Starting phenix.real_space_refine on Sat Dec 28 04:13:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wa1_32379/12_2024/7wa1_32379.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wa1_32379/12_2024/7wa1_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_32379/12_2024/7wa1_32379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wa1_32379/12_2024/7wa1_32379.map" model { file = "/net/cci-nas-00/data/ceres_data/7wa1_32379/12_2024/7wa1_32379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wa1_32379/12_2024/7wa1_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 4.62, per 1000 atoms: 0.72 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: 1.66 Conformation dependent library (CDL) restraints added in 874.5 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: 0.69 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: 2.00 Time building geometry restraints manager: 1.94 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.370 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.500 ------------------------------------------------------------------------------- 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 : 0.003 0.045 6625 Z= 0.192 Angle : 0.575 7.316 9003 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 *********************** 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 : 0.745 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: 1.1541 time to fit residues: 193.3132 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 : 0.812 ------------------------------------------------------------------------------- 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: 0.0570 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 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: 0.6498 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6625 Z= 0.184 Angle : 0.497 5.452 9003 Z= 0.260 Chirality : 0.041 0.134 929 Planarity : 0.005 0.048 1172 Dihedral : 4.576 28.882 875 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.75 % Allowed : 11.56 % 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: -1.39 (0.27), residues: 786 helix: -1.18 (0.23), residues: 378 sheet: -0.68 (0.64), residues: 58 loop : -0.43 (0.32), residues: 350 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 0.012 0.001 PHE A 369 TYR 0.017 0.001 TYR B 351 ARG 0.007 0.001 ARG A 113 *********************** 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 115 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6454 (mm-30) REVERT: A 31 LYS cc_start: 0.7941 (tppt) cc_final: 0.7493 (ttpt) REVERT: A 74 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6714 (mt-10) REVERT: A 156 LYS cc_start: 0.7422 (mptt) cc_final: 0.7077 (mmtt) REVERT: A 225 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7314 (t0) REVERT: B 403 ARG cc_start: 0.8325 (ptm-80) cc_final: 0.8090 (ptm160) REVERT: B 484 GLU cc_start: 0.7340 (pp20) cc_final: 0.7128 (pp20) outliers start: 19 outliers final: 10 residues processed: 108 average time/residue: 1.2617 time to fit residues: 143.6149 Evaluate side-chains 96 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 225 ASP 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 39 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 0.0870 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6625 Z= 0.175 Angle : 0.468 5.720 9003 Z= 0.242 Chirality : 0.041 0.136 929 Planarity : 0.004 0.036 1172 Dihedral : 4.253 30.128 873 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.32 % Allowed : 13.29 % 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: -0.59 (0.29), residues: 786 helix: -0.27 (0.26), residues: 387 sheet: -0.63 (0.65), residues: 59 loop : -0.28 (0.33), residues: 340 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 0.006 0.000 ARG A 113 *********************** 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 114 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6457 (mm-30) REVERT: A 31 LYS cc_start: 0.7863 (tppt) cc_final: 0.7481 (ttpp) REVERT: A 156 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7181 (mmtt) REVERT: B 399 SER cc_start: 0.8203 (OUTLIER) cc_final: 0.7889 (p) REVERT: B 403 ARG cc_start: 0.8375 (ptm-80) cc_final: 0.8169 (ptm160) REVERT: B 484 GLU cc_start: 0.7340 (pp20) cc_final: 0.7130 (pp20) outliers start: 23 outliers final: 10 residues processed: 108 average time/residue: 1.4423 time to fit residues: 163.6557 Evaluate side-chains 96 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 156 LYS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 THR 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 36 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6625 Z= 0.217 Angle : 0.485 5.450 9003 Z= 0.250 Chirality : 0.042 0.134 929 Planarity : 0.004 0.037 1172 Dihedral : 4.225 30.113 872 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.89 % Allowed : 14.31 % Favored : 82.80 % 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: 388 sheet: -0.56 (0.66), residues: 59 loop : -0.22 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 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 0.009 0.001 ARG A 113 *********************** 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 105 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.698 Fit side-chains REVERT: A 30 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6426 (mm-30) REVERT: A 31 LYS cc_start: 0.7860 (tppt) cc_final: 0.7475 (ttpp) REVERT: A 325 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6778 (tt0) REVERT: A 534 LYS cc_start: 0.8213 (mmmt) cc_final: 0.8004 (mptt) REVERT: B 399 SER cc_start: 0.8310 (OUTLIER) cc_final: 0.7990 (p) REVERT: B 424 LYS cc_start: 0.7962 (tptt) cc_final: 0.7672 (tptt) REVERT: B 484 GLU cc_start: 0.7331 (pp20) cc_final: 0.7101 (pp20) outliers start: 20 outliers final: 11 residues processed: 100 average time/residue: 1.2975 time to fit residues: 136.6067 Evaluate side-chains 91 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 364 VAL 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 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 1 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.0010 chunk 67 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6625 Z= 0.177 Angle : 0.470 6.518 9003 Z= 0.239 Chirality : 0.041 0.122 929 Planarity : 0.004 0.040 1172 Dihedral : 4.101 29.863 872 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.05 % Allowed : 13.58 % 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: 0.01 (0.30), residues: 786 helix: 0.36 (0.27), residues: 388 sheet: -0.38 (0.68), residues: 59 loop : -0.16 (0.33), residues: 339 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 0.013 0.001 PHE A 523 TYR 0.014 0.001 TYR A 521 ARG 0.010 0.000 ARG A 113 *********************** 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 114 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6397 (mm-30) REVERT: A 31 LYS cc_start: 0.7841 (tppt) cc_final: 0.7474 (ttpp) REVERT: A 325 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6795 (tt0) REVERT: B 347 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.6531 (t80) REVERT: B 399 SER cc_start: 0.8295 (OUTLIER) cc_final: 0.7823 (p) REVERT: B 424 LYS cc_start: 0.7965 (tptt) cc_final: 0.7662 (tptt) REVERT: B 484 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7089 (pp20) REVERT: B 493 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.6409 (tm-30) outliers start: 28 outliers final: 11 residues processed: 108 average time/residue: 1.3756 time to fit residues: 156.6967 Evaluate side-chains 97 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 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 B residue 347 PHE Chi-restraints excluded: chain B residue 356 LYS 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 Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6625 Z= 0.282 Angle : 0.517 5.466 9003 Z= 0.264 Chirality : 0.044 0.122 929 Planarity : 0.004 0.045 1172 Dihedral : 4.308 31.218 872 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.03 % Allowed : 15.46 % 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: 0.00 (0.30), residues: 786 helix: 0.34 (0.27), residues: 390 sheet: -0.40 (0.69), residues: 59 loop : -0.14 (0.33), residues: 337 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 0.015 0.002 PHE A 523 TYR 0.020 0.001 TYR A 521 ARG 0.010 0.001 ARG A 113 *********************** 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 107 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.694 Fit side-chains REVERT: A 30 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6404 (mm-30) REVERT: A 60 GLN cc_start: 0.7602 (tm-30) cc_final: 0.7323 (pt0) REVERT: A 98 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6433 (tmm-80) REVERT: B 399 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.8045 (p) REVERT: B 484 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7066 (pp20) REVERT: B 493 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.6415 (tm-30) outliers start: 21 outliers final: 11 residues processed: 102 average time/residue: 1.3841 time to fit residues: 148.8179 Evaluate side-chains 94 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 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 356 LYS 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 55 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6625 Z= 0.216 Angle : 0.487 5.402 9003 Z= 0.249 Chirality : 0.042 0.130 929 Planarity : 0.004 0.051 1172 Dihedral : 4.213 30.908 872 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.18 % Allowed : 16.04 % Favored : 80.78 % 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: 0.11 (0.30), residues: 786 helix: 0.46 (0.27), residues: 389 sheet: -0.47 (0.68), residues: 59 loop : -0.11 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.014 0.001 PHE A 523 TYR 0.018 0.001 TYR A 521 ARG 0.012 0.000 ARG A 113 *********************** 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 108 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.767 Fit side-chains REVERT: A 30 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6376 (mm-30) REVERT: A 60 GLN cc_start: 0.7564 (tm-30) cc_final: 0.7293 (pt0) REVERT: A 160 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: A 470 LYS cc_start: 0.8124 (ttmt) cc_final: 0.7906 (ttmm) REVERT: B 347 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.6666 (t80) REVERT: B 399 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.7883 (p) REVERT: B 424 LYS cc_start: 0.8015 (tmtm) cc_final: 0.7799 (tptt) REVERT: B 484 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.7068 (pp20) outliers start: 22 outliers final: 13 residues processed: 103 average time/residue: 1.2445 time to fit residues: 134.8897 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 : 0.661 ------------------------------------------------------------------------------- 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 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 356 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6625 Z= 0.198 Angle : 0.484 5.375 9003 Z= 0.247 Chirality : 0.042 0.125 929 Planarity : 0.004 0.054 1172 Dihedral : 4.165 30.876 872 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.75 % Allowed : 16.33 % Favored : 80.92 % 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: 0.18 (0.30), residues: 786 helix: 0.55 (0.27), residues: 388 sheet: -0.49 (0.68), residues: 59 loop : -0.09 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.014 0.001 PHE A 523 TYR 0.022 0.001 TYR A 521 ARG 0.013 0.000 ARG A 113 *********************** 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 102 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6345 (mm-30) REVERT: A 60 GLN cc_start: 0.7553 (tm-30) cc_final: 0.7282 (pt0) REVERT: B 347 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.6665 (t80) REVERT: B 399 SER cc_start: 0.8335 (OUTLIER) cc_final: 0.7886 (p) REVERT: B 484 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.7072 (pp20) outliers start: 19 outliers final: 13 residues processed: 98 average time/residue: 1.3787 time to fit residues: 142.3428 Evaluate side-chains 95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 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 A residue 471 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 356 LYS 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 30 optimal weight: 0.0570 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6625 Z= 0.177 Angle : 0.476 5.332 9003 Z= 0.243 Chirality : 0.041 0.126 929 Planarity : 0.004 0.056 1172 Dihedral : 4.095 30.846 872 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.61 % Allowed : 15.46 % Favored : 80.92 % 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: 0.28 (0.30), residues: 786 helix: 0.69 (0.27), residues: 382 sheet: -0.43 (0.68), residues: 59 loop : -0.12 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 523 TYR 0.021 0.001 TYR A 521 ARG 0.013 0.000 ARG A 113 *********************** 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 107 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6324 (mm-30) REVERT: A 60 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7125 (pt0) REVERT: A 64 ILE cc_start: 0.7786 (mp) cc_final: 0.7501 (pp) REVERT: B 347 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.6672 (t80) REVERT: B 399 SER cc_start: 0.8323 (OUTLIER) cc_final: 0.7891 (p) REVERT: B 484 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7070 (pp20) outliers start: 25 outliers final: 12 residues processed: 101 average time/residue: 1.1879 time to fit residues: 126.4823 Evaluate side-chains 94 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 347 PHE Chi-restraints excluded: chain B residue 356 LYS 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 77 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.0470 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6625 Z= 0.190 Angle : 0.483 5.351 9003 Z= 0.246 Chirality : 0.042 0.126 929 Planarity : 0.004 0.061 1172 Dihedral : 4.111 30.841 872 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.17 % Allowed : 16.76 % Favored : 81.07 % 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: 0.31 (0.30), residues: 786 helix: 0.72 (0.27), residues: 382 sheet: -0.44 (0.68), residues: 59 loop : -0.12 (0.33), 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 0.014 0.001 PHE A 523 TYR 0.022 0.001 TYR A 521 ARG 0.014 0.000 ARG A 113 ********************** 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 93 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6328 (mm-30) REVERT: A 60 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7275 (pt0) REVERT: A 249 MET cc_start: 0.8116 (mtp) cc_final: 0.7801 (mtm) REVERT: B 347 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.6664 (t80) REVERT: B 399 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.7892 (p) REVERT: B 484 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.7072 (pp20) outliers start: 15 outliers final: 11 residues processed: 89 average time/residue: 1.2258 time to fit residues: 115.6876 Evaluate side-chains 91 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 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 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 17 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 0.0370 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.144264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116324 restraints weight = 7318.754| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.94 r_work: 0.3195 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6625 Z= 0.185 Angle : 0.479 5.324 9003 Z= 0.244 Chirality : 0.042 0.126 929 Planarity : 0.004 0.062 1172 Dihedral : 4.097 30.735 872 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.31 % Allowed : 16.76 % Favored : 80.92 % 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: 0.34 (0.30), residues: 786 helix: 0.75 (0.27), residues: 382 sheet: -0.44 (0.67), residues: 59 loop : -0.10 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 523 TYR 0.012 0.001 TYR B 505 ARG 0.014 0.000 ARG A 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3164.78 seconds wall clock time: 58 minutes 13.83 seconds (3493.83 seconds total)