Starting phenix.real_space_refine on Sun Dec 29 13:21:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gso_34237/12_2024/8gso_34237_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gso_34237/12_2024/8gso_34237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gso_34237/12_2024/8gso_34237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gso_34237/12_2024/8gso_34237.map" model { file = "/net/cci-nas-00/data/ceres_data/8gso_34237/12_2024/8gso_34237_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gso_34237/12_2024/8gso_34237_neut.cif" } resolution = 3.3 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= 0.031 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 36 5.16 5 C 7060 2.51 5 N 1700 2.21 5 O 1828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10624 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5312 Classifications: {'peptide': 661} Link IDs: {'PTRANS': 30, 'TRANS': 630} Chain breaks: 1 Chain: "B" Number of atoms: 5312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5312 Classifications: {'peptide': 661} Link IDs: {'PTRANS': 30, 'TRANS': 630} Chain breaks: 1 Time building chain proxies: 7.01, per 1000 atoms: 0.66 Number of scatterers: 10624 At special positions: 0 Unit cell: (119.262, 112.59, 100.914, 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 36 16.00 O 1828 8.00 N 1700 7.00 C 7060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.05 Conformation dependent library (CDL) restraints added in 1.6 seconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2532 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 71.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 2 through 28 Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 80 through 110 Proline residue: A 104 - end of helix Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.536A pdb=" N ASN A 136 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 183 removed outlier: 4.529A pdb=" N VAL A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 229 through 232 removed outlier: 4.044A pdb=" N GLU A 232 " --> pdb=" O VAL A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.732A pdb=" N ASN A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 304 Processing helix chain 'A' and resid 317 through 326 Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 348 through 353 removed outlier: 4.368A pdb=" N ASN A 353 " --> pdb=" O GLN A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 389 Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.628A pdb=" N GLN A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A 395 " --> pdb=" O LYS A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 390 through 395' Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 416 through 438 removed outlier: 3.589A pdb=" N MET A 428 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 444 through 484 removed outlier: 4.020A pdb=" N LYS A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 483 " --> pdb=" O LYS A 479 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 484 " --> pdb=" O ASP A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 523 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 523 through 537 removed outlier: 4.428A pdb=" N LYS A 535 " --> pdb=" O HIS A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.583A pdb=" N VAL A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 572 Processing helix chain 'A' and resid 582 through 594 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 612 through 638 removed outlier: 4.234A pdb=" N LEU A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 645 No H-bonds generated for 'chain 'A' and resid 643 through 645' Processing helix chain 'A' and resid 646 through 665 removed outlier: 3.796A pdb=" N LEU A 654 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 689 through 693 removed outlier: 3.555A pdb=" N TYR A 693 " --> pdb=" O PHE A 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 28 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 60 through 67 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 80 through 110 Proline residue: B 104 - end of helix Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.536A pdb=" N ASN B 136 " --> pdb=" O GLN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 183 removed outlier: 4.529A pdb=" N VAL B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 229 through 232 removed outlier: 4.044A pdb=" N GLU B 232 " --> pdb=" O VAL B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.732A pdb=" N ASN B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 304 Processing helix chain 'B' and resid 317 through 326 Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 348 through 353 removed outlier: 4.368A pdb=" N ASN B 353 " --> pdb=" O GLN B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 389 Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 416 through 438 removed outlier: 3.589A pdb=" N MET B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 444 through 477 Processing helix chain 'B' and resid 489 through 523 Proline residue: B 499 - end of helix Processing helix chain 'B' and resid 523 through 537 removed outlier: 4.428A pdb=" N LYS B 535 " --> pdb=" O HIS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 549 removed outlier: 3.583A pdb=" N VAL B 544 " --> pdb=" O THR B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 572 Processing helix chain 'B' and resid 582 through 594 Processing helix chain 'B' and resid 595 through 598 Processing helix chain 'B' and resid 612 through 638 removed outlier: 4.234A pdb=" N LEU B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 645 No H-bonds generated for 'chain 'B' and resid 643 through 645' Processing helix chain 'B' and resid 646 through 665 removed outlier: 3.796A pdb=" N LEU B 654 " --> pdb=" O ILE B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 669 Processing helix chain 'B' and resid 689 through 693 removed outlier: 3.555A pdb=" N TYR B 693 " --> pdb=" O PHE B 690 " (cutoff:3.500A) 633 hydrogen bonds defined for protein. 1851 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: 3.51 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1544 1.27 - 1.40: 2908 1.40 - 1.54: 6299 1.54 - 1.68: 95 1.68 - 1.81: 60 Bond restraints: 10906 Sorted by residual: bond pdb=" C PHE A 95 " pdb=" O PHE A 95 " ideal model delta sigma weight residual 1.236 1.133 0.103 1.16e-02 7.43e+03 7.93e+01 bond pdb=" C PHE B 95 " pdb=" O PHE B 95 " ideal model delta sigma weight residual 1.236 1.133 0.103 1.16e-02 7.43e+03 7.93e+01 bond pdb=" C THR B 496 " pdb=" O THR B 496 " ideal model delta sigma weight residual 1.236 1.323 -0.087 1.16e-02 7.43e+03 5.68e+01 bond pdb=" C THR A 496 " pdb=" O THR A 496 " ideal model delta sigma weight residual 1.236 1.323 -0.087 1.16e-02 7.43e+03 5.68e+01 bond pdb=" N THR B 389 " pdb=" CA THR B 389 " ideal model delta sigma weight residual 1.463 1.559 -0.096 1.30e-02 5.92e+03 5.51e+01 ... (remaining 10901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 13746 2.93 - 5.87: 878 5.87 - 8.80: 149 8.80 - 11.74: 41 11.74 - 14.67: 10 Bond angle restraints: 14824 Sorted by residual: angle pdb=" C LEU A 107 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " ideal model delta sigma weight residual 119.56 108.73 10.83 1.02e+00 9.61e-01 1.13e+02 angle pdb=" C LEU B 107 " pdb=" N PRO B 108 " pdb=" CA PRO B 108 " ideal model delta sigma weight residual 119.56 108.73 10.83 1.02e+00 9.61e-01 1.13e+02 angle pdb=" N LYS B 145 " pdb=" CA LYS B 145 " pdb=" C LYS B 145 " ideal model delta sigma weight residual 109.96 95.29 14.67 1.49e+00 4.50e-01 9.69e+01 angle pdb=" N LYS A 145 " pdb=" CA LYS A 145 " pdb=" C LYS A 145 " ideal model delta sigma weight residual 109.96 95.29 14.67 1.49e+00 4.50e-01 9.69e+01 angle pdb=" N PHE B 632 " pdb=" CA PHE B 632 " pdb=" C PHE B 632 " ideal model delta sigma weight residual 113.88 101.88 12.00 1.23e+00 6.61e-01 9.51e+01 ... (remaining 14819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4960 17.46 - 34.91: 716 34.91 - 52.37: 485 52.37 - 69.82: 251 69.82 - 87.28: 22 Dihedral angle restraints: 6434 sinusoidal: 2526 harmonic: 3908 Sorted by residual: dihedral pdb=" C ILE B 397 " pdb=" N ILE B 397 " pdb=" CA ILE B 397 " pdb=" CB ILE B 397 " ideal model delta harmonic sigma weight residual -122.00 -136.17 14.17 0 2.50e+00 1.60e-01 3.21e+01 dihedral pdb=" C ILE B 379 " pdb=" N ILE B 379 " pdb=" CA ILE B 379 " pdb=" CB ILE B 379 " ideal model delta harmonic sigma weight residual -122.00 -135.10 13.10 0 2.50e+00 1.60e-01 2.75e+01 dihedral pdb=" C ILE A 379 " pdb=" N ILE A 379 " pdb=" CA ILE A 379 " pdb=" CB ILE A 379 " ideal model delta harmonic sigma weight residual -122.00 -135.10 13.10 0 2.50e+00 1.60e-01 2.75e+01 ... (remaining 6431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1305 0.111 - 0.221: 324 0.221 - 0.332: 57 0.332 - 0.442: 26 0.442 - 0.553: 10 Chirality restraints: 1722 Sorted by residual: chirality pdb=" CA PRO B 499 " pdb=" N PRO B 499 " pdb=" C PRO B 499 " pdb=" CB PRO B 499 " both_signs ideal model delta sigma weight residual False 2.72 2.17 0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" CA PRO A 499 " pdb=" N PRO A 499 " pdb=" C PRO A 499 " pdb=" CB PRO A 499 " both_signs ideal model delta sigma weight residual False 2.72 2.17 0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" CA ILE B 397 " pdb=" N ILE B 397 " pdb=" C ILE B 397 " pdb=" CB ILE B 397 " both_signs ideal model delta sigma weight residual False 2.43 1.91 0.52 2.00e-01 2.50e+01 6.74e+00 ... (remaining 1719 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 107 " 0.123 5.00e-02 4.00e+02 1.85e-01 5.50e+01 pdb=" N PRO A 108 " -0.321 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " 0.091 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " 0.106 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 107 " -0.123 5.00e-02 4.00e+02 1.85e-01 5.50e+01 pdb=" N PRO B 108 " 0.321 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " -0.091 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " -0.106 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 498 " 0.121 5.00e-02 4.00e+02 1.81e-01 5.25e+01 pdb=" N PRO A 499 " -0.313 5.00e-02 4.00e+02 pdb=" CA PRO A 499 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO A 499 " 0.105 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 20 1.93 - 2.68: 842 2.68 - 3.42: 15677 3.42 - 4.16: 27139 4.16 - 4.90: 46532 Nonbonded interactions: 90210 Sorted by model distance: nonbonded pdb=" CZ2 TRP A 240 " pdb=" CE LYS A 294 " model vdw 1.194 3.740 nonbonded pdb=" CZ2 TRP B 240 " pdb=" CE LYS B 294 " model vdw 1.194 3.740 nonbonded pdb=" NE1 TRP A 240 " pdb=" NZ LYS A 294 " model vdw 1.407 3.200 nonbonded pdb=" NE1 TRP B 240 " pdb=" NZ LYS B 294 " model vdw 1.407 3.200 nonbonded pdb=" CE2 TRP B 240 " pdb=" NZ LYS B 294 " model vdw 1.446 3.340 ... (remaining 90205 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 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: 0.000 Extract box with map and model: 1.140 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.720 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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: 35.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 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 : 0.013 0.103 10906 Z= 0.822 Angle : 1.663 14.670 14824 Z= 1.143 Chirality : 0.112 0.553 1722 Planarity : 0.014 0.185 1808 Dihedral : 25.120 87.276 3902 Min Nonbonded Distance : 1.194 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 6.70 % Allowed : 17.05 % Favored : 76.26 % Rotamer: Outliers : 41.49 % Allowed : 12.07 % Favored : 46.44 % Cbeta Deviations : 1.42 % 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: -5.21 (0.18), residues: 1314 helix: -2.57 (0.13), residues: 864 sheet: -6.27 (0.42), residues: 24 loop : -4.97 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 548 HIS 0.005 0.001 HIS B 617 PHE 0.030 0.002 PHE B 513 TYR 0.010 0.002 TYR B 555 ARG 0.002 0.000 ARG B 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 478 poor density : 314 time to evaluate : 1.129 Fit side-chains REVERT: A 2 GLU cc_start: 0.4885 (OUTLIER) cc_final: 0.4439 (tt0) REVERT: A 104 PRO cc_start: 0.6399 (OUTLIER) cc_final: 0.5087 (Cg_exo) REVERT: A 120 LYS cc_start: 0.5868 (OUTLIER) cc_final: 0.5664 (mmmt) REVERT: A 169 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7412 (tttm) REVERT: A 204 ASP cc_start: -0.0318 (OUTLIER) cc_final: -0.0536 (t0) REVERT: A 223 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7772 (p) REVERT: A 337 THR cc_start: 0.7627 (m) cc_final: 0.7148 (p) REVERT: A 420 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8096 (mt) REVERT: A 466 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7251 (mp) REVERT: A 481 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8489 (tt) REVERT: A 532 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.8004 (mt) REVERT: A 607 GLU cc_start: 0.7583 (tp30) cc_final: 0.7127 (mm-30) REVERT: A 619 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8112 (mmt90) REVERT: B 2 GLU cc_start: 0.4908 (OUTLIER) cc_final: 0.4550 (tt0) REVERT: B 104 PRO cc_start: 0.6415 (OUTLIER) cc_final: 0.5093 (Cg_exo) REVERT: B 169 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7415 (tttm) REVERT: B 204 ASP cc_start: -0.0315 (OUTLIER) cc_final: -0.0536 (t0) REVERT: B 223 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7776 (p) REVERT: B 337 THR cc_start: 0.7632 (m) cc_final: 0.7150 (p) REVERT: B 420 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8114 (mt) REVERT: B 466 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7244 (mp) REVERT: B 532 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7998 (mt) REVERT: B 607 GLU cc_start: 0.7579 (tp30) cc_final: 0.7124 (mm-30) REVERT: B 619 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8107 (mmt90) outliers start: 478 outliers final: 87 residues processed: 634 average time/residue: 0.2575 time to fit residues: 221.9244 Evaluate side-chains 299 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 192 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 104 PRO Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 499 PRO Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 PRO Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 499 PRO Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 619 ARG Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 660 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 136 ASN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 ASN A 596 ASN A 628 GLN B 40 ASN B 136 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 ASN B 596 ASN B 628 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10906 Z= 0.314 Angle : 0.898 8.618 14824 Z= 0.472 Chirality : 0.051 0.250 1722 Planarity : 0.008 0.088 1808 Dihedral : 13.115 66.186 1635 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 1.29 % Allowed : 13.85 % Favored : 84.86 % Rotamer: Outliers : 10.94 % Allowed : 23.26 % Favored : 65.80 % 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: -2.98 (0.22), residues: 1314 helix: -0.64 (0.16), residues: 898 sheet: -6.33 (0.37), residues: 24 loop : -4.89 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 49 HIS 0.003 0.001 HIS A 670 PHE 0.024 0.002 PHE B 369 TYR 0.013 0.002 TYR B 572 ARG 0.007 0.001 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 201 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.4770 (OUTLIER) cc_final: 0.4556 (tt0) REVERT: A 120 LYS cc_start: 0.5684 (OUTLIER) cc_final: 0.5374 (mmmt) REVERT: A 334 ASP cc_start: 0.5303 (t0) cc_final: 0.5067 (t0) REVERT: A 337 THR cc_start: 0.7680 (m) cc_final: 0.7145 (p) REVERT: A 420 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8382 (mt) REVERT: A 570 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.7559 (t80) REVERT: A 624 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8886 (tp) REVERT: B 334 ASP cc_start: 0.5301 (t0) cc_final: 0.5065 (t0) REVERT: B 337 THR cc_start: 0.7674 (m) cc_final: 0.7149 (p) REVERT: B 420 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8379 (mt) REVERT: B 570 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.7566 (t80) REVERT: B 624 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8890 (tp) outliers start: 126 outliers final: 54 residues processed: 305 average time/residue: 0.1831 time to fit residues: 85.2224 Evaluate side-chains 217 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 155 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 659 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 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 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10906 Z= 0.269 Angle : 0.775 8.648 14824 Z= 0.404 Chirality : 0.047 0.185 1722 Planarity : 0.006 0.074 1808 Dihedral : 10.228 72.254 1508 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.68 % Allowed : 14.16 % Favored : 85.16 % Rotamer: Outliers : 7.81 % Allowed : 26.22 % Favored : 65.97 % 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: -1.87 (0.23), residues: 1314 helix: 0.21 (0.17), residues: 890 sheet: -4.66 (1.19), residues: 10 loop : -4.55 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 613 HIS 0.004 0.001 HIS B 531 PHE 0.020 0.001 PHE A 513 TYR 0.009 0.001 TYR B 634 ARG 0.005 0.001 ARG B 678 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 187 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: A 478 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8423 (m) REVERT: A 573 SER cc_start: 0.8448 (t) cc_final: 0.8073 (m) REVERT: A 647 ILE cc_start: 0.7932 (tp) cc_final: 0.7463 (tt) REVERT: B 337 THR cc_start: 0.7653 (m) cc_final: 0.6997 (p) REVERT: B 573 SER cc_start: 0.8452 (t) cc_final: 0.8084 (m) REVERT: B 647 ILE cc_start: 0.7946 (tp) cc_final: 0.7474 (tt) outliers start: 90 outliers final: 59 residues processed: 260 average time/residue: 0.1772 time to fit residues: 69.6397 Evaluate side-chains 228 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 168 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 659 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.1980 chunk 90 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 80 optimal weight: 0.0870 chunk 120 optimal weight: 0.9980 chunk 127 optimal weight: 0.0060 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 0.0870 overall best weight: 0.2552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN A 617 HIS A 628 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10906 Z= 0.229 Angle : 0.738 8.589 14824 Z= 0.380 Chirality : 0.044 0.174 1722 Planarity : 0.006 0.065 1808 Dihedral : 9.295 75.445 1489 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.61 % Allowed : 12.40 % Favored : 86.99 % Rotamer: Outliers : 6.08 % Allowed : 29.25 % Favored : 64.67 % 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: -1.35 (0.24), residues: 1314 helix: 0.54 (0.18), residues: 892 sheet: -4.58 (1.14), residues: 10 loop : -4.20 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 548 HIS 0.004 0.001 HIS B 531 PHE 0.019 0.001 PHE A 513 TYR 0.012 0.001 TYR B 572 ARG 0.007 0.001 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 184 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7109 (ptp-170) REVERT: A 390 LEU cc_start: 0.7243 (tp) cc_final: 0.6863 (tp) REVERT: A 478 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8397 (m) REVERT: A 570 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7450 (t80) REVERT: A 573 SER cc_start: 0.8188 (t) cc_final: 0.7946 (m) REVERT: A 611 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7591 (tpt-90) REVERT: B 318 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7094 (ptp-170) REVERT: B 459 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7679 (t80) REVERT: B 570 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7577 (t80) REVERT: B 573 SER cc_start: 0.8215 (t) cc_final: 0.8015 (m) REVERT: B 611 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7598 (tpt-90) outliers start: 70 outliers final: 42 residues processed: 238 average time/residue: 0.1936 time to fit residues: 68.7235 Evaluate side-chains 217 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 659 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.6038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10906 Z= 0.254 Angle : 0.722 7.858 14824 Z= 0.373 Chirality : 0.045 0.165 1722 Planarity : 0.006 0.060 1808 Dihedral : 8.756 81.680 1485 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.68 % Allowed : 12.63 % Favored : 86.68 % Rotamer: Outliers : 7.03 % Allowed : 27.34 % Favored : 65.62 % 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: -1.00 (0.24), residues: 1314 helix: 0.79 (0.18), residues: 880 sheet: -4.34 (1.33), residues: 10 loop : -3.88 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 548 HIS 0.004 0.001 HIS B 531 PHE 0.021 0.001 PHE A 513 TYR 0.013 0.001 TYR B 634 ARG 0.004 0.000 ARG A 678 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 169 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.7086 (ppp) cc_final: 0.6789 (ppp) REVERT: A 390 LEU cc_start: 0.7372 (tp) cc_final: 0.6997 (tp) REVERT: A 573 SER cc_start: 0.8179 (t) cc_final: 0.7937 (m) REVERT: A 611 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7694 (tpt-90) REVERT: B 332 MET cc_start: 0.7089 (ppp) cc_final: 0.6788 (ppp) REVERT: B 573 SER cc_start: 0.8186 (t) cc_final: 0.7928 (m) REVERT: B 611 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7703 (tpt-90) outliers start: 81 outliers final: 46 residues processed: 226 average time/residue: 0.1929 time to fit residues: 66.0032 Evaluate side-chains 201 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 659 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 106 optimal weight: 0.0980 chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10906 Z= 0.241 Angle : 0.714 7.219 14824 Z= 0.369 Chirality : 0.045 0.214 1722 Planarity : 0.005 0.059 1808 Dihedral : 7.693 85.982 1462 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.18 % Favored : 87.29 % Rotamer: Outliers : 6.08 % Allowed : 27.60 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.71 (0.24), residues: 1314 helix: 0.87 (0.18), residues: 890 sheet: None (None), residues: 0 loop : -3.53 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 548 HIS 0.004 0.001 HIS B 531 PHE 0.020 0.001 PHE B 513 TYR 0.010 0.001 TYR A 634 ARG 0.003 0.000 ARG B 318 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 161 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.3985 (t0) cc_final: 0.3765 (t0) REVERT: A 334 ASP cc_start: 0.4806 (t0) cc_final: 0.4536 (t0) REVERT: A 390 LEU cc_start: 0.7375 (tp) cc_final: 0.7054 (tp) REVERT: A 611 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7598 (tpt-90) REVERT: B 198 ASP cc_start: 0.3997 (t0) cc_final: 0.3693 (t0) REVERT: B 334 ASP cc_start: 0.4813 (t0) cc_final: 0.4535 (t0) REVERT: B 573 SER cc_start: 0.8120 (t) cc_final: 0.7904 (m) REVERT: B 611 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7612 (tpt-90) outliers start: 70 outliers final: 53 residues processed: 211 average time/residue: 0.2081 time to fit residues: 64.4041 Evaluate side-chains 182 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 127 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 0.0870 chunk 127 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 0.0770 chunk 50 optimal weight: 0.0870 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10906 Z= 0.222 Angle : 0.702 8.125 14824 Z= 0.360 Chirality : 0.044 0.184 1722 Planarity : 0.005 0.057 1808 Dihedral : 7.119 58.624 1459 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.18 % Favored : 87.29 % Rotamer: Outliers : 5.56 % Allowed : 28.65 % Favored : 65.80 % 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: -0.52 (0.25), residues: 1314 helix: 1.05 (0.18), residues: 882 sheet: -4.84 (0.87), residues: 20 loop : -3.33 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 548 HIS 0.004 0.001 HIS B 531 PHE 0.019 0.001 PHE B 459 TYR 0.010 0.001 TYR A 634 ARG 0.003 0.000 ARG A 558 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 148 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: A 390 LEU cc_start: 0.7334 (tp) cc_final: 0.7024 (tp) REVERT: A 570 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7461 (t80) REVERT: A 611 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7677 (tpt-90) REVERT: B 611 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7686 (tpt-90) outliers start: 64 outliers final: 46 residues processed: 197 average time/residue: 0.2270 time to fit residues: 64.9756 Evaluate side-chains 181 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 132 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 0.0670 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.6758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10906 Z= 0.236 Angle : 0.716 10.409 14824 Z= 0.364 Chirality : 0.045 0.237 1722 Planarity : 0.005 0.053 1808 Dihedral : 6.699 57.710 1452 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.53 % Allowed : 11.95 % Favored : 87.52 % Rotamer: Outliers : 4.95 % Allowed : 28.73 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.47 (0.24), residues: 1314 helix: 1.08 (0.18), residues: 894 sheet: -4.63 (0.91), residues: 20 loop : -3.44 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 548 HIS 0.004 0.001 HIS A 531 PHE 0.021 0.001 PHE A 513 TYR 0.008 0.001 TYR A 634 ARG 0.004 0.000 ARG B 318 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 135 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7568 (t80) REVERT: A 611 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7785 (tpt-90) REVERT: B 611 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7797 (tpt-90) outliers start: 57 outliers final: 49 residues processed: 176 average time/residue: 0.2001 time to fit residues: 52.3710 Evaluate side-chains 181 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 129 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.6925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10906 Z= 0.238 Angle : 0.724 11.280 14824 Z= 0.366 Chirality : 0.045 0.215 1722 Planarity : 0.005 0.051 1808 Dihedral : 6.325 56.524 1448 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.33 % Favored : 87.29 % Rotamer: Outliers : 5.03 % Allowed : 28.39 % Favored : 66.58 % 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: -0.38 (0.24), residues: 1314 helix: 1.14 (0.18), residues: 896 sheet: -4.82 (0.87), residues: 20 loop : -3.40 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 548 HIS 0.004 0.001 HIS A 447 PHE 0.020 0.001 PHE B 513 TYR 0.008 0.001 TYR A 634 ARG 0.010 0.001 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 139 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.7500 (t80) REVERT: A 611 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7990 (tpt-90) REVERT: B 611 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8000 (tpt-90) outliers start: 58 outliers final: 49 residues processed: 182 average time/residue: 0.2019 time to fit residues: 54.6906 Evaluate side-chains 178 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 126 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.7041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10906 Z= 0.250 Angle : 0.740 10.252 14824 Z= 0.375 Chirality : 0.045 0.208 1722 Planarity : 0.005 0.048 1808 Dihedral : 6.302 56.162 1448 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.40 % Favored : 87.21 % Rotamer: Outliers : 4.77 % Allowed : 28.99 % Favored : 66.23 % 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: -0.35 (0.24), residues: 1314 helix: 1.14 (0.18), residues: 906 sheet: -4.65 (0.90), residues: 20 loop : -3.43 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 548 HIS 0.004 0.001 HIS A 531 PHE 0.022 0.001 PHE A 513 TYR 0.008 0.001 TYR A 364 ARG 0.009 0.001 ARG A 395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 137 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.6999 (ppp) cc_final: 0.6698 (ppp) REVERT: A 570 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7579 (t80) REVERT: B 332 MET cc_start: 0.7030 (ppp) cc_final: 0.6749 (ppp) outliers start: 55 outliers final: 45 residues processed: 176 average time/residue: 0.2194 time to fit residues: 57.7428 Evaluate side-chains 176 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 130 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 647 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 92 optimal weight: 0.0040 chunk 5 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.157195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.121517 restraints weight = 13336.729| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.34 r_work: 0.3305 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.7231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10906 Z= 0.218 Angle : 0.714 9.742 14824 Z= 0.362 Chirality : 0.044 0.207 1722 Planarity : 0.005 0.044 1808 Dihedral : 6.106 54.388 1446 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.56 % Favored : 87.06 % Rotamer: Outliers : 4.43 % Allowed : 29.34 % Favored : 66.23 % 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: -0.37 (0.24), residues: 1314 helix: 1.22 (0.18), residues: 894 sheet: -4.81 (0.85), residues: 20 loop : -3.57 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 548 HIS 0.005 0.001 HIS A 531 PHE 0.019 0.001 PHE B 513 TYR 0.010 0.001 TYR B 536 ARG 0.009 0.001 ARG A 395 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2559.16 seconds wall clock time: 48 minutes 12.92 seconds (2892.92 seconds total)