Starting phenix.real_space_refine on Fri Jun 6 11:47:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wa1_32379/06_2025/7wa1_32379.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wa1_32379/06_2025/7wa1_32379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wa1_32379/06_2025/7wa1_32379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wa1_32379/06_2025/7wa1_32379.map" model { file = "/net/cci-nas-00/data/ceres_data/7wa1_32379/06_2025/7wa1_32379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wa1_32379/06_2025/7wa1_32379.cif" } resolution = 2.9 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= -0.000 sd= 0.069 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 1540 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 4116 2.51 5 N 1080 2.21 5 O 1206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6440 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4899 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 30, 'TRANS': 564} Chain: "B" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1540 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} 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: 4.71, per 1000 atoms: 0.73 Number of scatterers: 6440 At special positions: 0 Unit cell: (70.914, 86.97, 121.089, 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 1206 8.00 N 1080 7.00 C 4116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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: 1.48 Conformation dependent library (CDL) restraints added in 908.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 378 " 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 6 sheets defined 55.3% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 3.680A pdb=" N TYR A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.703A pdb=" N GLN A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.576A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.639A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.729A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 171 removed outlier: 3.680A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.918A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.746A pdb=" N HIS A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.544A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (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 282 Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.530A pdb=" N MET A 297 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.639A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.967A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.500A pdb=" N ALA A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.689A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.544A pdb=" N ASN A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.513A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 removed outlier: 3.512A pdb=" N GLU A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) 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 484 removed outlier: 3.613A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.618A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.501A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 559 removed outlier: 3.897A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.662A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.853A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.413A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.789A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 280 hydrogen bonds defined for protein. 789 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: 1.83 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2077 1.34 - 1.46: 1667 1.46 - 1.58: 2823 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6625 Sorted by residual: bond pdb=" C GLU A 145 " pdb=" N PRO A 146 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.69e+00 bond pdb=" CA GLU A 145 " pdb=" C GLU A 145 " ideal model delta sigma weight residual 1.520 1.536 -0.016 1.23e-02 6.61e+03 1.72e+00 bond pdb=" C GLU A 589 " pdb=" N PRO A 590 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.28e-02 6.10e+03 1.44e+00 bond pdb=" CA GLU A 589 " pdb=" C GLU A 589 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.26e-02 6.30e+03 1.32e+00 bond pdb=" C LYS A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.28e-02 6.10e+03 1.27e+00 ... (remaining 6620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 8767 1.46 - 2.93: 199 2.93 - 4.39: 22 4.39 - 5.85: 9 5.85 - 7.32: 6 Bond angle restraints: 9003 Sorted by residual: angle pdb=" C PHE A 588 " pdb=" N GLU A 589 " pdb=" CA GLU A 589 " ideal model delta sigma weight residual 120.09 124.38 -4.29 1.25e+00 6.40e-01 1.18e+01 angle pdb=" C LEU B 486 " pdb=" N ASN B 487 " pdb=" CA ASN B 487 " ideal model delta sigma weight residual 123.91 129.26 -5.35 1.66e+00 3.63e-01 1.04e+01 angle pdb=" C SER B 371 " pdb=" N ALA B 372 " pdb=" CA ALA B 372 " ideal model delta sigma weight residual 122.40 126.12 -3.72 1.45e+00 4.76e-01 6.60e+00 angle pdb=" N ASP A 499 " pdb=" CA ASP A 499 " pdb=" C ASP A 499 " ideal model delta sigma weight residual 109.81 115.36 -5.55 2.21e+00 2.05e-01 6.30e+00 angle pdb=" CA TYR A 385 " pdb=" CB TYR A 385 " pdb=" CG TYR A 385 " ideal model delta sigma weight residual 113.90 118.37 -4.47 1.80e+00 3.09e-01 6.18e+00 ... (remaining 8998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 3646 16.17 - 32.34: 220 32.34 - 48.51: 46 48.51 - 64.68: 7 64.68 - 80.84: 4 Dihedral angle restraints: 3923 sinusoidal: 1600 harmonic: 2323 Sorted by residual: dihedral pdb=" CA ARG A 582 " pdb=" C ARG A 582 " pdb=" N PRO A 583 " pdb=" CA PRO A 583 " ideal model delta harmonic sigma weight residual 180.00 162.57 17.43 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ALA A 396 " pdb=" C ALA A 396 " pdb=" N ASN A 397 " pdb=" CA ASN A 397 " ideal model delta harmonic sigma weight residual 180.00 163.53 16.47 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA PRO A 146 " pdb=" C PRO A 146 " pdb=" N GLY A 147 " pdb=" CA GLY A 147 " ideal model delta harmonic sigma weight residual 180.00 -164.37 -15.63 0 5.00e+00 4.00e-02 9.77e+00 ... (remaining 3920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 526 0.032 - 0.064: 286 0.064 - 0.095: 64 0.095 - 0.127: 49 0.127 - 0.159: 4 Chirality restraints: 929 Sorted by residual: chirality pdb=" CA ARG A 177 " pdb=" N ARG A 177 " pdb=" C ARG A 177 " pdb=" CB ARG A 177 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA LYS A 234 " pdb=" N LYS A 234 " pdb=" C LYS A 234 " pdb=" CB LYS A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA TYR A 279 " pdb=" N TYR A 279 " pdb=" C TYR A 279 " pdb=" CB TYR A 279 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 926 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.043 5.00e-02 4.00e+02 6.49e-02 6.73e+00 pdb=" N PRO A 583 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO B 521 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 450 " 0.034 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO A 451 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " 0.029 5.00e-02 4.00e+02 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 91 2.66 - 3.22: 5508 3.22 - 3.78: 10267 3.78 - 4.34: 15088 4.34 - 4.90: 23982 Nonbonded interactions: 54936 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 801 " model vdw 2.103 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 801 " model vdw 2.106 2.230 nonbonded pdb=" NE2 HIS A 378 " pdb=" OE1 GLU A 402 " model vdw 2.160 3.120 nonbonded pdb=" CD GLU A 402 " pdb="ZN ZN A 801 " model vdw 2.228 2.460 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.285 3.040 ... (remaining 54931 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.080 Find NCS groups from input model: 0.050 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:16.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.200 6634 Z= 0.182 Angle : 0.575 7.316 9017 Z= 0.323 Chirality : 0.044 0.159 929 Planarity : 0.006 0.065 1172 Dihedral : 11.298 80.844 2412 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.59 % Allowed : 5.78 % Favored : 92.63 % 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: -3.55 (0.23), residues: 786 helix: -3.46 (0.14), residues: 384 sheet: -0.65 (0.68), residues: 56 loop : -1.04 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.012 0.001 PHE B 400 TYR 0.022 0.001 TYR A 385 ARG 0.004 0.000 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.29270 ( 280) hydrogen bonds : angle 9.71316 ( 789) metal coordination : bond 0.19746 ( 2) SS BOND : bond 0.00302 ( 7) SS BOND : angle 0.68771 ( 14) covalent geometry : bond 0.00301 ( 6625) covalent geometry : angle 0.57525 ( 9003) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.710 Fit side-chains REVERT: A 30 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6895 (mm-30) REVERT: A 31 LYS cc_start: 0.8142 (tppt) cc_final: 0.7767 (tmmt) REVERT: A 150 ASP cc_start: 0.7267 (t70) cc_final: 0.7051 (m-30) REVERT: A 586 ASN cc_start: 0.8020 (t0) cc_final: 0.7726 (t0) REVERT: B 395 VAL cc_start: 0.8263 (t) cc_final: 0.8011 (p) REVERT: B 474 GLN cc_start: 0.6309 (pt0) cc_final: 0.5887 (mt0) REVERT: B 484 GLU cc_start: 0.7379 (pp20) cc_final: 0.7176 (pp20) outliers start: 11 outliers final: 5 residues processed: 159 average time/residue: 1.1090 time to fit residues: 185.7585 Evaluate side-chains 101 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 32 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 96 GLN A 228 HIS A 299 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.146839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.119047 restraints weight = 7269.146| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.97 r_work: 0.3238 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6634 Z= 0.141 Angle : 0.504 5.423 9017 Z= 0.266 Chirality : 0.042 0.136 929 Planarity : 0.005 0.047 1172 Dihedral : 4.611 28.789 875 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.03 % Allowed : 11.27 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.37 (0.27), residues: 786 helix: -1.13 (0.23), residues: 383 sheet: -0.66 (0.64), residues: 58 loop : -0.46 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 369 TYR 0.017 0.001 TYR B 351 ARG 0.007 0.001 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.05246 ( 280) hydrogen bonds : angle 5.32472 ( 789) metal coordination : bond 0.00456 ( 2) SS BOND : bond 0.00316 ( 7) SS BOND : angle 0.52205 ( 14) covalent geometry : bond 0.00308 ( 6625) covalent geometry : angle 0.50442 ( 9003) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6615 (mm-30) REVERT: A 31 LYS cc_start: 0.8018 (tppt) cc_final: 0.7339 (ttpt) REVERT: A 60 GLN cc_start: 0.7211 (mm110) cc_final: 0.6696 (tm-30) REVERT: A 74 GLU cc_start: 0.7565 (mt-10) cc_final: 0.6843 (mt-10) REVERT: A 347 THR cc_start: 0.8471 (m) cc_final: 0.8256 (p) REVERT: B 403 ARG cc_start: 0.8539 (ptm-80) cc_final: 0.8306 (ptm160) REVERT: B 484 GLU cc_start: 0.7124 (pp20) cc_final: 0.6836 (pp20) outliers start: 21 outliers final: 10 residues processed: 107 average time/residue: 1.1635 time to fit residues: 131.2647 Evaluate side-chains 95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 0 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 89 GLN A 96 GLN A 599 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.146099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.118025 restraints weight = 7380.119| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.97 r_work: 0.3225 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6634 Z= 0.126 Angle : 0.471 5.420 9017 Z= 0.243 Chirality : 0.041 0.136 929 Planarity : 0.004 0.036 1172 Dihedral : 4.301 29.721 873 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.31 % Allowed : 13.44 % Favored : 84.25 % 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: -0.61 (0.29), residues: 786 helix: -0.28 (0.26), residues: 386 sheet: -0.54 (0.66), residues: 58 loop : -0.33 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 369 TYR 0.018 0.001 TYR A 521 ARG 0.008 0.001 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.04531 ( 280) hydrogen bonds : angle 4.90706 ( 789) metal coordination : bond 0.00073 ( 2) SS BOND : bond 0.00284 ( 7) SS BOND : angle 0.49445 ( 14) covalent geometry : bond 0.00281 ( 6625) covalent geometry : angle 0.47058 ( 9003) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6524 (mm-30) REVERT: A 31 LYS cc_start: 0.7915 (tppt) cc_final: 0.7418 (tmmt) REVERT: A 60 GLN cc_start: 0.7158 (mm110) cc_final: 0.6708 (pt0) REVERT: A 74 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7288 (mt-10) REVERT: A 156 LYS cc_start: 0.7497 (mptt) cc_final: 0.7003 (mmtt) REVERT: A 347 THR cc_start: 0.8511 (m) cc_final: 0.8255 (p) REVERT: A 470 LYS cc_start: 0.8321 (ptmt) cc_final: 0.8048 (ttpp) REVERT: B 484 GLU cc_start: 0.7109 (pp20) cc_final: 0.6821 (pp20) outliers start: 16 outliers final: 10 residues processed: 107 average time/residue: 1.3771 time to fit residues: 154.7939 Evaluate side-chains 99 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.145229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116977 restraints weight = 7454.712| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.98 r_work: 0.3197 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6634 Z= 0.128 Angle : 0.465 5.445 9017 Z= 0.239 Chirality : 0.041 0.135 929 Planarity : 0.004 0.036 1172 Dihedral : 4.152 29.955 872 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.18 % Allowed : 13.44 % Favored : 83.38 % 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: -0.26 (0.29), residues: 786 helix: 0.09 (0.26), residues: 389 sheet: -0.53 (0.66), residues: 59 loop : -0.23 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 523 TYR 0.013 0.001 TYR A 521 ARG 0.007 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 280) hydrogen bonds : angle 4.77326 ( 789) metal coordination : bond 0.00107 ( 2) SS BOND : bond 0.00275 ( 7) SS BOND : angle 0.51512 ( 14) covalent geometry : bond 0.00289 ( 6625) covalent geometry : angle 0.46514 ( 9003) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.701 Fit side-chains REVERT: A 30 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6517 (mm-30) REVERT: A 31 LYS cc_start: 0.7914 (tppt) cc_final: 0.7315 (ttpp) REVERT: A 60 GLN cc_start: 0.7189 (mm110) cc_final: 0.6715 (pt0) REVERT: A 74 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7198 (mt-10) REVERT: A 160 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: A 325 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: A 347 THR cc_start: 0.8551 (m) cc_final: 0.8287 (p) REVERT: A 455 MET cc_start: 0.8445 (tmt) cc_final: 0.8140 (tmt) REVERT: A 470 LYS cc_start: 0.8338 (ptmt) cc_final: 0.8009 (ttpp) REVERT: A 534 LYS cc_start: 0.8323 (mmmt) cc_final: 0.7823 (mptt) REVERT: B 399 SER cc_start: 0.8582 (OUTLIER) cc_final: 0.8165 (p) REVERT: B 484 GLU cc_start: 0.7071 (pp20) cc_final: 0.6772 (pp20) outliers start: 22 outliers final: 10 residues processed: 108 average time/residue: 1.2814 time to fit residues: 145.3144 Evaluate side-chains 93 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 0.0170 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.0020 chunk 73 optimal weight: 0.8980 overall best weight: 0.4626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.118328 restraints weight = 7352.265| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.96 r_work: 0.3231 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6634 Z= 0.105 Angle : 0.453 6.142 9017 Z= 0.231 Chirality : 0.041 0.122 929 Planarity : 0.004 0.039 1172 Dihedral : 4.013 29.721 872 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.60 % Allowed : 14.31 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.30), residues: 786 helix: 0.41 (0.27), residues: 389 sheet: -0.13 (0.77), residues: 49 loop : -0.09 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.012 0.001 PHE A 369 TYR 0.017 0.001 TYR A 521 ARG 0.010 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 280) hydrogen bonds : angle 4.61020 ( 789) metal coordination : bond 0.00072 ( 2) SS BOND : bond 0.00231 ( 7) SS BOND : angle 0.47772 ( 14) covalent geometry : bond 0.00232 ( 6625) covalent geometry : angle 0.45322 ( 9003) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6511 (mm-30) REVERT: A 31 LYS cc_start: 0.7941 (tppt) cc_final: 0.7382 (ttpp) REVERT: A 60 GLN cc_start: 0.7220 (mm110) cc_final: 0.6753 (pt0) REVERT: A 74 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7087 (mt-10) REVERT: A 156 LYS cc_start: 0.7724 (mptt) cc_final: 0.7147 (mmtt) REVERT: A 160 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: A 325 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: A 347 THR cc_start: 0.8558 (m) cc_final: 0.8329 (p) REVERT: A 456 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7997 (tt) REVERT: A 470 LYS cc_start: 0.8320 (ptmt) cc_final: 0.8052 (ttpp) REVERT: A 534 LYS cc_start: 0.8339 (mmmt) cc_final: 0.7891 (mptt) REVERT: B 399 SER cc_start: 0.8553 (OUTLIER) cc_final: 0.8181 (p) REVERT: B 424 LYS cc_start: 0.7996 (tptt) cc_final: 0.7680 (tptt) REVERT: B 484 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6783 (pp20) outliers start: 18 outliers final: 9 residues processed: 103 average time/residue: 1.9620 time to fit residues: 213.4052 Evaluate side-chains 96 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 484 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.141431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113145 restraints weight = 7425.057| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.95 r_work: 0.3135 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6634 Z= 0.207 Angle : 0.531 5.629 9017 Z= 0.272 Chirality : 0.045 0.123 929 Planarity : 0.004 0.043 1172 Dihedral : 4.395 31.271 872 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.34 % Allowed : 13.29 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.29), residues: 786 helix: 0.31 (0.26), residues: 386 sheet: -0.31 (0.69), residues: 59 loop : -0.21 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 163 HIS 0.007 0.001 HIS A 241 PHE 0.016 0.002 PHE A 523 TYR 0.017 0.002 TYR A 385 ARG 0.008 0.001 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.04690 ( 280) hydrogen bonds : angle 4.85786 ( 789) metal coordination : bond 0.00210 ( 2) SS BOND : bond 0.00427 ( 7) SS BOND : angle 0.67511 ( 14) covalent geometry : bond 0.00488 ( 6625) covalent geometry : angle 0.53032 ( 9003) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6486 (mm-30) REVERT: A 60 GLN cc_start: 0.7135 (mm110) cc_final: 0.6700 (pt0) REVERT: A 160 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8008 (tm-30) REVERT: A 325 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7321 (tt0) REVERT: A 347 THR cc_start: 0.8582 (m) cc_final: 0.8317 (p) REVERT: A 534 LYS cc_start: 0.8383 (mmmt) cc_final: 0.7886 (mptt) REVERT: B 465 GLU cc_start: 0.8045 (tt0) cc_final: 0.7727 (tt0) REVERT: B 484 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6713 (pp20) REVERT: B 493 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.6610 (tm-30) outliers start: 30 outliers final: 14 residues processed: 109 average time/residue: 1.2309 time to fit residues: 140.9457 Evaluate side-chains 99 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.142287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.114162 restraints weight = 7402.285| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.95 r_work: 0.3138 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6634 Z= 0.168 Angle : 0.499 5.471 9017 Z= 0.256 Chirality : 0.043 0.123 929 Planarity : 0.004 0.050 1172 Dihedral : 4.331 31.366 872 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.32 % Allowed : 14.88 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.05 (0.30), residues: 786 helix: 0.37 (0.27), residues: 390 sheet: -0.29 (0.69), residues: 59 loop : -0.13 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.014 0.001 PHE A 523 TYR 0.016 0.001 TYR A 521 ARG 0.011 0.001 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 280) hydrogen bonds : angle 4.79469 ( 789) metal coordination : bond 0.00185 ( 2) SS BOND : bond 0.00364 ( 7) SS BOND : angle 0.64150 ( 14) covalent geometry : bond 0.00391 ( 6625) covalent geometry : angle 0.49848 ( 9003) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6494 (mm-30) REVERT: A 60 GLN cc_start: 0.7140 (mm110) cc_final: 0.6714 (pt0) REVERT: A 160 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8009 (tm-30) REVERT: A 313 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7472 (ttmt) REVERT: A 347 THR cc_start: 0.8591 (m) cc_final: 0.8333 (p) REVERT: A 456 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8021 (tt) REVERT: A 534 LYS cc_start: 0.8369 (mmmt) cc_final: 0.7882 (mptt) REVERT: B 399 SER cc_start: 0.8647 (OUTLIER) cc_final: 0.8246 (p) REVERT: B 465 GLU cc_start: 0.8044 (tt0) cc_final: 0.7722 (tt0) REVERT: B 484 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6721 (pp20) REVERT: B 493 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.6632 (tm-30) outliers start: 23 outliers final: 12 residues processed: 107 average time/residue: 1.2665 time to fit residues: 142.4148 Evaluate side-chains 101 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 47 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.143999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.115850 restraints weight = 7440.883| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.96 r_work: 0.3196 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6634 Z= 0.126 Angle : 0.471 5.398 9017 Z= 0.241 Chirality : 0.042 0.121 929 Planarity : 0.004 0.052 1172 Dihedral : 4.167 30.635 872 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.89 % Allowed : 15.61 % Favored : 81.50 % 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: 0.24 (0.30), residues: 786 helix: 0.63 (0.27), residues: 382 sheet: -0.30 (0.69), residues: 59 loop : -0.14 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 523 TYR 0.019 0.001 TYR A 521 ARG 0.011 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 280) hydrogen bonds : angle 4.65955 ( 789) metal coordination : bond 0.00113 ( 2) SS BOND : bond 0.00300 ( 7) SS BOND : angle 0.58760 ( 14) covalent geometry : bond 0.00287 ( 6625) covalent geometry : angle 0.47031 ( 9003) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6450 (mm-30) REVERT: A 60 GLN cc_start: 0.7142 (mm110) cc_final: 0.6718 (pt0) REVERT: A 156 LYS cc_start: 0.7890 (mptt) cc_final: 0.7137 (mmtt) REVERT: A 160 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: A 313 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7479 (ttmt) REVERT: A 347 THR cc_start: 0.8587 (m) cc_final: 0.8349 (p) REVERT: A 456 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8004 (tt) REVERT: A 470 LYS cc_start: 0.8381 (ptmt) cc_final: 0.8044 (ttpp) REVERT: A 534 LYS cc_start: 0.8359 (mmmt) cc_final: 0.7879 (mptt) REVERT: B 399 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.8246 (p) REVERT: B 465 GLU cc_start: 0.7992 (tt0) cc_final: 0.7675 (tt0) REVERT: B 484 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6726 (pp20) outliers start: 20 outliers final: 12 residues processed: 103 average time/residue: 1.2184 time to fit residues: 131.9267 Evaluate side-chains 98 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 58 optimal weight: 0.0040 chunk 26 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117224 restraints weight = 7460.480| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.97 r_work: 0.3193 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6634 Z= 0.108 Angle : 0.455 5.310 9017 Z= 0.233 Chirality : 0.041 0.121 929 Planarity : 0.004 0.058 1172 Dihedral : 4.050 30.786 872 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.03 % Allowed : 15.61 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.30), residues: 786 helix: 0.78 (0.27), residues: 382 sheet: -0.23 (0.69), residues: 59 loop : -0.07 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 369 TYR 0.011 0.001 TYR B 351 ARG 0.014 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 280) hydrogen bonds : angle 4.55275 ( 789) metal coordination : bond 0.00068 ( 2) SS BOND : bond 0.00248 ( 7) SS BOND : angle 0.50817 ( 14) covalent geometry : bond 0.00240 ( 6625) covalent geometry : angle 0.45466 ( 9003) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.720 Fit side-chains REVERT: A 30 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6415 (mm-30) REVERT: A 60 GLN cc_start: 0.7139 (mm110) cc_final: 0.6558 (pt0) REVERT: A 64 ILE cc_start: 0.7638 (mp) cc_final: 0.7328 (pp) REVERT: A 160 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: A 249 MET cc_start: 0.8181 (mtp) cc_final: 0.7759 (mtm) REVERT: A 313 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7410 (ttmt) REVERT: A 325 GLU cc_start: 0.8178 (tp30) cc_final: 0.7341 (tt0) REVERT: A 347 THR cc_start: 0.8573 (m) cc_final: 0.8344 (p) REVERT: A 456 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7992 (tt) REVERT: A 470 LYS cc_start: 0.8362 (ptmt) cc_final: 0.8051 (ttpp) REVERT: A 534 LYS cc_start: 0.8327 (mmmt) cc_final: 0.7857 (mptt) REVERT: B 347 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.6279 (t80) REVERT: B 399 SER cc_start: 0.8610 (OUTLIER) cc_final: 0.8039 (p) REVERT: B 484 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6768 (pp20) outliers start: 21 outliers final: 12 residues processed: 111 average time/residue: 1.0903 time to fit residues: 127.9563 Evaluate side-chains 103 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.143864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115849 restraints weight = 7436.563| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.96 r_work: 0.3179 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6634 Z= 0.135 Angle : 0.481 5.386 9017 Z= 0.247 Chirality : 0.042 0.122 929 Planarity : 0.004 0.063 1172 Dihedral : 4.152 30.979 872 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.03 % Allowed : 15.61 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.30), residues: 786 helix: 0.76 (0.27), residues: 382 sheet: -0.26 (0.68), residues: 59 loop : -0.08 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.014 0.001 PHE A 523 TYR 0.021 0.001 TYR B 351 ARG 0.014 0.001 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 280) hydrogen bonds : angle 4.61412 ( 789) metal coordination : bond 0.00116 ( 2) SS BOND : bond 0.00295 ( 7) SS BOND : angle 0.53688 ( 14) covalent geometry : bond 0.00311 ( 6625) covalent geometry : angle 0.48080 ( 9003) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.757 Fit side-chains REVERT: A 30 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6417 (mm-30) REVERT: A 60 GLN cc_start: 0.7120 (mm110) cc_final: 0.6671 (pt0) REVERT: A 160 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: A 249 MET cc_start: 0.8164 (mtp) cc_final: 0.7750 (mtm) REVERT: A 313 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7402 (ttmt) REVERT: A 347 THR cc_start: 0.8565 (m) cc_final: 0.8323 (p) REVERT: A 456 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7979 (tt) REVERT: A 470 LYS cc_start: 0.8383 (ptmt) cc_final: 0.8057 (ttpp) REVERT: A 534 LYS cc_start: 0.8336 (mmmt) cc_final: 0.7856 (mptt) REVERT: B 399 SER cc_start: 0.8623 (OUTLIER) cc_final: 0.8259 (p) REVERT: B 484 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6737 (pp20) outliers start: 21 outliers final: 12 residues processed: 102 average time/residue: 1.1741 time to fit residues: 126.4907 Evaluate side-chains 99 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 484 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.145469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117456 restraints weight = 7533.290| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.97 r_work: 0.3220 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6634 Z= 0.110 Angle : 0.463 5.311 9017 Z= 0.237 Chirality : 0.041 0.122 929 Planarity : 0.004 0.061 1172 Dihedral : 4.058 30.363 872 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.75 % Allowed : 15.75 % Favored : 81.50 % 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: 0.48 (0.30), residues: 786 helix: 0.85 (0.27), residues: 382 sheet: -0.23 (0.68), residues: 59 loop : -0.03 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 369 TYR 0.021 0.001 TYR B 351 ARG 0.014 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 280) hydrogen bonds : angle 4.54280 ( 789) metal coordination : bond 0.00053 ( 2) SS BOND : bond 0.00240 ( 7) SS BOND : angle 0.51602 ( 14) covalent geometry : bond 0.00244 ( 6625) covalent geometry : angle 0.46333 ( 9003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5692.10 seconds wall clock time: 99 minutes 26.72 seconds (5966.72 seconds total)