Starting phenix.real_space_refine on Tue Mar 3 17:43:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wa1_32379/03_2026/7wa1_32379.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wa1_32379/03_2026/7wa1_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_2026/7wa1_32379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wa1_32379/03_2026/7wa1_32379.map" model { file = "/net/cci-nas-00/data/ceres_data/7wa1_32379/03_2026/7wa1_32379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wa1_32379/03_2026/7wa1_32379.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1540 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4116 2.51 5 N 1080 2.21 5 O 1206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.35, per 1000 atoms: 0.21 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: 0.43 Conformation dependent library (CDL) restraints added in 229.0 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: 0.20 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: 1.03 Time building geometry restraints manager: 0.58 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: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.810 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:7.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.200 6634 Z= 0.182 Angle : 0.575 7.316 9017 Z= 0.323 Chirality : 0.044 0.159 929 Planarity : 0.006 0.065 1172 Dihedral : 11.298 80.844 2412 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.55 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG A 460 TYR 0.022 0.001 TYR A 385 PHE 0.012 0.001 PHE B 400 TRP 0.008 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6625) covalent geometry : angle 0.57525 ( 9003) SS BOND : bond 0.00302 ( 7) SS BOND : angle 0.68771 ( 14) hydrogen bonds : bond 0.29270 ( 280) hydrogen bonds : angle 9.71316 ( 789) metal coordination : bond 0.19746 ( 2) *********************** 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 : 0.248 Fit side-chains REVERT: A 30 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6893 (mm-30) REVERT: A 31 LYS cc_start: 0.8142 (tppt) cc_final: 0.7765 (tmmt) REVERT: A 150 ASP cc_start: 0.7267 (t70) cc_final: 0.7051 (m-30) REVERT: A 383 MET cc_start: 0.9012 (mtp) cc_final: 0.8781 (mtm) 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: 0.5886 (mt0) REVERT: B 484 GLU cc_start: 0.7379 (pp20) cc_final: 0.7177 (pp20) outliers start: 11 outliers final: 5 residues processed: 159 average time/residue: 0.5115 time to fit residues: 85.4636 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 : 0.277 ------------------------------------------------------------------------------- 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 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0370 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.1260 ------------------------------------------------------------------------------- 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 A 599 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.144650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116729 restraints weight = 7456.049| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.96 r_work: 0.3203 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6634 Z= 0.176 Angle : 0.532 5.574 9017 Z= 0.279 Chirality : 0.043 0.137 929 Planarity : 0.005 0.050 1172 Dihedral : 4.749 29.553 875 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.89 % Allowed : 11.71 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.27), residues: 786 helix: -1.22 (0.23), residues: 376 sheet: -0.70 (0.64), residues: 58 loop : -0.42 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 113 TYR 0.017 0.002 TYR B 351 PHE 0.012 0.002 PHE A 369 TRP 0.011 0.001 TRP A 165 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6625) covalent geometry : angle 0.53184 ( 9003) SS BOND : bond 0.00365 ( 7) SS BOND : angle 0.60106 ( 14) hydrogen bonds : bond 0.05203 ( 280) hydrogen bonds : angle 5.45532 ( 789) metal coordination : bond 0.00358 ( 2) *********************** 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 113 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.165 Fit side-chains REVERT: A 30 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6589 (mm-30) REVERT: A 31 LYS cc_start: 0.8000 (tppt) cc_final: 0.7378 (ttpt) REVERT: A 60 GLN cc_start: 0.7230 (mm110) cc_final: 0.6707 (tm-30) REVERT: A 74 GLU cc_start: 0.7587 (mt-10) cc_final: 0.6865 (mt-10) REVERT: A 160 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7703 (tm-30) REVERT: A 190 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8311 (tmm) REVERT: A 325 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7202 (tt0) REVERT: A 347 THR cc_start: 0.8498 (m) cc_final: 0.8258 (p) REVERT: B 484 GLU cc_start: 0.7109 (pp20) cc_final: 0.6794 (pp20) outliers start: 20 outliers final: 11 residues processed: 106 average time/residue: 0.5397 time to fit residues: 60.1264 Evaluate side-chains 96 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 190 MET 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 511 SER Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.0470 chunk 71 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.0870 chunk 54 optimal weight: 1.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.146679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118821 restraints weight = 7319.846| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.95 r_work: 0.3238 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6634 Z= 0.110 Angle : 0.457 5.471 9017 Z= 0.237 Chirality : 0.041 0.122 929 Planarity : 0.004 0.037 1172 Dihedral : 4.294 29.393 873 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.61 % Allowed : 12.14 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.29), residues: 786 helix: -0.36 (0.25), residues: 387 sheet: -0.46 (0.66), residues: 58 loop : -0.33 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 113 TYR 0.016 0.001 TYR A 521 PHE 0.014 0.001 PHE A 369 TRP 0.015 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 6625) covalent geometry : angle 0.45730 ( 9003) SS BOND : bond 0.00252 ( 7) SS BOND : angle 0.46960 ( 14) hydrogen bonds : bond 0.04413 ( 280) hydrogen bonds : angle 4.89887 ( 789) metal coordination : bond 0.00078 ( 2) *********************** 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 115 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6531 (mm-30) REVERT: A 31 LYS cc_start: 0.7936 (tppt) cc_final: 0.7450 (tmmt) REVERT: A 60 GLN cc_start: 0.7164 (mm110) cc_final: 0.6730 (pt0) REVERT: A 74 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7318 (mt-10) REVERT: A 156 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7014 (mmtt) REVERT: A 225 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7740 (t0) REVERT: A 347 THR cc_start: 0.8524 (m) cc_final: 0.8274 (p) REVERT: A 470 LYS cc_start: 0.8309 (ptmt) cc_final: 0.8091 (ttpp) REVERT: B 399 SER cc_start: 0.8469 (OUTLIER) cc_final: 0.8080 (p) REVERT: B 484 GLU cc_start: 0.7097 (pp20) cc_final: 0.6797 (pp20) outliers start: 25 outliers final: 9 residues processed: 107 average time/residue: 0.5841 time to fit residues: 65.6058 Evaluate side-chains 98 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 225 ASP 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 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 27 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 52 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 47 optimal weight: 0.0470 chunk 11 optimal weight: 5.9990 chunk 58 optimal weight: 0.0670 overall best weight: 0.5216 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.146146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.118132 restraints weight = 7449.937| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.97 r_work: 0.3204 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6634 Z= 0.111 Angle : 0.457 5.697 9017 Z= 0.234 Chirality : 0.041 0.121 929 Planarity : 0.004 0.036 1172 Dihedral : 4.095 30.026 872 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.93 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.29), residues: 786 helix: 0.05 (0.26), residues: 390 sheet: -0.22 (0.76), residues: 49 loop : -0.14 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 113 TYR 0.013 0.001 TYR A 521 PHE 0.013 0.001 PHE A 369 TRP 0.022 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 6625) covalent geometry : angle 0.45720 ( 9003) SS BOND : bond 0.00250 ( 7) SS BOND : angle 0.49561 ( 14) hydrogen bonds : bond 0.04121 ( 280) hydrogen bonds : angle 4.69779 ( 789) metal coordination : bond 0.00093 ( 2) *********************** 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 111 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.257 Fit side-chains REVERT: A 30 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6476 (mm-30) REVERT: A 31 LYS cc_start: 0.7921 (tppt) cc_final: 0.7329 (ttpp) REVERT: A 60 GLN cc_start: 0.7171 (mm110) cc_final: 0.6700 (pt0) REVERT: A 74 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7206 (mt-10) REVERT: A 347 THR cc_start: 0.8518 (m) cc_final: 0.8264 (p) REVERT: A 470 LYS cc_start: 0.8282 (ptmt) cc_final: 0.8022 (ttpp) REVERT: A 534 LYS cc_start: 0.8293 (mmmt) cc_final: 0.7793 (mptt) REVERT: B 399 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8162 (p) REVERT: B 484 GLU cc_start: 0.7127 (pp20) cc_final: 0.6835 (pp20) REVERT: B 493 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.6326 (tm-30) outliers start: 19 outliers final: 11 residues processed: 107 average time/residue: 0.5855 time to fit residues: 65.6939 Evaluate side-chains 96 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 190 MET 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 Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 0.0070 overall best weight: 0.7200 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.145076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116961 restraints weight = 7516.024| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.98 r_work: 0.3215 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6634 Z= 0.128 Angle : 0.466 5.398 9017 Z= 0.239 Chirality : 0.042 0.125 929 Planarity : 0.004 0.041 1172 Dihedral : 4.111 30.132 872 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.90 % Allowed : 13.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.30), residues: 786 helix: 0.32 (0.27), residues: 388 sheet: -0.17 (0.69), residues: 59 loop : -0.16 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 113 TYR 0.019 0.001 TYR A 521 PHE 0.013 0.001 PHE A 523 TRP 0.027 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6625) covalent geometry : angle 0.46631 ( 9003) SS BOND : bond 0.00283 ( 7) SS BOND : angle 0.52127 ( 14) hydrogen bonds : bond 0.04166 ( 280) hydrogen bonds : angle 4.64857 ( 789) metal coordination : bond 0.00104 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6535 (mm-30) REVERT: A 31 LYS cc_start: 0.7946 (tppt) cc_final: 0.7393 (ttpp) REVERT: A 60 GLN cc_start: 0.7207 (mm110) cc_final: 0.6741 (pt0) REVERT: A 74 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7055 (mt-10) REVERT: A 156 LYS cc_start: 0.7819 (mptt) cc_final: 0.7079 (mmtt) REVERT: A 347 THR cc_start: 0.8618 (m) cc_final: 0.8394 (p) REVERT: A 534 LYS cc_start: 0.8356 (mmmt) cc_final: 0.7901 (mptt) REVERT: B 399 SER cc_start: 0.8607 (OUTLIER) cc_final: 0.8233 (p) REVERT: B 424 LYS cc_start: 0.8009 (tptt) cc_final: 0.7687 (tptt) REVERT: B 484 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6807 (pp20) outliers start: 27 outliers final: 13 residues processed: 108 average time/residue: 0.5389 time to fit residues: 61.1355 Evaluate side-chains 99 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 190 MET 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 477 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 484 GLU 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 2 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 65 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 0.0770 chunk 53 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.144935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117006 restraints weight = 7423.015| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.96 r_work: 0.3203 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6634 Z= 0.123 Angle : 0.462 5.364 9017 Z= 0.236 Chirality : 0.041 0.125 929 Planarity : 0.004 0.044 1172 Dihedral : 4.070 30.273 872 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.47 % Allowed : 14.02 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.30), residues: 786 helix: 0.45 (0.27), residues: 389 sheet: -0.12 (0.70), residues: 59 loop : -0.08 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 113 TYR 0.021 0.001 TYR A 521 PHE 0.013 0.001 PHE A 523 TRP 0.028 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6625) covalent geometry : angle 0.46221 ( 9003) SS BOND : bond 0.00282 ( 7) SS BOND : angle 0.52861 ( 14) hydrogen bonds : bond 0.04057 ( 280) hydrogen bonds : angle 4.58977 ( 789) metal coordination : bond 0.00111 ( 2) *********************** 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 111 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6441 (mm-30) REVERT: A 60 GLN cc_start: 0.7135 (mm110) cc_final: 0.6676 (pt0) REVERT: A 74 GLU cc_start: 0.7230 (mt-10) cc_final: 0.7000 (mt-10) REVERT: A 160 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: A 347 THR cc_start: 0.8554 (m) cc_final: 0.8298 (p) REVERT: A 534 LYS cc_start: 0.8318 (mmmt) cc_final: 0.7839 (mptt) REVERT: B 347 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.6269 (t80) REVERT: B 399 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.8003 (p) REVERT: B 424 LYS cc_start: 0.7975 (tptt) cc_final: 0.7622 (tptt) REVERT: B 484 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6767 (pp20) REVERT: B 493 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.6732 (tm-30) outliers start: 24 outliers final: 14 residues processed: 105 average time/residue: 0.5843 time to fit residues: 64.4382 Evaluate side-chains 99 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 190 MET 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 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 483 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 71 optimal weight: 0.0000 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.144752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116799 restraints weight = 7413.960| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.96 r_work: 0.3200 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6634 Z= 0.124 Angle : 0.470 5.331 9017 Z= 0.239 Chirality : 0.041 0.125 929 Planarity : 0.004 0.051 1172 Dihedral : 4.069 30.633 872 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.61 % Allowed : 14.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.30), residues: 786 helix: 0.55 (0.27), residues: 388 sheet: 0.05 (0.78), residues: 49 loop : -0.03 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 113 TYR 0.010 0.001 TYR A 385 PHE 0.013 0.001 PHE A 523 TRP 0.029 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6625) covalent geometry : angle 0.47004 ( 9003) SS BOND : bond 0.00284 ( 7) SS BOND : angle 0.53733 ( 14) hydrogen bonds : bond 0.04014 ( 280) hydrogen bonds : angle 4.59300 ( 789) metal coordination : bond 0.00117 ( 2) *********************** 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 117 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6509 (mm-30) REVERT: A 60 GLN cc_start: 0.7165 (mm110) cc_final: 0.6736 (pt0) REVERT: A 156 LYS cc_start: 0.7883 (mptt) cc_final: 0.7102 (mmtt) REVERT: A 160 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8050 (tm-30) REVERT: A 313 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7593 (ttmt) REVERT: A 347 THR cc_start: 0.8590 (m) cc_final: 0.8353 (p) REVERT: A 534 LYS cc_start: 0.8347 (mmmt) cc_final: 0.7891 (mptt) REVERT: B 347 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.6322 (t80) REVERT: B 399 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8039 (p) REVERT: B 424 LYS cc_start: 0.8050 (tptt) cc_final: 0.7786 (tptt) REVERT: B 453 TYR cc_start: 0.8895 (p90) cc_final: 0.8650 (p90) REVERT: B 484 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6833 (pp20) REVERT: B 493 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.6838 (tm-30) outliers start: 25 outliers final: 13 residues processed: 113 average time/residue: 0.5695 time to fit residues: 67.6210 Evaluate side-chains 104 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 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 477 SER 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 30 optimal weight: 0.0170 chunk 62 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.0470 chunk 43 optimal weight: 0.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.145071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.117229 restraints weight = 7509.400| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.96 r_work: 0.3219 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6634 Z= 0.116 Angle : 0.464 5.305 9017 Z= 0.236 Chirality : 0.041 0.125 929 Planarity : 0.004 0.055 1172 Dihedral : 4.036 30.368 872 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.30), residues: 786 helix: 0.62 (0.27), residues: 388 sheet: 0.06 (0.78), residues: 49 loop : 0.01 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 113 TYR 0.020 0.001 TYR B 351 PHE 0.013 0.001 PHE A 523 TRP 0.031 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6625) covalent geometry : angle 0.46357 ( 9003) SS BOND : bond 0.00260 ( 7) SS BOND : angle 0.51768 ( 14) hydrogen bonds : bond 0.03933 ( 280) hydrogen bonds : angle 4.55095 ( 789) metal coordination : bond 0.00074 ( 2) *********************** 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 116 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.148 Fit side-chains REVERT: A 30 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6477 (mm-30) REVERT: A 60 GLN cc_start: 0.7174 (mm110) cc_final: 0.6630 (pt0) REVERT: A 64 ILE cc_start: 0.7722 (mp) cc_final: 0.7402 (pp) REVERT: A 74 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6830 (mt-10) REVERT: A 156 LYS cc_start: 0.7908 (mptt) cc_final: 0.7122 (mmtt) REVERT: A 160 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8047 (tm-30) REVERT: A 313 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7585 (ttmt) REVERT: A 347 THR cc_start: 0.8593 (m) cc_final: 0.8368 (p) REVERT: A 534 LYS cc_start: 0.8332 (mmmt) cc_final: 0.7883 (mptt) REVERT: B 347 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.6308 (t80) REVERT: B 399 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.8065 (p) REVERT: B 424 LYS cc_start: 0.8059 (tptt) cc_final: 0.7717 (tptt) REVERT: B 484 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6840 (pp20) REVERT: B 513 LEU cc_start: 0.7936 (mm) cc_final: 0.7728 (mm) outliers start: 24 outliers final: 12 residues processed: 111 average time/residue: 0.5568 time to fit residues: 64.8814 Evaluate side-chains 102 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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 477 SER 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 62 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.144026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116051 restraints weight = 7549.602| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.97 r_work: 0.3181 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 6634 Z= 0.138 Angle : 0.483 5.366 9017 Z= 0.246 Chirality : 0.042 0.128 929 Planarity : 0.004 0.057 1172 Dihedral : 4.123 30.906 872 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.60 % Allowed : 15.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.30), residues: 786 helix: 0.58 (0.27), residues: 388 sheet: -0.14 (0.68), residues: 59 loop : -0.02 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 113 TYR 0.020 0.001 TYR B 351 PHE 0.014 0.001 PHE A 523 TRP 0.031 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6625) covalent geometry : angle 0.48321 ( 9003) SS BOND : bond 0.00308 ( 7) SS BOND : angle 0.54927 ( 14) hydrogen bonds : bond 0.04095 ( 280) hydrogen bonds : angle 4.60348 ( 789) metal coordination : bond 0.00117 ( 2) *********************** 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: 18 poor density : 89 time to evaluate : 0.264 Fit side-chains REVERT: A 30 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6420 (mm-30) REVERT: A 60 GLN cc_start: 0.7135 (mm110) cc_final: 0.6700 (pt0) REVERT: A 74 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6735 (mt-10) REVERT: A 160 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: A 249 MET cc_start: 0.8213 (mtp) cc_final: 0.7810 (mtm) REVERT: A 313 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7458 (ttmt) REVERT: A 347 THR cc_start: 0.8576 (m) cc_final: 0.8328 (p) REVERT: A 534 LYS cc_start: 0.8322 (mmmt) cc_final: 0.7842 (mptt) REVERT: B 399 SER cc_start: 0.8614 (OUTLIER) cc_final: 0.8238 (p) REVERT: B 424 LYS cc_start: 0.8047 (tptt) cc_final: 0.7701 (tptt) REVERT: B 484 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6811 (pp20) REVERT: B 513 LEU cc_start: 0.7870 (mm) cc_final: 0.7668 (mm) outliers start: 18 outliers final: 12 residues processed: 104 average time/residue: 0.5607 time to fit residues: 61.3238 Evaluate side-chains 101 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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 477 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115676 restraints weight = 7426.293| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.95 r_work: 0.3176 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6634 Z= 0.143 Angle : 0.493 5.348 9017 Z= 0.251 Chirality : 0.042 0.127 929 Planarity : 0.004 0.063 1172 Dihedral : 4.174 30.976 872 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.03 % Allowed : 15.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.30), residues: 786 helix: 0.57 (0.27), residues: 388 sheet: -0.12 (0.68), residues: 59 loop : -0.02 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 113 TYR 0.021 0.001 TYR B 351 PHE 0.014 0.001 PHE A 523 TRP 0.033 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6625) covalent geometry : angle 0.49256 ( 9003) SS BOND : bond 0.00315 ( 7) SS BOND : angle 0.58424 ( 14) hydrogen bonds : bond 0.04137 ( 280) hydrogen bonds : angle 4.62850 ( 789) metal coordination : bond 0.00130 ( 2) ********************** 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 108 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.246 Fit side-chains REVERT: A 30 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6400 (mm-30) REVERT: A 60 GLN cc_start: 0.7138 (mm110) cc_final: 0.6584 (pt0) REVERT: A 64 ILE cc_start: 0.7638 (mp) cc_final: 0.7311 (pp) REVERT: A 74 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6769 (mt-10) REVERT: A 160 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8022 (tm-30) REVERT: A 249 MET cc_start: 0.8175 (mtp) cc_final: 0.7796 (mtm) REVERT: A 313 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7479 (ttmt) REVERT: A 347 THR cc_start: 0.8584 (m) cc_final: 0.8334 (p) REVERT: A 456 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7926 (tt) REVERT: A 534 LYS cc_start: 0.8323 (mmmt) cc_final: 0.7849 (mptt) REVERT: B 399 SER cc_start: 0.8618 (OUTLIER) cc_final: 0.8233 (p) REVERT: B 424 LYS cc_start: 0.8040 (tptt) cc_final: 0.7701 (tptt) REVERT: B 484 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6817 (pp20) outliers start: 21 outliers final: 13 residues processed: 105 average time/residue: 0.5497 time to fit residues: 60.7503 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 : 0.301 ------------------------------------------------------------------------------- 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 409 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 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 = 0.144235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116233 restraints weight = 7426.888| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.95 r_work: 0.3196 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 0.030 6634 Z= 0.127 Angle : 0.477 5.323 9017 Z= 0.244 Chirality : 0.042 0.140 929 Planarity : 0.004 0.062 1172 Dihedral : 4.164 30.764 872 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.03 % Allowed : 15.90 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.30), residues: 786 helix: 0.62 (0.27), residues: 388 sheet: -0.11 (0.68), residues: 59 loop : 0.02 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 113 TYR 0.021 0.001 TYR B 351 PHE 0.013 0.001 PHE A 523 TRP 0.034 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6625) covalent geometry : angle 0.47738 ( 9003) SS BOND : bond 0.00287 ( 7) SS BOND : angle 0.52187 ( 14) hydrogen bonds : bond 0.04065 ( 280) hydrogen bonds : angle 4.59453 ( 789) metal coordination : bond 0.00091 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2459.90 seconds wall clock time: 42 minutes 33.33 seconds (2553.33 seconds total)