Starting phenix.real_space_refine on Wed Feb 12 09:37:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wa1_32379/02_2025/7wa1_32379.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wa1_32379/02_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_32379/02_2025/7wa1_32379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wa1_32379/02_2025/7wa1_32379.map" model { file = "/net/cci-nas-00/data/ceres_data/7wa1_32379/02_2025/7wa1_32379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wa1_32379/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.89, per 1000 atoms: 0.76 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: 1.50 Conformation dependent library (CDL) restraints added in 886.2 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: 0.79 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: 1.72 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.990 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.160 ------------------------------------------------------------------------------- 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 : 0.766 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: 1.1651 time to fit residues: 194.8243 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 : 0.723 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.147362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.119793 restraints weight = 7270.966| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.96 r_work: 0.3247 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.713 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6591 (mm-30) REVERT: A 31 LYS cc_start: 0.8043 (tppt) cc_final: 0.7372 (ttpt) REVERT: A 60 GLN cc_start: 0.7239 (mm110) cc_final: 0.6716 (tm-30) REVERT: A 74 GLU cc_start: 0.7565 (mt-10) cc_final: 0.6845 (mt-10) REVERT: A 156 LYS cc_start: 0.7413 (mptt) cc_final: 0.6942 (mmtt) REVERT: A 225 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7791 (t0) REVERT: A 347 THR cc_start: 0.8463 (m) cc_final: 0.8246 (p) REVERT: B 403 ARG cc_start: 0.8504 (ptm-80) cc_final: 0.8279 (ptm160) REVERT: B 484 GLU cc_start: 0.7135 (pp20) cc_final: 0.6849 (pp20) outliers start: 19 outliers final: 10 residues processed: 108 average time/residue: 1.2432 time to fit residues: 141.1120 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 : 0.762 ------------------------------------------------------------------------------- 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 42 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.146545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.118605 restraints weight = 7361.030| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.96 r_work: 0.3228 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6625 Z= 0.170 Angle : 0.465 5.564 9003 Z= 0.240 Chirality : 0.041 0.135 929 Planarity : 0.004 0.037 1172 Dihedral : 4.263 29.910 873 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.60 % Allowed : 13.58 % Favored : 83.82 % 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: -0.30 (0.25), residues: 386 sheet: -0.52 (0.65), residues: 58 loop : -0.31 (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 0.007 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 110 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6540 (mm-30) REVERT: A 31 LYS cc_start: 0.7905 (tppt) cc_final: 0.7294 (ttpt) REVERT: A 60 GLN cc_start: 0.7149 (mm110) cc_final: 0.6684 (pt0) REVERT: A 74 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7256 (mt-10) REVERT: A 156 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.6962 (mmtt) REVERT: A 347 THR cc_start: 0.8478 (m) cc_final: 0.8222 (p) REVERT: A 470 LYS cc_start: 0.8318 (ptmt) cc_final: 0.8041 (ttpp) REVERT: B 403 ARG cc_start: 0.8523 (ptm-80) cc_final: 0.8261 (ptm160) REVERT: B 484 GLU cc_start: 0.7120 (pp20) cc_final: 0.6866 (pp20) outliers start: 18 outliers final: 10 residues processed: 105 average time/residue: 1.2897 time to fit residues: 142.1899 Evaluate side-chains 97 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 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: 0.1980 chunk 67 optimal weight: 0.0370 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.147131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.119010 restraints weight = 7438.714| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.98 r_work: 0.3238 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6625 Z= 0.145 Angle : 0.448 5.365 9003 Z= 0.230 Chirality : 0.040 0.133 929 Planarity : 0.004 0.037 1172 Dihedral : 4.038 29.950 872 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.75 % Allowed : 13.73 % Favored : 83.53 % 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: -0.14 (0.29), residues: 786 helix: 0.12 (0.26), residues: 390 sheet: -0.45 (0.74), residues: 49 loop : -0.09 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.013 0.001 PHE A 369 TYR 0.013 0.001 TYR B 505 ARG 0.008 0.000 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 108 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.737 Fit side-chains REVERT: A 30 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6548 (mm-30) REVERT: A 31 LYS cc_start: 0.7945 (tppt) cc_final: 0.7387 (ttpp) REVERT: A 60 GLN cc_start: 0.7191 (mm110) cc_final: 0.6731 (pt0) REVERT: A 74 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7226 (mt-10) REVERT: A 160 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: A 347 THR cc_start: 0.8517 (m) cc_final: 0.8266 (p) REVERT: A 470 LYS cc_start: 0.8302 (ptmt) cc_final: 0.7993 (ttpp) REVERT: B 399 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8152 (p) REVERT: B 484 GLU cc_start: 0.7111 (pp20) cc_final: 0.6842 (pp20) outliers start: 19 outliers final: 8 residues processed: 104 average time/residue: 1.2997 time to fit residues: 141.9900 Evaluate side-chains 92 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 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 A 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.117208 restraints weight = 7372.488| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.97 r_work: 0.3206 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6625 Z= 0.186 Angle : 0.468 6.149 9003 Z= 0.238 Chirality : 0.041 0.121 929 Planarity : 0.004 0.039 1172 Dihedral : 4.059 30.242 872 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.03 % Allowed : 14.31 % Favored : 82.66 % 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: 0.10 (0.30), residues: 786 helix: 0.40 (0.27), residues: 388 sheet: -0.21 (0.69), residues: 59 loop : -0.10 (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 0.018 0.001 TYR A 521 ARG 0.010 0.001 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 109 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6469 (mm-30) REVERT: A 60 GLN cc_start: 0.7168 (mm110) cc_final: 0.6693 (pt0) REVERT: A 74 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7120 (mt-10) REVERT: A 156 LYS cc_start: 0.7667 (mptt) cc_final: 0.7109 (mmtt) REVERT: A 160 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: A 347 THR cc_start: 0.8539 (m) cc_final: 0.8281 (p) REVERT: A 470 LYS cc_start: 0.8312 (ptmt) cc_final: 0.8007 (ttpp) REVERT: A 534 LYS cc_start: 0.8310 (mmmt) cc_final: 0.7842 (mptt) REVERT: B 399 SER cc_start: 0.8598 (OUTLIER) cc_final: 0.8185 (p) REVERT: B 424 LYS cc_start: 0.7969 (tptt) cc_final: 0.7630 (tptt) REVERT: B 484 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6775 (pp20) REVERT: B 493 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.6353 (tm-30) outliers start: 21 outliers final: 11 residues processed: 105 average time/residue: 1.2430 time to fit residues: 137.3413 Evaluate side-chains 95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 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 33 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 12 optimal weight: 0.0770 chunk 24 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 59 optimal weight: 0.0270 chunk 67 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.146951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.119023 restraints weight = 7339.728| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.95 r_work: 0.3241 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6625 Z= 0.141 Angle : 0.445 5.324 9003 Z= 0.227 Chirality : 0.040 0.122 929 Planarity : 0.004 0.043 1172 Dihedral : 3.930 29.677 872 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.89 % Allowed : 15.03 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.30), residues: 786 helix: 0.61 (0.27), residues: 388 sheet: -0.03 (0.79), residues: 49 loop : -0.01 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.012 0.001 PHE A 523 TYR 0.022 0.001 TYR A 521 ARG 0.011 0.000 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: 20 poor density : 87 time to evaluate : 0.710 Fit side-chains REVERT: A 30 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6445 (mm-30) REVERT: A 60 GLN cc_start: 0.7181 (mm110) cc_final: 0.6563 (pt0) REVERT: A 64 ILE cc_start: 0.7652 (mp) cc_final: 0.7328 (pp) REVERT: A 74 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7022 (mt-10) REVERT: A 156 LYS cc_start: 0.7655 (mptt) cc_final: 0.7112 (mmtt) REVERT: A 160 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: A 347 THR cc_start: 0.8516 (m) cc_final: 0.8282 (p) REVERT: A 470 LYS cc_start: 0.8264 (ptmt) cc_final: 0.7990 (ttpp) REVERT: A 534 LYS cc_start: 0.8301 (mmmt) cc_final: 0.7834 (mptt) REVERT: B 399 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8211 (p) REVERT: B 424 LYS cc_start: 0.7977 (tptt) cc_final: 0.7643 (tptt) REVERT: B 484 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6783 (pp20) outliers start: 20 outliers final: 9 residues processed: 102 average time/residue: 1.3645 time to fit residues: 146.0485 Evaluate side-chains 93 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 334 THR Chi-restraints excluded: chain A residue 409 SER 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 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: 2.9990 chunk 40 optimal weight: 0.0270 chunk 13 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 overall best weight: 1.0244 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.143553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.115564 restraints weight = 7398.024| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.96 r_work: 0.3168 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6625 Z= 0.239 Angle : 0.497 5.444 9003 Z= 0.253 Chirality : 0.043 0.133 929 Planarity : 0.004 0.052 1172 Dihedral : 4.158 31.339 872 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.47 % Allowed : 14.88 % Favored : 81.65 % 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: 0.23 (0.30), residues: 786 helix: 0.57 (0.27), residues: 388 sheet: -0.28 (0.69), residues: 59 loop : -0.08 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.015 0.001 PHE A 523 TYR 0.022 0.001 TYR B 505 ARG 0.012 0.001 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 114 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6456 (mm-30) REVERT: A 60 GLN cc_start: 0.7126 (mm110) cc_final: 0.6688 (pt0) REVERT: A 160 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: A 313 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7526 (ttmt) REVERT: A 347 THR cc_start: 0.8592 (m) cc_final: 0.8340 (p) REVERT: A 470 LYS cc_start: 0.8379 (ptmt) cc_final: 0.8049 (ttpp) REVERT: A 534 LYS cc_start: 0.8334 (mmmt) cc_final: 0.7855 (mptt) REVERT: B 347 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.6249 (t80) REVERT: B 399 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8012 (p) REVERT: B 453 TYR cc_start: 0.8896 (p90) cc_final: 0.8602 (p90) REVERT: B 484 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6787 (pp20) REVERT: B 493 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.6651 (tm-30) outliers start: 24 outliers final: 12 residues processed: 108 average time/residue: 1.2929 time to fit residues: 146.6621 Evaluate side-chains 102 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 294 THR 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 47 optimal weight: 0.0370 chunk 45 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.145008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117131 restraints weight = 7417.775| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.96 r_work: 0.3216 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6625 Z= 0.176 Angle : 0.470 5.348 9003 Z= 0.240 Chirality : 0.041 0.129 929 Planarity : 0.004 0.054 1172 Dihedral : 4.043 30.500 872 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.61 % Allowed : 15.17 % Favored : 81.21 % 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: 0.39 (0.30), residues: 786 helix: 0.74 (0.27), residues: 382 sheet: -0.22 (0.76), residues: 49 loop : -0.05 (0.33), residues: 355 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 0.024 0.001 TYR B 505 ARG 0.012 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 113 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6483 (mm-30) REVERT: A 60 GLN cc_start: 0.7158 (mm110) cc_final: 0.6728 (pt0) REVERT: A 160 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: A 313 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7608 (ttmt) REVERT: A 347 THR cc_start: 0.8620 (m) cc_final: 0.8393 (p) REVERT: A 470 LYS cc_start: 0.8383 (ptmt) cc_final: 0.8068 (ttpp) REVERT: A 534 LYS cc_start: 0.8342 (mmmt) cc_final: 0.7893 (mptt) REVERT: B 347 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.6294 (t80) REVERT: B 399 SER cc_start: 0.8617 (OUTLIER) cc_final: 0.8064 (p) REVERT: B 453 TYR cc_start: 0.8863 (p90) cc_final: 0.8654 (p90) REVERT: B 484 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6812 (pp20) REVERT: B 493 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.6862 (tm-30) outliers start: 25 outliers final: 12 residues processed: 106 average time/residue: 1.2146 time to fit residues: 135.4443 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 : 0.781 ------------------------------------------------------------------------------- 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 364 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.0980 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 0.0020 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.145423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.117563 restraints weight = 7458.309| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.97 r_work: 0.3199 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2848 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= 0.167 Angle : 0.470 5.357 9003 Z= 0.239 Chirality : 0.041 0.126 929 Planarity : 0.004 0.057 1172 Dihedral : 4.018 30.564 872 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.89 % Allowed : 15.90 % Favored : 81.21 % 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: 0.47 (0.30), residues: 786 helix: 0.81 (0.27), residues: 382 sheet: -0.23 (0.75), residues: 49 loop : -0.01 (0.33), residues: 355 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 523 TYR 0.025 0.001 TYR B 505 ARG 0.014 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: 20 poor density : 87 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6413 (mm-30) REVERT: A 60 GLN cc_start: 0.7107 (mm110) cc_final: 0.6509 (pt0) REVERT: A 64 ILE cc_start: 0.7614 (mp) cc_final: 0.7289 (pp) REVERT: A 160 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: A 313 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7522 (ttmt) REVERT: A 347 THR cc_start: 0.8581 (m) cc_final: 0.8339 (p) REVERT: A 470 LYS cc_start: 0.8356 (ptmt) cc_final: 0.8049 (ttpp) REVERT: A 534 LYS cc_start: 0.8311 (mmmt) cc_final: 0.7833 (mptt) REVERT: B 347 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.6239 (t80) REVERT: B 399 SER cc_start: 0.8619 (OUTLIER) cc_final: 0.8022 (p) REVERT: B 453 TYR cc_start: 0.8831 (p90) cc_final: 0.8602 (p90) REVERT: B 484 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6772 (pp20) REVERT: B 493 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.6928 (tm-30) outliers start: 20 outliers final: 12 residues processed: 101 average time/residue: 1.2622 time to fit residues: 134.0465 Evaluate side-chains 102 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 364 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.144153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.116286 restraints weight = 7442.669| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.96 r_work: 0.3202 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2884 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= 0.209 Angle : 0.493 5.366 9003 Z= 0.251 Chirality : 0.042 0.128 929 Planarity : 0.004 0.063 1172 Dihedral : 4.107 31.014 872 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.89 % Allowed : 15.90 % Favored : 81.21 % 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: 0.77 (0.27), residues: 382 sheet: -0.32 (0.68), residues: 59 loop : -0.05 (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 0.027 0.001 TYR B 505 ARG 0.014 0.001 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 106 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.783 Fit side-chains REVERT: A 30 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6419 (mm-30) REVERT: A 60 GLN cc_start: 0.7121 (mm110) cc_final: 0.6693 (pt0) REVERT: A 160 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7936 (tm-30) REVERT: A 313 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7507 (ttmt) REVERT: A 347 THR cc_start: 0.8591 (m) cc_final: 0.8343 (p) REVERT: A 470 LYS cc_start: 0.8389 (ptmt) cc_final: 0.8070 (ttpp) REVERT: A 534 LYS cc_start: 0.8332 (mmmt) cc_final: 0.7858 (mptt) REVERT: B 399 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.8250 (p) REVERT: B 453 TYR cc_start: 0.8863 (p90) cc_final: 0.8656 (p90) REVERT: B 484 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6779 (pp20) outliers start: 20 outliers final: 11 residues processed: 101 average time/residue: 1.2540 time to fit residues: 133.6383 Evaluate side-chains 100 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 0.0370 chunk 73 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.144935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117104 restraints weight = 7561.111| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.97 r_work: 0.3190 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 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 0.031 6625 Z= 0.178 Angle : 0.477 5.353 9003 Z= 0.243 Chirality : 0.041 0.127 929 Planarity : 0.004 0.062 1172 Dihedral : 4.056 30.690 872 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.17 % Allowed : 16.33 % 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: 0.83 (0.27), residues: 382 sheet: -0.30 (0.68), residues: 59 loop : 0.00 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 523 TYR 0.025 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: 5011.59 seconds wall clock time: 89 minutes 11.20 seconds (5351.20 seconds total)