Starting phenix.real_space_refine on Wed Mar 12 09:39:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wa1_32379/03_2025/7wa1_32379.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wa1_32379/03_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_32379/03_2025/7wa1_32379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wa1_32379/03_2025/7wa1_32379.map" model { file = "/net/cci-nas-00/data/ceres_data/7wa1_32379/03_2025/7wa1_32379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wa1_32379/03_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-5624/modules/chem_data/mon_lib" Total number of atoms: 6440 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4899 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 30, 'TRANS': 564} Chain: "B" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1540 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.71, per 1000 atoms: 0.73 Number of scatterers: 6440 At special positions: 0 Unit cell: (70.914, 86.97, 121.089, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1206 8.00 N 1080 7.00 C 4116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.77 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: 2.01 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: 3.030 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.080 Find NCS groups from input model: 0.060 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:15.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.280 ------------------------------------------------------------------------------- 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 : 0.737 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: 1.1712 time to fit residues: 196.0320 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 : 0.664 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.119751 restraints weight = 7270.989| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.97 r_work: 0.3236 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 116 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6544 (mm-30) REVERT: A 31 LYS cc_start: 0.8010 (tppt) cc_final: 0.7319 (ttpt) REVERT: A 60 GLN cc_start: 0.7210 (mm110) cc_final: 0.6671 (tm-30) REVERT: A 74 GLU cc_start: 0.7549 (mt-10) cc_final: 0.6824 (mt-10) REVERT: A 156 LYS cc_start: 0.7388 (mptt) cc_final: 0.6908 (mmtt) REVERT: A 160 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7985 (tm-30) REVERT: A 225 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7772 (t0) REVERT: A 347 THR cc_start: 0.8432 (m) cc_final: 0.8205 (p) REVERT: B 403 ARG cc_start: 0.8481 (ptm-80) cc_final: 0.8253 (ptm160) REVERT: B 484 GLU cc_start: 0.7112 (pp20) cc_final: 0.6820 (pp20) outliers start: 19 outliers final: 10 residues processed: 109 average time/residue: 1.2847 time to fit residues: 147.1989 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 : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 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: 0.8980 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 89 GLN A 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.144894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116728 restraints weight = 7376.232| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.96 r_work: 0.3206 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2317 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= 0.204 Angle : 0.483 5.957 9003 Z= 0.250 Chirality : 0.042 0.136 929 Planarity : 0.004 0.036 1172 Dihedral : 4.348 30.249 873 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.61 % Allowed : 12.43 % Favored : 83.96 % 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: -0.66 (0.29), residues: 786 helix: -0.33 (0.25), residues: 387 sheet: -0.65 (0.65), residues: 59 loop : -0.31 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 369 TYR 0.016 0.001 TYR A 521 ARG 0.006 0.001 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: 25 poor density : 89 time to evaluate : 0.706 Fit side-chains REVERT: A 30 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6550 (mm-30) REVERT: A 31 LYS cc_start: 0.7933 (tppt) cc_final: 0.7362 (ttpp) REVERT: A 60 GLN cc_start: 0.7190 (mm110) cc_final: 0.6724 (pt0) REVERT: A 74 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7293 (mt-10) REVERT: A 156 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7137 (mmtt) REVERT: A 160 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.8027 (tm-30) REVERT: A 347 THR cc_start: 0.8563 (m) cc_final: 0.8292 (p) REVERT: A 470 LYS cc_start: 0.8370 (ptmt) cc_final: 0.8025 (ttpp) REVERT: A 534 LYS cc_start: 0.8333 (mmmt) cc_final: 0.7873 (mptt) REVERT: B 399 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.8121 (p) REVERT: B 403 ARG cc_start: 0.8566 (ptm-80) cc_final: 0.8358 (ptm160) REVERT: B 484 GLU cc_start: 0.7086 (pp20) cc_final: 0.6777 (pp20) outliers start: 25 outliers final: 11 residues processed: 107 average time/residue: 1.3850 time to fit residues: 155.5662 Evaluate side-chains 98 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 160 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 364 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 Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.0970 chunk 63 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.146303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118139 restraints weight = 7452.894| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.97 r_work: 0.3203 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6625 Z= 0.150 Angle : 0.452 5.369 9003 Z= 0.232 Chirality : 0.041 0.133 929 Planarity : 0.004 0.037 1172 Dihedral : 4.100 29.866 872 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.46 % Allowed : 14.02 % 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: -0.20 (0.29), residues: 786 helix: 0.15 (0.26), residues: 388 sheet: -0.50 (0.67), residues: 59 loop : -0.21 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 369 TYR 0.019 0.001 TYR A 521 ARG 0.009 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 103 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.756 Fit side-chains REVERT: A 30 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6495 (mm-30) REVERT: A 31 LYS cc_start: 0.7913 (tppt) cc_final: 0.7294 (ttpp) REVERT: A 60 GLN cc_start: 0.7182 (mm110) cc_final: 0.6701 (pt0) REVERT: A 74 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7196 (mt-10) REVERT: A 160 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: A 325 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: A 347 THR cc_start: 0.8513 (m) cc_final: 0.8259 (p) REVERT: A 455 MET cc_start: 0.8451 (tmt) cc_final: 0.8141 (tmt) REVERT: A 470 LYS cc_start: 0.8342 (ptmt) cc_final: 0.8047 (ttpp) REVERT: A 534 LYS cc_start: 0.8304 (mmmt) cc_final: 0.7811 (mptt) REVERT: B 399 SER cc_start: 0.8567 (OUTLIER) cc_final: 0.8164 (p) REVERT: B 484 GLU cc_start: 0.7098 (pp20) cc_final: 0.6811 (pp20) outliers start: 17 outliers final: 8 residues processed: 98 average time/residue: 1.2452 time to fit residues: 128.4004 Evaluate side-chains 90 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 325 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR 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: 3.9990 chunk 66 optimal weight: 0.0980 chunk 54 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 0.0170 chunk 73 optimal weight: 0.9980 overall best weight: 0.3818 ------------------------------------------------------------------------------- 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 = 0.147164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.119160 restraints weight = 7345.810| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.96 r_work: 0.3230 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6625 Z= 0.135 Angle : 0.445 6.416 9003 Z= 0.227 Chirality : 0.040 0.121 929 Planarity : 0.004 0.041 1172 Dihedral : 3.950 30.042 872 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.03 % Allowed : 14.02 % Favored : 82.95 % 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: 0.19 (0.30), residues: 786 helix: 0.47 (0.27), residues: 388 sheet: -0.12 (0.77), residues: 49 loop : -0.06 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.013 0.001 PHE A 369 TYR 0.015 0.001 TYR A 521 ARG 0.011 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 113 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6438 (mm-30) REVERT: A 60 GLN cc_start: 0.7175 (mm110) cc_final: 0.6549 (pt0) REVERT: A 64 ILE cc_start: 0.7648 (mp) cc_final: 0.7315 (pp) REVERT: A 74 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7039 (mt-10) REVERT: A 156 LYS cc_start: 0.7620 (mptt) cc_final: 0.7110 (mmtt) REVERT: A 160 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: A 347 THR cc_start: 0.8494 (m) cc_final: 0.8246 (p) REVERT: A 455 MET cc_start: 0.8439 (tmt) cc_final: 0.8204 (tmt) REVERT: A 470 LYS cc_start: 0.8285 (ptmt) cc_final: 0.7999 (ttpp) REVERT: A 534 LYS cc_start: 0.8297 (mmmt) cc_final: 0.7826 (mptt) REVERT: B 399 SER cc_start: 0.8559 (OUTLIER) cc_final: 0.8167 (p) REVERT: B 424 LYS cc_start: 0.7955 (tptt) cc_final: 0.7627 (tptt) REVERT: B 484 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6773 (pp20) outliers start: 21 outliers final: 10 residues processed: 108 average time/residue: 1.6714 time to fit residues: 189.4526 Evaluate side-chains 95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 356 LYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 484 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 0.0040 chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 59 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.7994 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.144915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116894 restraints weight = 7375.607| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.95 r_work: 0.3188 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2654 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= 0.199 Angle : 0.471 5.376 9003 Z= 0.240 Chirality : 0.042 0.121 929 Planarity : 0.004 0.048 1172 Dihedral : 4.013 30.434 871 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.32 % Allowed : 14.74 % Favored : 81.94 % 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: 0.56 (0.27), residues: 388 sheet: -0.11 (0.78), residues: 49 loop : -0.03 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.014 0.001 PHE A 523 TYR 0.018 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: 23 poor density : 84 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6417 (mm-30) REVERT: A 60 GLN cc_start: 0.7156 (mm110) cc_final: 0.6669 (pt0) REVERT: A 74 GLU cc_start: 0.7271 (mt-10) cc_final: 0.7008 (mt-10) REVERT: A 160 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: A 347 THR cc_start: 0.8542 (m) cc_final: 0.8289 (p) REVERT: A 470 LYS cc_start: 0.8355 (ptmt) cc_final: 0.8055 (ttpp) REVERT: A 534 LYS cc_start: 0.8319 (mmmt) cc_final: 0.7843 (mptt) REVERT: B 347 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.6230 (t80) REVERT: B 399 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.7994 (p) REVERT: B 424 LYS cc_start: 0.8001 (tptt) cc_final: 0.7650 (tptt) REVERT: B 484 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6769 (pp20) REVERT: B 493 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.6769 (tm-30) outliers start: 23 outliers final: 12 residues processed: 103 average time/residue: 1.6799 time to fit residues: 182.2669 Evaluate side-chains 96 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 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 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 493 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.141975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.113723 restraints weight = 7411.354| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.95 r_work: 0.3154 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6625 Z= 0.297 Angle : 0.526 5.561 9003 Z= 0.269 Chirality : 0.044 0.127 929 Planarity : 0.004 0.050 1172 Dihedral : 4.302 31.908 871 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.47 % Allowed : 14.60 % Favored : 81.94 % 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: 0.07 (0.30), residues: 786 helix: 0.43 (0.27), residues: 386 sheet: -0.35 (0.68), residues: 59 loop : -0.15 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 163 HIS 0.007 0.001 HIS A 241 PHE 0.015 0.002 PHE A 523 TYR 0.018 0.002 TYR A 521 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 106 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.753 Fit side-chains REVERT: A 30 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6442 (mm-30) REVERT: A 60 GLN cc_start: 0.7144 (mm110) cc_final: 0.6715 (pt0) REVERT: A 160 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: A 313 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7478 (ttmt) REVERT: A 347 THR cc_start: 0.8592 (m) cc_final: 0.8337 (p) REVERT: A 534 LYS cc_start: 0.8369 (mmmt) cc_final: 0.7882 (mptt) REVERT: B 399 SER cc_start: 0.8646 (OUTLIER) cc_final: 0.8246 (p) REVERT: B 484 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6757 (pp20) REVERT: B 493 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.6743 (tm-30) outliers start: 24 outliers final: 15 residues processed: 100 average time/residue: 1.2776 time to fit residues: 134.0789 Evaluate side-chains 98 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 518 ARG 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 493 GLN Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 54 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 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.144404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116391 restraints weight = 7438.354| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.96 r_work: 0.3204 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6625 Z= 0.173 Angle : 0.467 5.330 9003 Z= 0.239 Chirality : 0.041 0.124 929 Planarity : 0.004 0.053 1172 Dihedral : 4.078 30.329 871 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.89 % Allowed : 15.17 % Favored : 81.94 % 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: 0.29 (0.30), residues: 786 helix: 0.61 (0.27), residues: 388 sheet: -0.37 (0.68), residues: 59 loop : -0.03 (0.34), residues: 339 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 0.019 0.001 TYR A 521 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 104 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6424 (mm-30) REVERT: A 60 GLN cc_start: 0.7122 (mm110) cc_final: 0.6693 (pt0) REVERT: A 160 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: A 313 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7470 (ttmt) REVERT: A 347 THR cc_start: 0.8563 (m) cc_final: 0.8323 (p) REVERT: A 470 LYS cc_start: 0.8375 (ptmt) cc_final: 0.8033 (ttpp) REVERT: A 534 LYS cc_start: 0.8319 (mmmt) cc_final: 0.7838 (mptt) REVERT: B 399 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8230 (p) REVERT: B 484 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6747 (pp20) outliers start: 20 outliers final: 14 residues processed: 100 average time/residue: 1.2496 time to fit residues: 131.2831 Evaluate side-chains 100 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 65 optimal weight: 0.0170 chunk 31 optimal weight: 0.3980 chunk 58 optimal weight: 0.0020 chunk 26 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.3226 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.146735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118887 restraints weight = 7429.027| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.96 r_work: 0.3217 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6625 Z= 0.135 Angle : 0.448 5.246 9003 Z= 0.229 Chirality : 0.040 0.124 929 Planarity : 0.004 0.051 1172 Dihedral : 3.909 30.208 871 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.46 % Allowed : 15.90 % 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: 0.53 (0.30), residues: 786 helix: 0.85 (0.27), residues: 385 sheet: -0.22 (0.76), residues: 49 loop : 0.03 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.013 0.001 PHE A 369 TYR 0.018 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 101 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.686 Fit side-chains REVERT: A 30 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6392 (mm-30) REVERT: A 60 GLN cc_start: 0.7109 (mm110) cc_final: 0.6507 (pt0) REVERT: A 64 ILE cc_start: 0.7602 (mp) cc_final: 0.7288 (pp) REVERT: A 160 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: A 249 MET cc_start: 0.8168 (mtp) cc_final: 0.7777 (mtm) REVERT: A 313 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7380 (ttmt) REVERT: A 325 GLU cc_start: 0.8177 (tp30) cc_final: 0.7323 (tt0) REVERT: A 347 THR cc_start: 0.8519 (m) cc_final: 0.8285 (p) REVERT: A 470 LYS cc_start: 0.8336 (ptmt) cc_final: 0.8028 (ttpp) REVERT: A 534 LYS cc_start: 0.8287 (mmmt) cc_final: 0.7812 (mptt) REVERT: B 399 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.8227 (p) REVERT: B 484 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6735 (pp20) outliers start: 17 outliers final: 10 residues processed: 98 average time/residue: 1.2534 time to fit residues: 129.1667 Evaluate side-chains 94 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 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 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 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 73 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.144492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.116535 restraints weight = 7403.726| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.96 r_work: 0.3197 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6625 Z= 0.198 Angle : 0.479 5.354 9003 Z= 0.245 Chirality : 0.042 0.126 929 Planarity : 0.004 0.062 1172 Dihedral : 4.026 30.994 871 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.17 % Allowed : 16.47 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.30), residues: 786 helix: 0.84 (0.27), residues: 382 sheet: -0.27 (0.68), residues: 59 loop : -0.02 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.014 0.001 PHE A 523 TYR 0.019 0.001 TYR A 521 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 94 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.759 Fit side-chains REVERT: A 30 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6396 (mm-30) REVERT: A 60 GLN cc_start: 0.7110 (mm110) cc_final: 0.6660 (pt0) REVERT: A 160 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: A 249 MET cc_start: 0.8131 (mtp) cc_final: 0.7721 (mtm) REVERT: A 313 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7405 (ttmt) REVERT: A 347 THR cc_start: 0.8534 (m) cc_final: 0.8297 (p) REVERT: A 470 LYS cc_start: 0.8371 (ptmt) cc_final: 0.8064 (ttpp) REVERT: A 534 LYS cc_start: 0.8306 (mmmt) cc_final: 0.7830 (mptt) REVERT: B 347 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.6239 (t80) REVERT: B 399 SER cc_start: 0.8614 (OUTLIER) cc_final: 0.8016 (p) REVERT: B 484 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6733 (pp20) outliers start: 15 outliers final: 10 residues processed: 93 average time/residue: 1.2625 time to fit residues: 123.5150 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 : 0.714 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 0.0770 chunk 73 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.144702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116816 restraints weight = 7533.095| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.97 r_work: 0.3198 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2914 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= 0.186 Angle : 0.471 5.349 9003 Z= 0.242 Chirality : 0.042 0.125 929 Planarity : 0.004 0.062 1172 Dihedral : 4.021 30.711 871 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: 0.49 (0.30), residues: 786 helix: 0.85 (0.27), residues: 382 sheet: -0.29 (0.68), residues: 59 loop : -0.01 (0.34), 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 0.019 0.001 TYR A 521 ARG 0.014 0.001 ARG A 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5700.45 seconds wall clock time: 101 minutes 7.21 seconds (6067.21 seconds total)