Starting phenix.real_space_refine on Wed Sep 17 07:13:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yfd_39220/09_2025/8yfd_39220.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yfd_39220/09_2025/8yfd_39220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yfd_39220/09_2025/8yfd_39220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yfd_39220/09_2025/8yfd_39220.map" model { file = "/net/cci-nas-00/data/ceres_data/8yfd_39220/09_2025/8yfd_39220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yfd_39220/09_2025/8yfd_39220.cif" } resolution = 3.57 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= -0.001 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 4414 2.51 5 N 1054 2.21 5 O 1088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6588 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3294 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain: "B" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3294 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Time building chain proxies: 1.84, per 1000 atoms: 0.28 Number of scatterers: 6588 At special positions: 0 Unit cell: (79.2, 67.1, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1088 8.00 N 1054 7.00 C 4414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " 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: 0.58 Conformation dependent library (CDL) restraints added in 346.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 73.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 230 through 258 removed outlier: 3.619A pdb=" N THR A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 296 removed outlier: 4.856A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 337 removed outlier: 3.629A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 removed outlier: 3.948A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 390 through 402 removed outlier: 3.637A pdb=" N PHE A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.920A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 471 Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 476 through 501 removed outlier: 4.326A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 3.559A pdb=" N ILE A 520 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 527 " --> pdb=" O CYS A 523 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 532 " --> pdb=" O TRP A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 571 removed outlier: 4.026A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 583 removed outlier: 3.713A pdb=" N GLN A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 622 Proline residue: A 598 - end of helix removed outlier: 4.225A pdb=" N VAL A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE A 602 " --> pdb=" O PRO A 598 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 258 Processing helix chain 'B' and resid 265 through 296 removed outlier: 3.673A pdb=" N ILE B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.743A pdb=" N ILE B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 337 removed outlier: 3.555A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 346 through 360 removed outlier: 3.759A pdb=" N LEU B 359 " --> pdb=" O MET B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 382 removed outlier: 3.513A pdb=" N PHE B 379 " --> pdb=" O LEU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 399 Processing helix chain 'B' and resid 404 through 420 removed outlier: 3.518A pdb=" N LEU B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR B 412 " --> pdb=" O MET B 408 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU B 420 " --> pdb=" O PHE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 471 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 473 through 501 removed outlier: 4.112A pdb=" N GLY B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.638A pdb=" N PHE B 511 " --> pdb=" O THR B 507 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR B 512 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 513 " --> pdb=" O VAL B 509 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL B 516 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 521 " --> pdb=" O PHE B 517 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE B 527 " --> pdb=" O CYS B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 571 removed outlier: 4.180A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 580 Processing helix chain 'B' and resid 588 through 622 removed outlier: 4.247A pdb=" N ILE B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA B 593 " --> pdb=" O GLY B 589 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 595 " --> pdb=" O ILE B 591 " (cutoff:3.500A) Proline residue: B 598 - end of helix removed outlier: 4.040A pdb=" N VAL B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 602 " --> pdb=" O PRO B 598 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1230 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: 0.96 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1955 1.35 - 1.46: 1935 1.46 - 1.58: 2874 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 6808 Sorted by residual: bond pdb=" CA THR A 261 " pdb=" CB THR A 261 " ideal model delta sigma weight residual 1.526 1.547 -0.021 1.53e-02 4.27e+03 1.88e+00 bond pdb=" N PRO A 475 " pdb=" CA PRO A 475 " ideal model delta sigma weight residual 1.474 1.465 0.009 7.40e-03 1.83e+04 1.40e+00 bond pdb=" CA HIS A 504 " pdb=" C HIS A 504 " ideal model delta sigma weight residual 1.532 1.522 0.011 9.60e-03 1.09e+04 1.21e+00 bond pdb=" CA ILE B 339 " pdb=" CB ILE B 339 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 1.04e+00 bond pdb=" CA TYR B 367 " pdb=" C TYR B 367 " ideal model delta sigma weight residual 1.532 1.523 0.010 9.60e-03 1.09e+04 1.01e+00 ... (remaining 6803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 9087 2.12 - 4.25: 152 4.25 - 6.37: 23 6.37 - 8.50: 4 8.50 - 10.62: 2 Bond angle restraints: 9268 Sorted by residual: angle pdb=" N ASP A 262 " pdb=" CA ASP A 262 " pdb=" C ASP A 262 " ideal model delta sigma weight residual 114.64 107.72 6.92 1.52e+00 4.33e-01 2.07e+01 angle pdb=" C THR B 383 " pdb=" N ALA B 384 " pdb=" CA ALA B 384 " ideal model delta sigma weight residual 121.80 130.88 -9.08 2.44e+00 1.68e-01 1.39e+01 angle pdb=" C ARG B 308 " pdb=" N SER B 309 " pdb=" CA SER B 309 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 9.99e+00 angle pdb=" CA TRP B 395 " pdb=" CB TRP B 395 " pdb=" CG TRP B 395 " ideal model delta sigma weight residual 113.60 119.47 -5.87 1.90e+00 2.77e-01 9.53e+00 angle pdb=" CA TYR B 290 " pdb=" CB TYR B 290 " pdb=" CG TYR B 290 " ideal model delta sigma weight residual 113.90 119.46 -5.56 1.80e+00 3.09e-01 9.53e+00 ... (remaining 9263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 3194 16.45 - 32.91: 458 32.91 - 49.36: 179 49.36 - 65.81: 34 65.81 - 82.26: 3 Dihedral angle restraints: 3868 sinusoidal: 1532 harmonic: 2336 Sorted by residual: dihedral pdb=" CA GLN B 399 " pdb=" C GLN B 399 " pdb=" N LEU B 400 " pdb=" CA LEU B 400 " ideal model delta harmonic sigma weight residual 180.00 155.83 24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA ALA B 384 " pdb=" C ALA B 384 " pdb=" N PRO B 385 " pdb=" CA PRO B 385 " ideal model delta harmonic sigma weight residual 180.00 -158.86 -21.14 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ILE A 342 " pdb=" C ILE A 342 " pdb=" N PRO A 343 " pdb=" CA PRO A 343 " ideal model delta harmonic sigma weight residual -180.00 -160.24 -19.76 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 3865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 653 0.034 - 0.067: 264 0.067 - 0.101: 75 0.101 - 0.135: 17 0.135 - 0.168: 3 Chirality restraints: 1012 Sorted by residual: chirality pdb=" CA GLN B 399 " pdb=" N GLN B 399 " pdb=" C GLN B 399 " pdb=" CB GLN B 399 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CG LEU B 311 " pdb=" CB LEU B 311 " pdb=" CD1 LEU B 311 " pdb=" CD2 LEU B 311 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CB THR A 507 " pdb=" CA THR A 507 " pdb=" OG1 THR A 507 " pdb=" CG2 THR A 507 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 1009 not shown) Planarity restraints: 1134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 395 " -0.021 2.00e-02 2.50e+03 1.62e-02 6.59e+00 pdb=" CG TRP B 395 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 395 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 395 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 395 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 395 " -0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP B 395 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 395 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 395 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 395 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 310 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C ASN B 310 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN B 310 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU B 311 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 384 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO B 385 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 385 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 385 " 0.026 5.00e-02 4.00e+02 ... (remaining 1131 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 431 2.74 - 3.28: 6891 3.28 - 3.82: 10931 3.82 - 4.36: 11858 4.36 - 4.90: 20548 Nonbonded interactions: 50659 Sorted by model distance: nonbonded pdb=" O ILE A 579 " pdb=" OG1 THR A 583 " model vdw 2.195 3.040 nonbonded pdb=" O SER A 578 " pdb=" OG1 THR A 582 " model vdw 2.231 3.040 nonbonded pdb=" O ARG B 308 " pdb=" OG SER B 309 " model vdw 2.241 3.040 nonbonded pdb=" O ARG A 466 " pdb=" OG1 THR A 470 " model vdw 2.274 3.040 nonbonded pdb=" O ILE A 271 " pdb=" OH TYR A 352 " model vdw 2.278 3.040 ... (remaining 50654 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.120 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 0.032 6810 Z= 0.149 Angle : 0.678 10.623 9272 Z= 0.384 Chirality : 0.040 0.168 1012 Planarity : 0.004 0.047 1134 Dihedral : 17.761 82.263 2358 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.09 % Favored : 93.53 % Rotamer: Outliers : 0.57 % Allowed : 29.97 % Favored : 69.46 % 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 aren not related in a simple way. whole: 0.20 (0.32), residues: 788 helix: 1.21 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -2.80 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 472 TYR 0.015 0.001 TYR A 518 PHE 0.012 0.001 PHE A 394 TRP 0.044 0.002 TRP B 395 HIS 0.004 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6808) covalent geometry : angle 0.67750 ( 9268) SS BOND : bond 0.00084 ( 2) SS BOND : angle 1.46552 ( 4) hydrogen bonds : bond 0.12708 ( 410) hydrogen bonds : angle 5.45319 ( 1230) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 0.251 Fit side-chains REVERT: A 489 MET cc_start: 0.7149 (tmm) cc_final: 0.6595 (tmm) outliers start: 4 outliers final: 4 residues processed: 142 average time/residue: 0.0791 time to fit residues: 15.4928 Evaluate side-chains 129 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 398 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.0770 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN B 310 ASN B 479 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.176815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.142580 restraints weight = 9825.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146230 restraints weight = 6142.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.148599 restraints weight = 4639.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149507 restraints weight = 3914.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.150732 restraints weight = 3597.572| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6810 Z= 0.125 Angle : 0.569 8.946 9272 Z= 0.297 Chirality : 0.040 0.144 1012 Planarity : 0.005 0.064 1134 Dihedral : 5.747 58.696 879 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.35 % Favored : 93.40 % Rotamer: Outliers : 5.11 % Allowed : 25.00 % Favored : 69.89 % 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 aren not related in a simple way. whole: 0.61 (0.31), residues: 788 helix: 1.60 (0.22), residues: 564 sheet: None (None), residues: 0 loop : -2.86 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 448 TYR 0.012 0.001 TYR A 518 PHE 0.015 0.001 PHE A 394 TRP 0.039 0.001 TRP B 395 HIS 0.005 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6808) covalent geometry : angle 0.56877 ( 9268) SS BOND : bond 0.00164 ( 2) SS BOND : angle 1.33294 ( 4) hydrogen bonds : bond 0.04568 ( 410) hydrogen bonds : angle 3.91293 ( 1230) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.255 Fit side-chains REVERT: A 345 TYR cc_start: 0.6948 (OUTLIER) cc_final: 0.6258 (m-80) REVERT: A 497 SER cc_start: 0.8359 (m) cc_final: 0.8046 (p) REVERT: A 518 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7349 (m-80) REVERT: B 245 ILE cc_start: 0.7303 (mm) cc_final: 0.7072 (mm) REVERT: B 452 GLN cc_start: 0.8015 (tp40) cc_final: 0.7732 (tp40) REVERT: B 502 ARG cc_start: 0.7948 (tmm-80) cc_final: 0.7522 (tmm-80) REVERT: B 508 MET cc_start: 0.7506 (mtm) cc_final: 0.7164 (mpp) REVERT: B 613 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6838 (pp20) outliers start: 36 outliers final: 18 residues processed: 159 average time/residue: 0.0758 time to fit residues: 16.7837 Evaluate side-chains 143 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 453 CYS Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 0.0970 chunk 58 optimal weight: 0.0010 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.0770 chunk 18 optimal weight: 0.9980 overall best weight: 0.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS A 608 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.176807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142813 restraints weight = 9694.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.146426 restraints weight = 6020.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.148755 restraints weight = 4538.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.149802 restraints weight = 3818.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.151064 restraints weight = 3485.591| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6810 Z= 0.117 Angle : 0.553 9.250 9272 Z= 0.286 Chirality : 0.039 0.187 1012 Planarity : 0.004 0.065 1134 Dihedral : 5.135 57.525 876 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.84 % Favored : 93.91 % Rotamer: Outliers : 5.40 % Allowed : 26.28 % Favored : 68.32 % 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 aren not related in a simple way. whole: 0.85 (0.31), residues: 788 helix: 1.80 (0.22), residues: 565 sheet: None (None), residues: 0 loop : -2.88 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 448 TYR 0.013 0.001 TYR A 496 PHE 0.015 0.001 PHE A 394 TRP 0.029 0.001 TRP B 395 HIS 0.004 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 6808) covalent geometry : angle 0.55240 ( 9268) SS BOND : bond 0.00183 ( 2) SS BOND : angle 1.46367 ( 4) hydrogen bonds : bond 0.04315 ( 410) hydrogen bonds : angle 3.69619 ( 1230) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 497 SER cc_start: 0.8314 (m) cc_final: 0.8024 (p) REVERT: B 245 ILE cc_start: 0.7244 (mm) cc_final: 0.6917 (mm) REVERT: B 502 ARG cc_start: 0.7862 (tmm-80) cc_final: 0.7532 (ttm-80) REVERT: B 613 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6303 (tm-30) outliers start: 38 outliers final: 19 residues processed: 165 average time/residue: 0.0715 time to fit residues: 16.4659 Evaluate side-chains 137 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 0.0370 chunk 27 optimal weight: 0.3980 chunk 22 optimal weight: 0.2980 chunk 48 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 0.0870 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS A 608 ASN B 399 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.177508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.143612 restraints weight = 9740.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.147262 restraints weight = 6045.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149584 restraints weight = 4532.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.150737 restraints weight = 3820.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.151588 restraints weight = 3460.797| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6810 Z= 0.114 Angle : 0.549 9.370 9272 Z= 0.282 Chirality : 0.039 0.152 1012 Planarity : 0.004 0.062 1134 Dihedral : 4.671 54.233 874 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.35 % Favored : 93.40 % Rotamer: Outliers : 5.40 % Allowed : 25.99 % Favored : 68.61 % 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 aren not related in a simple way. whole: 0.95 (0.32), residues: 788 helix: 1.90 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -2.95 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 448 TYR 0.011 0.001 TYR A 496 PHE 0.012 0.001 PHE A 394 TRP 0.030 0.001 TRP B 395 HIS 0.007 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6808) covalent geometry : angle 0.54870 ( 9268) SS BOND : bond 0.00097 ( 2) SS BOND : angle 1.32666 ( 4) hydrogen bonds : bond 0.04078 ( 410) hydrogen bonds : angle 3.65721 ( 1230) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 SER cc_start: 0.8315 (m) cc_final: 0.8015 (p) REVERT: A 605 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7726 (t80) REVERT: B 245 ILE cc_start: 0.7229 (mm) cc_final: 0.6914 (mm) REVERT: B 502 ARG cc_start: 0.7886 (tmm-80) cc_final: 0.7609 (ttm-80) REVERT: B 508 MET cc_start: 0.7271 (mtm) cc_final: 0.6949 (mpp) REVERT: B 587 HIS cc_start: 0.6526 (OUTLIER) cc_final: 0.6137 (t-90) REVERT: B 613 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6307 (tm-30) outliers start: 38 outliers final: 28 residues processed: 155 average time/residue: 0.0774 time to fit residues: 16.3790 Evaluate side-chains 152 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 74 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 73 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.176061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141464 restraints weight = 9943.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145093 restraints weight = 6237.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147097 restraints weight = 4714.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.148792 restraints weight = 4027.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.149421 restraints weight = 3617.581| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6810 Z= 0.128 Angle : 0.557 9.336 9272 Z= 0.284 Chirality : 0.040 0.228 1012 Planarity : 0.004 0.059 1134 Dihedral : 4.601 52.082 874 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.71 % Favored : 94.04 % Rotamer: Outliers : 5.26 % Allowed : 26.56 % Favored : 68.18 % 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 aren not related in a simple way. whole: 0.94 (0.31), residues: 788 helix: 1.90 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -2.95 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 448 TYR 0.011 0.001 TYR A 496 PHE 0.016 0.001 PHE A 394 TRP 0.027 0.001 TRP B 395 HIS 0.005 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6808) covalent geometry : angle 0.55631 ( 9268) SS BOND : bond 0.00164 ( 2) SS BOND : angle 1.34404 ( 4) hydrogen bonds : bond 0.04271 ( 410) hydrogen bonds : angle 3.65870 ( 1230) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 SER cc_start: 0.8325 (m) cc_final: 0.8041 (p) REVERT: A 512 TYR cc_start: 0.7905 (m-10) cc_final: 0.7515 (m-80) REVERT: A 518 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7444 (m-80) REVERT: A 605 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7853 (t80) REVERT: B 245 ILE cc_start: 0.7223 (mm) cc_final: 0.6916 (mm) REVERT: B 335 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.7024 (m-80) REVERT: B 408 MET cc_start: 0.7782 (mmm) cc_final: 0.7549 (mmm) REVERT: B 502 ARG cc_start: 0.7949 (tmm-80) cc_final: 0.7719 (tmm-80) REVERT: B 508 MET cc_start: 0.7250 (mtm) cc_final: 0.6946 (mpp) REVERT: B 613 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6298 (tm-30) outliers start: 37 outliers final: 26 residues processed: 151 average time/residue: 0.0728 time to fit residues: 15.5268 Evaluate side-chains 146 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 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 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.174257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139655 restraints weight = 9934.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143275 restraints weight = 6186.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145624 restraints weight = 4655.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.147082 restraints weight = 3922.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.147350 restraints weight = 3530.214| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6810 Z= 0.134 Angle : 0.562 9.339 9272 Z= 0.290 Chirality : 0.041 0.180 1012 Planarity : 0.004 0.056 1134 Dihedral : 4.542 49.031 874 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.84 % Favored : 93.91 % Rotamer: Outliers : 5.68 % Allowed : 26.85 % Favored : 67.47 % 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 aren not related in a simple way. whole: 0.85 (0.31), residues: 788 helix: 1.82 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -2.96 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 448 TYR 0.010 0.001 TYR A 496 PHE 0.018 0.001 PHE A 394 TRP 0.027 0.001 TRP B 395 HIS 0.005 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6808) covalent geometry : angle 0.56112 ( 9268) SS BOND : bond 0.00193 ( 2) SS BOND : angle 1.43469 ( 4) hydrogen bonds : bond 0.04480 ( 410) hydrogen bonds : angle 3.72723 ( 1230) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.6265 (m-80) REVERT: A 497 SER cc_start: 0.8362 (m) cc_final: 0.8110 (p) REVERT: A 512 TYR cc_start: 0.7818 (m-10) cc_final: 0.7474 (m-10) REVERT: B 245 ILE cc_start: 0.7234 (mm) cc_final: 0.6950 (mm) REVERT: B 331 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8145 (tt) REVERT: B 335 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.7013 (m-80) REVERT: B 508 MET cc_start: 0.7033 (mtm) cc_final: 0.6798 (mpp) REVERT: B 613 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6307 (tm-30) outliers start: 40 outliers final: 28 residues processed: 152 average time/residue: 0.0630 time to fit residues: 13.6732 Evaluate side-chains 149 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.173548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138500 restraints weight = 9982.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.141951 restraints weight = 6347.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144308 restraints weight = 4840.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.145558 restraints weight = 4110.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.146269 restraints weight = 3740.111| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6810 Z= 0.140 Angle : 0.576 9.430 9272 Z= 0.298 Chirality : 0.040 0.168 1012 Planarity : 0.004 0.055 1134 Dihedral : 4.542 48.129 874 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.84 % Favored : 93.91 % Rotamer: Outliers : 5.11 % Allowed : 27.70 % Favored : 67.19 % 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 aren not related in a simple way. whole: 0.81 (0.31), residues: 788 helix: 1.78 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -2.94 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 448 TYR 0.010 0.001 TYR A 496 PHE 0.024 0.001 PHE A 358 TRP 0.030 0.001 TRP B 395 HIS 0.005 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 6808) covalent geometry : angle 0.57594 ( 9268) SS BOND : bond 0.00164 ( 2) SS BOND : angle 1.29480 ( 4) hydrogen bonds : bond 0.04571 ( 410) hydrogen bonds : angle 3.77361 ( 1230) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 345 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.6348 (m-80) REVERT: A 497 SER cc_start: 0.8375 (m) cc_final: 0.8123 (p) REVERT: A 512 TYR cc_start: 0.7831 (m-10) cc_final: 0.7450 (m-80) REVERT: A 518 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: B 245 ILE cc_start: 0.7232 (mm) cc_final: 0.6940 (mm) REVERT: B 408 MET cc_start: 0.7557 (mmm) cc_final: 0.7242 (mmm) REVERT: B 508 MET cc_start: 0.6945 (mtm) cc_final: 0.6719 (mpp) REVERT: B 613 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6374 (tm-30) outliers start: 36 outliers final: 25 residues processed: 147 average time/residue: 0.0696 time to fit residues: 14.4919 Evaluate side-chains 150 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.0370 chunk 43 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.175068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.140843 restraints weight = 9855.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144439 restraints weight = 6137.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146791 restraints weight = 4623.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.147968 restraints weight = 3895.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.148456 restraints weight = 3539.349| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6810 Z= 0.121 Angle : 0.567 9.510 9272 Z= 0.291 Chirality : 0.040 0.164 1012 Planarity : 0.004 0.052 1134 Dihedral : 4.516 47.199 874 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.47 % Favored : 93.27 % Rotamer: Outliers : 5.11 % Allowed : 26.99 % Favored : 67.90 % 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 aren not related in a simple way. whole: 0.92 (0.31), residues: 788 helix: 1.88 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -2.95 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 448 TYR 0.009 0.001 TYR A 496 PHE 0.021 0.001 PHE A 358 TRP 0.032 0.001 TRP B 395 HIS 0.005 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6808) covalent geometry : angle 0.56626 ( 9268) SS BOND : bond 0.00163 ( 2) SS BOND : angle 1.45964 ( 4) hydrogen bonds : bond 0.04361 ( 410) hydrogen bonds : angle 3.68773 ( 1230) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 TYR cc_start: 0.7000 (OUTLIER) cc_final: 0.6305 (m-80) REVERT: A 497 SER cc_start: 0.8345 (m) cc_final: 0.8105 (p) REVERT: B 245 ILE cc_start: 0.7249 (mm) cc_final: 0.6961 (mm) REVERT: B 283 PHE cc_start: 0.7987 (m-10) cc_final: 0.7746 (m-10) REVERT: B 331 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8232 (tt) REVERT: B 613 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6322 (tm-30) outliers start: 36 outliers final: 28 residues processed: 151 average time/residue: 0.0683 time to fit residues: 14.5581 Evaluate side-chains 155 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 453 CYS Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN ** B 452 GLN ** 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 = 0.4034 r_free = 0.4034 target = 0.174430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139871 restraints weight = 9997.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143464 restraints weight = 6257.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145797 restraints weight = 4735.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146582 restraints weight = 4002.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147302 restraints weight = 3704.877| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6810 Z= 0.135 Angle : 0.583 9.516 9272 Z= 0.299 Chirality : 0.040 0.161 1012 Planarity : 0.004 0.050 1134 Dihedral : 4.524 46.046 874 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.35 % Favored : 93.40 % Rotamer: Outliers : 5.11 % Allowed : 27.70 % Favored : 67.19 % 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 aren not related in a simple way. whole: 0.88 (0.31), residues: 788 helix: 1.85 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -2.97 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 448 TYR 0.009 0.001 TYR A 496 PHE 0.020 0.001 PHE A 358 TRP 0.041 0.002 TRP B 395 HIS 0.005 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6808) covalent geometry : angle 0.58187 ( 9268) SS BOND : bond 0.00177 ( 2) SS BOND : angle 1.57057 ( 4) hydrogen bonds : bond 0.04510 ( 410) hydrogen bonds : angle 3.74371 ( 1230) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 345 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.6332 (m-80) REVERT: A 497 SER cc_start: 0.8362 (m) cc_final: 0.8122 (p) REVERT: A 518 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7296 (m-80) REVERT: B 245 ILE cc_start: 0.7217 (mm) cc_final: 0.6916 (mm) REVERT: B 283 PHE cc_start: 0.7997 (m-10) cc_final: 0.7711 (m-10) REVERT: B 331 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8223 (tt) REVERT: B 613 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6407 (tm-30) outliers start: 36 outliers final: 27 residues processed: 144 average time/residue: 0.0697 time to fit residues: 14.1623 Evaluate side-chains 151 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 75 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.174232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139372 restraints weight = 9922.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.142971 restraints weight = 6287.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.144904 restraints weight = 4792.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146421 restraints weight = 4107.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147059 restraints weight = 3745.570| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6810 Z= 0.130 Angle : 0.584 9.589 9272 Z= 0.299 Chirality : 0.040 0.160 1012 Planarity : 0.004 0.049 1134 Dihedral : 4.491 44.917 874 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.85 % Favored : 92.89 % Rotamer: Outliers : 5.11 % Allowed : 27.70 % Favored : 67.19 % 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 aren not related in a simple way. whole: 0.91 (0.31), residues: 788 helix: 1.88 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -2.99 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 448 TYR 0.009 0.001 TYR A 496 PHE 0.020 0.001 PHE A 358 TRP 0.044 0.002 TRP B 395 HIS 0.005 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6808) covalent geometry : angle 0.58326 ( 9268) SS BOND : bond 0.00157 ( 2) SS BOND : angle 1.58944 ( 4) hydrogen bonds : bond 0.04497 ( 410) hydrogen bonds : angle 3.72338 ( 1230) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 TYR cc_start: 0.7038 (OUTLIER) cc_final: 0.6310 (m-80) REVERT: A 497 SER cc_start: 0.8313 (m) cc_final: 0.8091 (p) REVERT: A 518 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: B 245 ILE cc_start: 0.7212 (mm) cc_final: 0.6910 (mm) REVERT: B 283 PHE cc_start: 0.7989 (m-10) cc_final: 0.7733 (m-10) REVERT: B 314 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.6756 (mp10) REVERT: B 331 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8199 (tt) REVERT: B 452 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7780 (mm-40) REVERT: B 613 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6406 (tm-30) outliers start: 36 outliers final: 28 residues processed: 149 average time/residue: 0.0674 time to fit residues: 14.2479 Evaluate side-chains 155 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 345 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 69 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 46 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.175323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.140908 restraints weight = 9843.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144591 restraints weight = 6154.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.146937 restraints weight = 4653.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.148001 restraints weight = 3927.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.149233 restraints weight = 3586.106| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6810 Z= 0.123 Angle : 0.580 9.649 9272 Z= 0.298 Chirality : 0.039 0.162 1012 Planarity : 0.004 0.049 1134 Dihedral : 4.452 43.838 874 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.35 % Favored : 93.40 % Rotamer: Outliers : 4.69 % Allowed : 28.27 % Favored : 67.05 % 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 aren not related in a simple way. whole: 0.97 (0.31), residues: 788 helix: 1.93 (0.22), residues: 567 sheet: None (None), residues: 0 loop : -3.00 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 448 TYR 0.009 0.001 TYR A 352 PHE 0.020 0.001 PHE A 358 TRP 0.043 0.002 TRP B 395 HIS 0.005 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6808) covalent geometry : angle 0.57892 ( 9268) SS BOND : bond 0.00157 ( 2) SS BOND : angle 1.53765 ( 4) hydrogen bonds : bond 0.04373 ( 410) hydrogen bonds : angle 3.69808 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1234.77 seconds wall clock time: 22 minutes 3.06 seconds (1323.06 seconds total)