Starting phenix.real_space_refine on Thu Nov 14 14:35:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yex_39204/11_2024/8yex_39204.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yex_39204/11_2024/8yex_39204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yex_39204/11_2024/8yex_39204.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yex_39204/11_2024/8yex_39204.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yex_39204/11_2024/8yex_39204.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yex_39204/11_2024/8yex_39204.cif" } resolution = 3.68 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= 0.053 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 30 5.16 5 C 4384 2.51 5 N 1044 2.21 5 O 1074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 6532 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3266 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 14, 'TRANS': 377} Chain: "B" Number of atoms: 3266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3266 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 14, 'TRANS': 377} Time building chain proxies: 4.60, per 1000 atoms: 0.70 Number of scatterers: 6532 At special positions: 0 Unit cell: (78.1, 68.2, 130.9, 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 30 16.00 O 1074 8.00 N 1044 7.00 C 4384 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: 1.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 76.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 230 through 259 removed outlier: 3.768A pdb=" N THR A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 296 removed outlier: 3.816A pdb=" N ILE A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 337 removed outlier: 3.726A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.526A pdb=" N ALA A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 384 through 387 Processing helix chain 'A' and resid 390 through 402 Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.854A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 471 removed outlier: 4.392A pdb=" N ILE A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 472 through 502 removed outlier: 4.254A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 532 removed outlier: 3.799A pdb=" N PHE A 511 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 532 " --> pdb=" O TRP A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 583 removed outlier: 3.802A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 619 removed outlier: 4.404A pdb=" N ASP A 590 " --> pdb=" O PRO A 586 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) Proline residue: A 598 - end of helix removed outlier: 4.446A pdb=" N VAL A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE A 602 " --> pdb=" O PRO A 598 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 259 removed outlier: 3.902A pdb=" N THR B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 296 removed outlier: 3.513A pdb=" N ILE B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 removed outlier: 3.679A pdb=" N ILE B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 337 removed outlier: 3.812A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.063A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (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 503 removed outlier: 3.903A pdb=" N ALA B 480 " --> pdb=" O HIS B 476 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 530 removed outlier: 3.959A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER B 521 " --> pdb=" O PHE B 517 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR B 524 " --> pdb=" O ILE B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 583 removed outlier: 3.838A pdb=" N VAL B 567 " --> pdb=" O ILE B 563 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B 581 " --> pdb=" O ILE B 577 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 597 Processing helix chain 'B' and resid 599 through 619 removed outlier: 4.013A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1293 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: 1.70 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1932 1.34 - 1.46: 1951 1.46 - 1.58: 2826 1.58 - 1.70: 1 1.70 - 1.83: 42 Bond restraints: 6752 Sorted by residual: bond pdb=" CB PRO B 338 " pdb=" CG PRO B 338 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 4.03e+00 bond pdb=" C PHE A 474 " pdb=" N PRO A 475 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.20e-02 6.94e+03 2.15e+00 bond pdb=" CG LEU A 284 " pdb=" CD1 LEU A 284 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.97e+00 bond pdb=" CB PHE B 354 " pdb=" CG PHE B 354 " ideal model delta sigma weight residual 1.502 1.532 -0.030 2.30e-02 1.89e+03 1.67e+00 bond pdb=" CB TRP B 423 " pdb=" CG TRP B 423 " ideal model delta sigma weight residual 1.498 1.537 -0.039 3.10e-02 1.04e+03 1.59e+00 ... (remaining 6747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 8914 1.91 - 3.83: 216 3.83 - 5.74: 45 5.74 - 7.65: 11 7.65 - 9.57: 6 Bond angle restraints: 9192 Sorted by residual: angle pdb=" CA PRO B 338 " pdb=" N PRO B 338 " pdb=" CD PRO B 338 " ideal model delta sigma weight residual 112.00 107.08 4.92 1.40e+00 5.10e-01 1.24e+01 angle pdb=" N VAL A 346 " pdb=" CA VAL A 346 " pdb=" C VAL A 346 " ideal model delta sigma weight residual 112.96 110.03 2.93 1.00e+00 1.00e+00 8.57e+00 angle pdb=" N VAL B 341 " pdb=" CA VAL B 341 " pdb=" C VAL B 341 " ideal model delta sigma weight residual 111.67 108.97 2.70 9.50e-01 1.11e+00 8.11e+00 angle pdb=" CA GLU A 304 " pdb=" CB GLU A 304 " pdb=" CG GLU A 304 " ideal model delta sigma weight residual 114.10 119.75 -5.65 2.00e+00 2.50e-01 7.97e+00 angle pdb=" CA PRO B 598 " pdb=" C PRO B 598 " pdb=" O PRO B 598 " ideal model delta sigma weight residual 121.38 119.21 2.17 7.70e-01 1.69e+00 7.96e+00 ... (remaining 9187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3243 17.86 - 35.72: 453 35.72 - 53.57: 121 53.57 - 71.43: 9 71.43 - 89.29: 8 Dihedral angle restraints: 3834 sinusoidal: 1518 harmonic: 2316 Sorted by residual: dihedral pdb=" CB CYS B 415 " pdb=" SG CYS B 415 " pdb=" SG CYS B 440 " pdb=" CB CYS B 440 " ideal model delta sinusoidal sigma weight residual 93.00 157.38 -64.38 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CA PHE B 517 " pdb=" C PHE B 517 " pdb=" N TYR B 518 " pdb=" CA TYR B 518 " ideal model delta harmonic sigma weight residual 180.00 161.99 18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ALA A 473 " pdb=" C ALA A 473 " pdb=" N PHE A 474 " pdb=" CA PHE A 474 " ideal model delta harmonic sigma weight residual -180.00 -163.06 -16.94 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 3831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 719 0.044 - 0.087: 224 0.087 - 0.130: 54 0.130 - 0.174: 8 0.174 - 0.217: 1 Chirality restraints: 1006 Sorted by residual: chirality pdb=" CB ILE A 461 " pdb=" CA ILE A 461 " pdb=" CG1 ILE A 461 " pdb=" CG2 ILE A 461 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CG LEU B 536 " pdb=" CB LEU B 536 " pdb=" CD1 LEU B 536 " pdb=" CD2 LEU B 536 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CG LEU A 284 " pdb=" CB LEU A 284 " pdb=" CD1 LEU A 284 " pdb=" CD2 LEU A 284 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.41e-01 ... (remaining 1003 not shown) Planarity restraints: 1120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 337 " -0.064 5.00e-02 4.00e+02 9.49e-02 1.44e+01 pdb=" N PRO B 338 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 338 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 338 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 368 " -0.012 2.00e-02 2.50e+03 1.75e-02 6.12e+00 pdb=" CG TYR B 368 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR B 368 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 368 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR B 368 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 368 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 368 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 368 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 540 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C ASN A 540 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN A 540 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA A 541 " 0.011 2.00e-02 2.50e+03 ... (remaining 1117 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 137 2.69 - 3.24: 6951 3.24 - 3.80: 10704 3.80 - 4.35: 12674 4.35 - 4.90: 20693 Nonbonded interactions: 51159 Sorted by model distance: nonbonded pdb=" O VAL B 478 " pdb=" OH TYR B 524 " model vdw 2.139 3.040 nonbonded pdb=" OH TYR A 443 " pdb=" O THR A 580 " model vdw 2.183 3.040 nonbonded pdb=" OD2 ASP B 529 " pdb=" NH2 ARG B 570 " model vdw 2.187 3.120 nonbonded pdb=" O SER A 578 " pdb=" OG1 THR A 582 " model vdw 2.219 3.040 nonbonded pdb=" O CYS B 440 " pdb=" NH2 ARG B 448 " model vdw 2.220 3.120 ... (remaining 51154 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: 0.750 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.900 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 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 : 0.004 0.100 6752 Z= 0.266 Angle : 0.794 9.565 9192 Z= 0.427 Chirality : 0.045 0.217 1006 Planarity : 0.005 0.095 1120 Dihedral : 17.185 89.290 2336 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.72 % Allowed : 32.23 % 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 (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: 0.80 (0.31), residues: 780 helix: 1.42 (0.22), residues: 564 sheet: None (None), residues: 0 loop : -1.89 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 607 HIS 0.004 0.001 HIS A 504 PHE 0.024 0.002 PHE A 487 TYR 0.042 0.002 TYR B 368 ARG 0.007 0.001 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 149 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 284 LEU cc_start: 0.8820 (mt) cc_final: 0.8481 (mt) REVERT: B 308 ARG cc_start: 0.8362 (mmp80) cc_final: 0.7995 (mmp80) outliers start: 5 outliers final: 2 residues processed: 150 average time/residue: 0.1622 time to fit residues: 33.5927 Evaluate side-chains 144 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 590 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6752 Z= 0.228 Angle : 0.651 8.474 9192 Z= 0.335 Chirality : 0.043 0.138 1006 Planarity : 0.004 0.047 1120 Dihedral : 4.564 38.288 868 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.30 % Allowed : 26.65 % Favored : 70.06 % 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: 0.99 (0.31), residues: 780 helix: 1.59 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -1.97 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 292 HIS 0.004 0.001 HIS A 504 PHE 0.025 0.001 PHE B 511 TYR 0.025 0.002 TYR A 524 ARG 0.007 0.001 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 PHE cc_start: 0.8287 (t80) cc_final: 0.7922 (t80) REVERT: A 558 TYR cc_start: 0.2947 (OUTLIER) cc_final: 0.2041 (t80) REVERT: A 615 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7816 (mm-30) REVERT: B 308 ARG cc_start: 0.8408 (mmp80) cc_final: 0.8086 (mmp80) outliers start: 23 outliers final: 9 residues processed: 169 average time/residue: 0.1855 time to fit residues: 43.2324 Evaluate side-chains 149 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain B residue 417 TYR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 486 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 0.0470 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6752 Z= 0.179 Angle : 0.618 8.787 9192 Z= 0.314 Chirality : 0.042 0.141 1006 Planarity : 0.004 0.035 1120 Dihedral : 4.267 17.125 864 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.44 % Allowed : 25.21 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.31), residues: 780 helix: 1.80 (0.22), residues: 570 sheet: None (None), residues: 0 loop : -1.93 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 514 HIS 0.008 0.001 HIS B 499 PHE 0.016 0.001 PHE B 474 TYR 0.019 0.002 TYR A 524 ARG 0.005 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 PHE cc_start: 0.8403 (t80) cc_final: 0.8033 (t80) REVERT: A 531 LYS cc_start: 0.7642 (tptp) cc_final: 0.7261 (tptp) REVERT: A 532 MET cc_start: 0.7299 (mmm) cc_final: 0.7043 (mmm) REVERT: A 558 TYR cc_start: 0.2900 (OUTLIER) cc_final: 0.1876 (t80) REVERT: B 308 ARG cc_start: 0.8395 (mmp80) cc_final: 0.8095 (mmp80) REVERT: B 495 LEU cc_start: 0.9151 (mm) cc_final: 0.8834 (pp) outliers start: 31 outliers final: 13 residues processed: 177 average time/residue: 0.1524 time to fit residues: 38.4327 Evaluate side-chains 147 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 417 TYR Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6752 Z= 0.286 Angle : 0.680 8.992 9192 Z= 0.346 Chirality : 0.045 0.188 1006 Planarity : 0.004 0.038 1120 Dihedral : 4.319 17.323 864 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 5.59 % Allowed : 27.08 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.31), residues: 780 helix: 1.61 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -1.86 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 607 HIS 0.005 0.001 HIS B 499 PHE 0.026 0.002 PHE B 511 TYR 0.018 0.002 TYR B 483 ARG 0.005 0.001 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 PHE cc_start: 0.8453 (t80) cc_final: 0.8071 (t80) REVERT: A 462 GLN cc_start: 0.8771 (mt0) cc_final: 0.8510 (mt0) REVERT: A 531 LYS cc_start: 0.7664 (tptp) cc_final: 0.7105 (tptp) REVERT: A 532 MET cc_start: 0.7312 (mmm) cc_final: 0.7043 (mmm) REVERT: A 558 TYR cc_start: 0.3042 (OUTLIER) cc_final: 0.2167 (t80) REVERT: B 308 ARG cc_start: 0.8463 (mmp80) cc_final: 0.8141 (mmp80) outliers start: 39 outliers final: 24 residues processed: 171 average time/residue: 0.1413 time to fit residues: 34.2031 Evaluate side-chains 157 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 417 TYR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.0570 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 452 GLN B 476 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6752 Z= 0.191 Angle : 0.635 9.438 9192 Z= 0.321 Chirality : 0.043 0.149 1006 Planarity : 0.004 0.039 1120 Dihedral : 4.303 16.963 864 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.87 % Allowed : 27.94 % Favored : 68.19 % 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: 1.19 (0.31), residues: 780 helix: 1.67 (0.21), residues: 570 sheet: None (None), residues: 0 loop : -1.72 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 607 HIS 0.003 0.001 HIS A 504 PHE 0.020 0.001 PHE A 416 TYR 0.018 0.002 TYR A 496 ARG 0.004 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 PHE cc_start: 0.8604 (t80) cc_final: 0.8091 (t80) REVERT: A 531 LYS cc_start: 0.7610 (tptp) cc_final: 0.7114 (tptp) REVERT: A 532 MET cc_start: 0.7289 (mmm) cc_final: 0.7071 (mmm) REVERT: A 558 TYR cc_start: 0.2999 (OUTLIER) cc_final: 0.1982 (t80) REVERT: B 308 ARG cc_start: 0.8450 (mmp80) cc_final: 0.8124 (mmp80) REVERT: B 495 LEU cc_start: 0.9100 (mm) cc_final: 0.8806 (pp) REVERT: B 615 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7754 (mm-30) outliers start: 27 outliers final: 15 residues processed: 160 average time/residue: 0.1408 time to fit residues: 32.3951 Evaluate side-chains 147 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 417 TYR Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.0870 chunk 39 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 310 ASN B 452 GLN B 462 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6752 Z= 0.192 Angle : 0.629 10.152 9192 Z= 0.315 Chirality : 0.043 0.175 1006 Planarity : 0.004 0.040 1120 Dihedral : 4.264 17.280 864 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.58 % Allowed : 28.37 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.31), residues: 780 helix: 1.81 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -1.71 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 607 HIS 0.003 0.001 HIS A 504 PHE 0.031 0.001 PHE B 357 TYR 0.014 0.001 TYR A 467 ARG 0.003 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 PHE cc_start: 0.8578 (t80) cc_final: 0.8074 (t80) REVERT: A 531 LYS cc_start: 0.7575 (tptp) cc_final: 0.7064 (tptp) REVERT: A 558 TYR cc_start: 0.2986 (OUTLIER) cc_final: 0.1922 (t80) REVERT: B 308 ARG cc_start: 0.8420 (mmp80) cc_final: 0.8098 (mmp80) REVERT: B 495 LEU cc_start: 0.9071 (mm) cc_final: 0.8789 (pp) outliers start: 25 outliers final: 17 residues processed: 165 average time/residue: 0.1406 time to fit residues: 32.8331 Evaluate side-chains 152 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 417 TYR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 529 ASP 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: 5.9990 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 0.0970 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 GLN B 462 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6752 Z= 0.184 Angle : 0.626 10.475 9192 Z= 0.313 Chirality : 0.043 0.180 1006 Planarity : 0.004 0.041 1120 Dihedral : 4.247 17.381 864 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.15 % Allowed : 28.08 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.31), residues: 780 helix: 1.84 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -1.66 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 514 HIS 0.003 0.001 HIS B 504 PHE 0.016 0.001 PHE B 322 TYR 0.015 0.001 TYR A 467 ARG 0.004 0.000 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 TRP cc_start: 0.7999 (m-10) cc_final: 0.7749 (m-10) REVERT: A 322 PHE cc_start: 0.8559 (t80) cc_final: 0.8004 (t80) REVERT: A 398 ASP cc_start: 0.7596 (t0) cc_final: 0.6814 (t0) REVERT: A 531 LYS cc_start: 0.7493 (tptp) cc_final: 0.7250 (tptp) REVERT: A 558 TYR cc_start: 0.2955 (OUTLIER) cc_final: 0.1910 (t80) REVERT: B 308 ARG cc_start: 0.8452 (mmp80) cc_final: 0.8057 (mmp80) REVERT: B 495 LEU cc_start: 0.9084 (mm) cc_final: 0.8811 (pp) outliers start: 29 outliers final: 18 residues processed: 166 average time/residue: 0.1479 time to fit residues: 34.6477 Evaluate side-chains 158 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 417 TYR Chi-restraints excluded: chain B residue 419 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 0.0670 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN B 310 ASN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6752 Z= 0.188 Angle : 0.625 11.217 9192 Z= 0.316 Chirality : 0.043 0.164 1006 Planarity : 0.004 0.042 1120 Dihedral : 4.221 18.043 864 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.30 % Allowed : 29.37 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.31), residues: 780 helix: 1.84 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -1.64 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 607 HIS 0.003 0.001 HIS B 476 PHE 0.027 0.001 PHE B 511 TYR 0.018 0.001 TYR B 560 ARG 0.003 0.000 ARG A 548 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 PHE cc_start: 0.8563 (t80) cc_final: 0.8032 (t80) REVERT: A 462 GLN cc_start: 0.8782 (mt0) cc_final: 0.8564 (mt0) REVERT: A 558 TYR cc_start: 0.2960 (OUTLIER) cc_final: 0.1928 (t80) REVERT: B 308 ARG cc_start: 0.8468 (mmp80) cc_final: 0.8101 (mmp80) outliers start: 23 outliers final: 19 residues processed: 155 average time/residue: 0.1371 time to fit residues: 30.5494 Evaluate side-chains 157 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 417 TYR Chi-restraints excluded: chain B residue 419 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6752 Z= 0.198 Angle : 0.640 11.125 9192 Z= 0.326 Chirality : 0.043 0.156 1006 Planarity : 0.004 0.044 1120 Dihedral : 4.216 18.114 864 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.30 % Allowed : 29.23 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.31), residues: 780 helix: 1.84 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -1.61 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 607 HIS 0.003 0.001 HIS B 476 PHE 0.018 0.001 PHE B 322 TYR 0.016 0.001 TYR A 467 ARG 0.003 0.000 ARG A 548 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 PHE cc_start: 0.8564 (t80) cc_final: 0.8047 (t80) REVERT: A 462 GLN cc_start: 0.8775 (mt0) cc_final: 0.8541 (mt0) REVERT: A 558 TYR cc_start: 0.2781 (OUTLIER) cc_final: 0.1689 (t80) REVERT: B 308 ARG cc_start: 0.8475 (mmp80) cc_final: 0.8062 (mmp80) outliers start: 23 outliers final: 20 residues processed: 153 average time/residue: 0.1370 time to fit residues: 29.9126 Evaluate side-chains 157 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 417 TYR Chi-restraints excluded: chain B residue 419 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 ASN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6752 Z= 0.192 Angle : 0.632 10.985 9192 Z= 0.322 Chirality : 0.043 0.153 1006 Planarity : 0.004 0.044 1120 Dihedral : 4.196 18.634 864 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.15 % Allowed : 30.09 % Favored : 66.76 % 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: 1.46 (0.31), residues: 780 helix: 1.86 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -1.57 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 607 HIS 0.003 0.001 HIS B 476 PHE 0.027 0.001 PHE B 511 TYR 0.016 0.001 TYR A 496 ARG 0.004 0.000 ARG A 548 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 PHE cc_start: 0.8582 (t80) cc_final: 0.8105 (t80) REVERT: A 462 GLN cc_start: 0.8770 (mt0) cc_final: 0.8540 (mt0) REVERT: A 531 LYS cc_start: 0.7151 (tptp) cc_final: 0.6736 (tptp) REVERT: A 558 TYR cc_start: 0.2751 (OUTLIER) cc_final: 0.1553 (t80) REVERT: B 308 ARG cc_start: 0.8486 (mmp80) cc_final: 0.8071 (mmp80) outliers start: 22 outliers final: 20 residues processed: 149 average time/residue: 0.1389 time to fit residues: 29.7187 Evaluate side-chains 157 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 417 TYR Chi-restraints excluded: chain B residue 419 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.0010 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 7 optimal weight: 0.0970 chunk 11 optimal weight: 20.0000 chunk 54 optimal weight: 0.0870 chunk 3 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.175672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.135561 restraints weight = 13321.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.140208 restraints weight = 7129.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.143066 restraints weight = 5039.258| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6752 Z= 0.173 Angle : 0.640 10.903 9192 Z= 0.322 Chirality : 0.043 0.163 1006 Planarity : 0.004 0.043 1120 Dihedral : 4.163 18.284 864 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.72 % Allowed : 30.80 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.31), residues: 780 helix: 1.86 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -1.61 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 607 HIS 0.003 0.001 HIS A 504 PHE 0.025 0.001 PHE B 357 TYR 0.017 0.001 TYR A 496 ARG 0.005 0.000 ARG B 308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1596.46 seconds wall clock time: 30 minutes 0.21 seconds (1800.21 seconds total)