 r_work: 0.3365 rms_B_bonded: 2.74 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: 0.8156 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6618 Z= 0.122 Angle : 0.566 10.703 8995 Z= 0.288 Chirality : 0.040 0.136 933 Planarity : 0.004 0.034 1166 Dihedral : 4.123 21.764 865 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.87 % Allowed : 34.67 % Favored : 61.46 % 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: 2.24 (0.27), residues: 396 sheet: 2.07 (0.87), residues: 29 loop : -0.68 (0.31), residues: 362 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 0.017 0.001 TYR A 385 ARG 0.002 0.000 ARG A 518 Details of bonding type rmsd hydrogen bonds : bond 0.05331 ( 301) hydrogen bonds : angle 3.90864 ( 876) metal coordination : bond 0.00096 ( 2) SS BOND : bond 0.00092 ( 2) SS BOND : angle 0.23486 ( 4) covalent geometry : bond 0.00266 ( 6614) covalent geometry : angle 0.56645 ( 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 215 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: B 493 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: A 115 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8170 (tpm-80) REVERT: A 162 LEU cc_start: 0.8713 (tm) cc_final: 0.8471 (tt) REVERT: A 181 GLU cc_start: 0.8228 (mm-30) cc_final: 0.8005 (mt-10) REVERT: A 189 GLU cc_start: 0.8377 (tp30) cc_final: 0.8129 (tp30) REVERT: A 209 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: A 288 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8247 (mmtp) REVERT: A 435 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7504 (mm-30) REVERT: A 480 MET cc_start: 0.8692 (mtp) cc_final: 0.8485 (mtt) REVERT: A 531 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8273 (tm-30) outliers start: 27 outliers final: 10 residues processed: 203 average time/residue: 1.0950 time to fit residues: 234.4925 Evaluate side-chains 197 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 54 ILE Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 288 LYS 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: 0.9980 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 71 optimal weight: 0.0670 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.130767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.110168 restraints weight = 10321.781| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.36 r_work: 0.3352 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6618 Z= 0.137 Angle : 0.588 11.381 8995 Z= 0.300 Chirality : 0.041 0.137 933 Planarity : 0.004 0.034 1166 Dihedral : 4.117 20.000 865 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.30 % Allowed : 35.39 % 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: 1.33 (0.30), residues: 787 helix: 2.11 (0.27), residues: 404 sheet: 2.11 (0.87), residues: 29 loop : -0.71 (0.31), 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 0.018 0.001 TYR A 385 ARG 0.002 0.000 ARG A 518 Details of bonding type rmsd hydrogen bonds : bond 0.05781 ( 301) hydrogen bonds : angle 3.96575 ( 876) metal coordination : bond 0.00118 ( 2) SS BOND : bond 0.00100 ( 2) SS BOND : angle 0.34783 ( 4) covalent geometry : bond 0.00303 ( 6614) covalent geometry : angle 0.58826 ( 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 214 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: B 493 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: B 495 TYR cc_start: 0.8676 (m-80) cc_final: 0.8386 (m-80) REVERT: A 115 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8130 (tpm-80) REVERT: A 162 LEU cc_start: 0.8728 (tm) cc_final: 0.8479 (tt) REVERT: A 189 GLU cc_start: 0.8375 (tp30) cc_final: 0.8104 (tp30) REVERT: A 288 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8272 (mmtp) REVERT: A 435 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7486 (mm-30) REVERT: A 480 MET cc_start: 0.8706 (mtp) cc_final: 0.8506 (mtt) REVERT: A 531 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8287 (tm-30) REVERT: A 586 ASN cc_start: 0.8851 (t0) cc_final: 0.8626 (t160) REVERT: A 595 LEU cc_start: 0.8597 (mp) cc_final: 0.8383 (mt) outliers start: 23 outliers final: 11 residues processed: 207 average time/residue: 1.1614 time to fit residues: 253.1736 Evaluate side-chains 200 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 288 LYS Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 556 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: 0.3980 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.131623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.110911 restraints weight = 10361.501| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.40 r_work: 0.3357 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6618 Z= 0.128 Angle : 0.584 8.630 8995 Z= 0.297 Chirality : 0.040 0.139 933 Planarity : 0.004 0.034 1166 Dihedral : 4.089 20.047 865 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.72 % Allowed : 36.68 % 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: 1.44 (0.30), residues: 787 helix: 2.25 (0.27), residues: 396 sheet: 2.11 (0.87), residues: 29 loop : -0.64 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.003 0.001 HIS A 378 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 0.05398 ( 301) hydrogen bonds : angle 3.92607 ( 876) metal coordination : bond 0.00096 ( 2) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.33227 ( 4) covalent geometry : bond 0.00283 ( 6614) covalent geometry : angle 0.58382 ( 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 205 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.698 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: 0.8654 (m-80) cc_final: 0.8356 (m-80) REVERT: A 115 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8035 (tpm-80) REVERT: A 162 LEU cc_start: 0.8706 (tm) cc_final: 0.8467 (tt) REVERT: A 189 GLU cc_start: 0.8365 (tp30) cc_final: 0.8106 (tp30) REVERT: A 288 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8251 (mmtp) REVERT: A 435 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7436 (mm-30) REVERT: A 480 MET cc_start: 0.8685 (mtp) cc_final: 0.8467 (mtt) REVERT: A 531 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8275 (tm-30) REVERT: A 582 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7932 (mpp80) REVERT: A 586 ASN cc_start: 0.8842 (t0) cc_final: 0.8630 (t160) REVERT: A 595 LEU cc_start: 0.8592 (mp) cc_final: 0.8374 (mt) outliers start: 19 outliers final: 11 residues processed: 200 average time/residue: 1.1065 time to fit residues: 232.6310 Evaluate side-chains 199 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 119 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 556 GLU 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: 10.0000 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 15 optimal weight: 0.0470 chunk 71 optimal weight: 0.0070 chunk 11 optimal weight: 4.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.130557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.109767 restraints weight = 10332.131| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.39 r_work: 0.3339 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6618 Z= 0.147 Angle : 0.612 12.418 8995 Z= 0.313 Chirality : 0.041 0.136 933 Planarity : 0.004 0.034 1166 Dihedral : 4.142 20.170 865 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.87 % Allowed : 36.68 % Favored : 60.46 % 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: 2.23 (0.27), residues: 396 sheet: 2.08 (0.86), residues: 29 loop : -0.68 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.004 0.001 HIS A 378 PHE 0.039 0.001 PHE B 497 TYR 0.018 0.001 TYR A 385 ARG 0.003 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.06036 ( 301) hydrogen bonds : angle 3.98781 ( 876) metal coordination : bond 0.00136 ( 2) SS BOND : bond 0.00140 ( 2) SS BOND : angle 0.30709 ( 4) covalent geometry : bond 0.00329 ( 6614) covalent geometry : angle 0.61217 ( 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 208 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: B 493 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: B 495 TYR cc_start: 0.8619 (m-80) cc_final: 0.8308 (m-80) REVERT: A 115 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8101 (tpm-80) REVERT: A 148 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8432 (mm) REVERT: A 162 LEU cc_start: 0.8744 (tm) cc_final: 0.8499 (tt) REVERT: A 189 GLU cc_start: 0.8369 (tp30) cc_final: 0.8082 (tp30) REVERT: A 194 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8267 (t0) REVERT: A 288 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8280 (mmtp) REVERT: A 435 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7520 (mm-30) REVERT: A 531 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8311 (tm-30) REVERT: A 595 LEU cc_start: 0.8597 (mp) cc_final: 0.8383 (mt) outliers start: 20 outliers final: 13 residues processed: 201 average time/residue: 1.0691 time to fit residues: 226.9205 Evaluate side-chains 204 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 37 GLU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 589 GLU 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 24 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 13 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN B 481 ASN A 101 GLN A 213 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 = 0.3730 r_free = 0.3730 target = 0.129671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.108679 restraints weight = 10668.287| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.47 r_work: 0.3330 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6618 Z= 0.150 Angle : 0.595 9.178 8995 Z= 0.308 Chirality : 0.041 0.134 933 Planarity : 0.004 0.035 1166 Dihedral : 4.155 19.101 865 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.72 % Allowed : 36.53 % 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: 1.39 (0.30), residues: 787 helix: 2.22 (0.27), residues: 396 sheet: 2.08 (0.85), residues: 29 loop : -0.68 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.036 0.001 PHE B 497 TYR 0.018 0.001 TYR A 385 ARG 0.008 0.000 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.06139 ( 301) hydrogen bonds : angle 4.00896 ( 876) metal coordination : bond 0.00126 ( 2) SS BOND : bond 0.00106 ( 2) SS BOND : angle 0.20190 ( 4) covalent geometry : bond 0.00335 ( 6614) covalent geometry : angle 0.59497 ( 8991) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6216.61 seconds wall clock time: 106 minutes 34.66 seconds (6394.66 seconds total)