Starting phenix.real_space_refine on Thu Nov 14 14:43:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfd_39220/11_2024/8yfd_39220.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfd_39220/11_2024/8yfd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfd_39220/11_2024/8yfd_39220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfd_39220/11_2024/8yfd_39220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfd_39220/11_2024/8yfd_39220.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfd_39220/11_2024/8yfd_39220.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 4.45, per 1000 atoms: 0.68 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: 1.68 Conformation dependent library (CDL) restraints added in 957.6 milliseconds 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: 0.56 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: 1.67 Time building geometry restraints manager: 1.99 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: 0.00 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: 3.990 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.750 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.250 ------------------------------------------------------------------------------- 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 6808 Z= 0.186 Angle : 0.678 10.623 9268 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 : 9.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.32), 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 TRP 0.044 0.002 TRP B 395 HIS 0.004 0.001 HIS B 441 PHE 0.012 0.001 PHE A 394 TYR 0.015 0.001 TYR A 518 ARG 0.004 0.000 ARG A 472 *********************** 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 : 0.702 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: 0.1732 time to fit residues: 33.7557 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 : 0.943 ------------------------------------------------------------------------------- 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 65 optimal weight: 0.9980 chunk 59 optimal weight: 0.0370 chunk 32 optimal weight: 0.0670 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 ASN B 479 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6808 Z= 0.163 Angle : 0.572 9.126 9268 Z= 0.298 Chirality : 0.040 0.142 1012 Planarity : 0.005 0.065 1134 Dihedral : 5.756 59.523 879 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.35 % Favored : 93.40 % Rotamer: Outliers : 4.55 % Allowed : 25.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.31), residues: 788 helix: 1.60 (0.22), residues: 564 sheet: None (None), residues: 0 loop : -2.88 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 395 HIS 0.005 0.001 HIS B 441 PHE 0.015 0.001 PHE A 394 TYR 0.013 0.001 TYR A 518 ARG 0.004 0.000 ARG A 448 *********************** 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 169 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.772 Fit side-chains REVERT: A 263 ARG cc_start: 0.5762 (tpt170) cc_final: 0.5533 (ttt90) REVERT: A 497 SER cc_start: 0.8358 (m) cc_final: 0.8049 (p) REVERT: A 518 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7331 (m-80) REVERT: B 245 ILE cc_start: 0.7271 (mm) cc_final: 0.7055 (mm) REVERT: B 452 GLN cc_start: 0.7996 (tp40) cc_final: 0.7708 (tp40) REVERT: B 508 MET cc_start: 0.7592 (mtm) cc_final: 0.7196 (mpp) REVERT: B 613 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6813 (pp20) outliers start: 32 outliers final: 15 residues processed: 157 average time/residue: 0.1696 time to fit residues: 36.7543 Evaluate side-chains 137 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 378 LEU 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 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 39 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 70 optimal weight: 0.0030 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6808 Z= 0.169 Angle : 0.550 9.207 9268 Z= 0.284 Chirality : 0.039 0.135 1012 Planarity : 0.004 0.065 1134 Dihedral : 5.120 57.383 876 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.71 % Favored : 94.04 % Rotamer: Outliers : 5.82 % Allowed : 25.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.32), residues: 788 helix: 1.80 (0.22), residues: 565 sheet: None (None), residues: 0 loop : -2.86 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 395 HIS 0.004 0.001 HIS B 441 PHE 0.016 0.001 PHE A 394 TYR 0.014 0.001 TYR A 496 ARG 0.003 0.000 ARG A 448 *********************** 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 172 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 263 ARG cc_start: 0.5534 (tpt170) cc_final: 0.5284 (ttt90) REVERT: A 345 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.6186 (m-80) REVERT: A 497 SER cc_start: 0.8300 (m) cc_final: 0.8023 (p) REVERT: B 245 ILE cc_start: 0.7254 (mm) cc_final: 0.6931 (mm) REVERT: B 502 ARG cc_start: 0.7942 (tmm-80) cc_final: 0.7593 (ttm-80) REVERT: B 613 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6352 (tm-30) outliers start: 41 outliers final: 23 residues processed: 161 average time/residue: 0.1584 time to fit residues: 35.2390 Evaluate side-chains 144 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 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 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 551 ILE Chi-restraints excluded: chain B residue 592 ILE 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 36 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 37 optimal weight: 0.4980 chunk 67 optimal weight: 8.9990 chunk 20 optimal weight: 0.0170 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS B 462 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6808 Z= 0.178 Angle : 0.567 9.316 9268 Z= 0.291 Chirality : 0.040 0.188 1012 Planarity : 0.004 0.062 1134 Dihedral : 4.696 54.149 874 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.07 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.31), residues: 788 helix: 1.83 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -2.91 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 395 HIS 0.007 0.001 HIS A 441 PHE 0.016 0.001 PHE A 394 TYR 0.012 0.001 TYR A 496 ARG 0.002 0.000 ARG A 448 *********************** 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 : 0.735 Fit side-chains revert: symmetry clash REVERT: A 345 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.6174 (m-80) REVERT: A 497 SER cc_start: 0.8295 (m) cc_final: 0.8008 (p) REVERT: B 245 ILE cc_start: 0.7207 (mm) cc_final: 0.6904 (mm) REVERT: B 502 ARG cc_start: 0.7974 (tmm-80) cc_final: 0.7655 (ttm-80) REVERT: B 587 HIS cc_start: 0.6410 (OUTLIER) cc_final: 0.6173 (t-90) REVERT: B 613 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6356 (tm-30) outliers start: 38 outliers final: 25 residues processed: 156 average time/residue: 0.1604 time to fit residues: 34.3177 Evaluate side-chains 147 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 341 VAL Chi-restraints excluded: chain A residue 345 TYR 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 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 B residue 265 ILE 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 398 ASP 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 587 HIS 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 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 462 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6808 Z= 0.254 Angle : 0.595 9.159 9268 Z= 0.310 Chirality : 0.042 0.210 1012 Planarity : 0.004 0.060 1134 Dihedral : 4.727 50.594 874 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.71 % Favored : 94.04 % Rotamer: Outliers : 5.82 % Allowed : 26.42 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.31), residues: 788 helix: 1.64 (0.22), residues: 569 sheet: None (None), residues: 0 loop : -2.91 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 395 HIS 0.004 0.001 HIS B 441 PHE 0.021 0.001 PHE A 394 TYR 0.011 0.002 TYR B 558 ARG 0.003 0.000 ARG A 448 *********************** 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 165 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.6356 (m-80) REVERT: A 497 SER cc_start: 0.8305 (m) cc_final: 0.8031 (p) REVERT: A 512 TYR cc_start: 0.7835 (m-10) cc_final: 0.7508 (m-80) REVERT: B 245 ILE cc_start: 0.7284 (mm) cc_final: 0.7008 (mm) REVERT: B 331 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8264 (tt) REVERT: B 335 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.7041 (m-80) REVERT: B 502 ARG cc_start: 0.7946 (tmm-80) cc_final: 0.7713 (tmm-80) REVERT: B 613 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6565 (tm-30) outliers start: 41 outliers final: 27 residues processed: 151 average time/residue: 0.1757 time to fit residues: 36.6631 Evaluate side-chains 148 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 289 THR 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 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 547 LEU Chi-restraints excluded: chain B residue 310 ASN 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 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 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6808 Z= 0.189 Angle : 0.568 9.366 9268 Z= 0.294 Chirality : 0.040 0.185 1012 Planarity : 0.004 0.058 1134 Dihedral : 4.627 48.235 874 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.22 % Favored : 93.53 % Rotamer: Outliers : 5.82 % Allowed : 26.42 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.31), residues: 788 helix: 1.82 (0.22), residues: 565 sheet: None (None), residues: 0 loop : -3.00 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 395 HIS 0.005 0.001 HIS B 441 PHE 0.016 0.001 PHE A 394 TYR 0.010 0.001 TYR A 496 ARG 0.002 0.000 ARG A 570 *********************** 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 168 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 TYR cc_start: 0.7024 (OUTLIER) cc_final: 0.6282 (m-80) REVERT: A 497 SER cc_start: 0.8290 (m) cc_final: 0.8030 (p) REVERT: A 512 TYR cc_start: 0.7761 (m-10) cc_final: 0.7389 (m-80) REVERT: B 245 ILE cc_start: 0.7229 (mm) cc_final: 0.6940 (mm) REVERT: B 331 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8202 (tt) REVERT: B 335 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.7025 (m-80) REVERT: B 452 GLN cc_start: 0.7763 (tp40) cc_final: 0.7350 (tp40) REVERT: B 502 ARG cc_start: 0.7962 (tmm-80) cc_final: 0.7719 (tmm-80) REVERT: B 613 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6528 (tm-30) outliers start: 41 outliers final: 26 residues processed: 155 average time/residue: 0.1465 time to fit residues: 31.7276 Evaluate side-chains 148 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 299 HIS 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 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 613 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 47 optimal weight: 0.0370 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 0.0980 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 0.0970 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6808 Z= 0.173 Angle : 0.565 9.514 9268 Z= 0.292 Chirality : 0.039 0.171 1012 Planarity : 0.004 0.055 1134 Dihedral : 4.560 47.560 874 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.71 % Favored : 94.04 % Rotamer: Outliers : 4.83 % Allowed : 27.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.31), residues: 788 helix: 1.93 (0.22), residues: 565 sheet: None (None), residues: 0 loop : -3.00 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 395 HIS 0.005 0.001 HIS B 441 PHE 0.025 0.001 PHE A 358 TYR 0.010 0.001 TYR A 496 ARG 0.002 0.000 ARG A 570 *********************** 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 160 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 TYR cc_start: 0.6959 (OUTLIER) cc_final: 0.6249 (m-80) REVERT: A 497 SER cc_start: 0.8338 (m) cc_final: 0.8070 (p) REVERT: B 245 ILE cc_start: 0.7197 (mm) cc_final: 0.6912 (mm) REVERT: B 283 PHE cc_start: 0.7970 (m-10) cc_final: 0.7692 (m-10) REVERT: B 331 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8241 (tt) REVERT: B 502 ARG cc_start: 0.7989 (tmm-80) cc_final: 0.7753 (tmm-80) REVERT: B 508 MET cc_start: 0.6947 (mtm) cc_final: 0.6703 (mpp) REVERT: B 613 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6463 (tm-30) outliers start: 34 outliers final: 24 residues processed: 149 average time/residue: 0.1545 time to fit residues: 32.0006 Evaluate side-chains 148 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 345 TYR 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 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 530 LEU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 582 THR 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 14 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 0.0050 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6808 Z= 0.197 Angle : 0.575 9.493 9268 Z= 0.296 Chirality : 0.040 0.167 1012 Planarity : 0.004 0.053 1134 Dihedral : 4.508 45.382 874 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.35 % Favored : 93.40 % Rotamer: Outliers : 5.11 % Allowed : 27.13 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.31), residues: 788 helix: 1.90 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -2.99 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 395 HIS 0.005 0.001 HIS B 441 PHE 0.021 0.001 PHE A 358 TYR 0.010 0.001 TYR A 496 ARG 0.002 0.000 ARG A 448 *********************** 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 161 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 TYR cc_start: 0.7008 (OUTLIER) cc_final: 0.6258 (m-80) REVERT: A 497 SER cc_start: 0.8323 (m) cc_final: 0.8097 (p) REVERT: A 518 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.7298 (m-80) REVERT: B 245 ILE cc_start: 0.7177 (mm) cc_final: 0.6928 (mm) REVERT: B 283 PHE cc_start: 0.7995 (m-10) cc_final: 0.7735 (m-10) REVERT: B 314 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.6734 (mp10) REVERT: B 331 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8280 (tt) REVERT: B 502 ARG cc_start: 0.8017 (tmm-80) cc_final: 0.7776 (tmm-80) REVERT: B 508 MET cc_start: 0.6977 (mtm) cc_final: 0.6733 (mpp) REVERT: B 613 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6534 (tm-30) outliers start: 36 outliers final: 26 residues processed: 150 average time/residue: 0.1817 time to fit residues: 37.9646 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 : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 299 HIS 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6808 Z= 0.242 Angle : 0.597 9.457 9268 Z= 0.310 Chirality : 0.041 0.171 1012 Planarity : 0.004 0.050 1134 Dihedral : 4.569 44.467 874 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.35 % Favored : 93.40 % Rotamer: Outliers : 5.26 % Allowed : 27.13 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.31), residues: 788 helix: 1.75 (0.22), residues: 569 sheet: None (None), residues: 0 loop : -3.00 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 395 HIS 0.005 0.001 HIS B 441 PHE 0.020 0.001 PHE A 358 TYR 0.009 0.001 TYR A 352 ARG 0.002 0.000 ARG A 448 *********************** 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 163 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.6324 (m-80) REVERT: A 352 TYR cc_start: 0.7365 (m-80) cc_final: 0.7103 (m-80) REVERT: A 497 SER cc_start: 0.8333 (m) cc_final: 0.8097 (p) REVERT: B 245 ILE cc_start: 0.7222 (mm) cc_final: 0.6969 (mm) REVERT: B 331 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8263 (tt) REVERT: B 502 ARG cc_start: 0.7939 (tmm-80) cc_final: 0.7731 (tmm-80) REVERT: B 508 MET cc_start: 0.7002 (mtm) cc_final: 0.6754 (mpp) REVERT: B 613 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6575 (tm-30) outliers start: 37 outliers final: 28 residues processed: 153 average time/residue: 0.1935 time to fit residues: 41.5214 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 : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 299 HIS 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 61 optimal weight: 0.0000 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6808 Z= 0.184 Angle : 0.592 9.602 9268 Z= 0.307 Chirality : 0.040 0.164 1012 Planarity : 0.004 0.050 1134 Dihedral : 4.510 42.835 874 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.73 % Favored : 93.02 % Rotamer: Outliers : 4.69 % Allowed : 28.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.31), residues: 788 helix: 1.85 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -3.04 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 395 HIS 0.005 0.001 HIS B 441 PHE 0.020 0.001 PHE A 358 TYR 0.009 0.001 TYR A 496 ARG 0.004 0.000 ARG B 448 ********************** 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 161 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.6240 (m-80) REVERT: A 497 SER cc_start: 0.8316 (m) cc_final: 0.8096 (p) REVERT: A 518 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7403 (m-80) REVERT: B 245 ILE cc_start: 0.7184 (mm) cc_final: 0.6935 (mm) REVERT: B 331 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8275 (tt) REVERT: B 452 GLN cc_start: 0.8488 (mm110) cc_final: 0.8275 (mm-40) REVERT: B 502 ARG cc_start: 0.7932 (tmm-80) cc_final: 0.7727 (tmm-80) REVERT: B 508 MET cc_start: 0.6924 (mtm) cc_final: 0.6695 (mpp) REVERT: B 613 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6495 (tm-30) outliers start: 33 outliers final: 27 residues processed: 150 average time/residue: 0.1516 time to fit residues: 31.7383 Evaluate side-chains 156 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 345 TYR 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 429 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 0.0010 chunk 25 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN B 399 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.174406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140424 restraints weight = 9733.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.143915 restraints weight = 6129.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.146242 restraints weight = 4645.027| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6808 Z= 0.187 Angle : 0.594 9.636 9268 Z= 0.307 Chirality : 0.040 0.162 1012 Planarity : 0.004 0.050 1134 Dihedral : 4.498 42.116 874 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.47 % Favored : 93.27 % Rotamer: Outliers : 4.69 % Allowed : 27.98 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.31), residues: 788 helix: 1.85 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -3.05 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 395 HIS 0.011 0.001 HIS A 441 PHE 0.020 0.001 PHE A 358 TYR 0.010 0.001 TYR A 352 ARG 0.002 0.000 ARG A 448 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1638.22 seconds wall clock time: 30 minutes 48.96 seconds (1848.96 seconds total)