Starting phenix.real_space_refine on Sun Dec 29 13:21:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gro_34210/12_2024/8gro_34210_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gro_34210/12_2024/8gro_34210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gro_34210/12_2024/8gro_34210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gro_34210/12_2024/8gro_34210.map" model { file = "/net/cci-nas-00/data/ceres_data/8gro_34210/12_2024/8gro_34210_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gro_34210/12_2024/8gro_34210_neut.cif" } resolution = 3.5 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= 0.024 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): 0.10s 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: 6.66, per 1000 atoms: 0.63 Number of scatterers: 10624 At special positions: 0 Unit cell: (114.258, 114.258, 103.416, 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: 3.80 Conformation dependent library (CDL) restraints added in 1.5 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 71.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 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 389 through 396 removed outlier: 4.069A pdb=" N ILE A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 416 through 438 removed outlier: 3.588A 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 482 removed outlier: 3.824A pdb=" N LYS A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A 480 " --> pdb=" O ASN A 476 " (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: 3.795A 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: 3.556A 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 389 through 397 removed outlier: 4.428A pdb=" N ILE B 396 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 416 through 438 removed outlier: 3.588A 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 480 removed outlier: 3.941A pdb=" N LYS B 479 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) 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: 3.795A 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: 3.556A pdb=" N TYR B 693 " --> pdb=" O PHE B 690 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1872 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: 3.49 Time building geometry restraints manager: 4.12 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: 1542 1.27 - 1.40: 2908 1.40 - 1.54: 6311 1.54 - 1.68: 85 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 1.132 0.104 1.16e-02 7.43e+03 7.97e+01 bond pdb=" C PHE B 95 " pdb=" O PHE B 95 " ideal model delta sigma weight residual 1.236 1.132 0.104 1.16e-02 7.43e+03 7.97e+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 5.58e+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 5.58e+01 bond pdb=" N THR A 389 " pdb=" CA THR A 389 " ideal model delta sigma weight residual 1.463 1.559 -0.096 1.30e-02 5.92e+03 5.50e+01 ... (remaining 10901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 13733 2.93 - 5.87: 887 5.87 - 8.80: 154 8.80 - 11.74: 42 11.74 - 14.67: 8 Bond angle restraints: 14824 Sorted by residual: angle pdb=" C LEU B 107 " pdb=" N PRO B 108 " pdb=" CA PRO B 108 " ideal model delta sigma weight residual 119.56 108.71 10.85 1.02e+00 9.61e-01 1.13e+02 angle pdb=" C LEU A 107 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " ideal model delta sigma weight residual 119.56 108.71 10.85 1.02e+00 9.61e-01 1.13e+02 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 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 PHE B 632 " pdb=" CA PHE B 632 " pdb=" C PHE B 632 " ideal model delta sigma weight residual 113.88 101.90 11.98 1.23e+00 6.61e-01 9.49e+01 ... (remaining 14819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4945 17.46 - 34.92: 726 34.92 - 52.38: 482 52.38 - 69.84: 259 69.84 - 87.30: 22 Dihedral angle restraints: 6434 sinusoidal: 2526 harmonic: 3908 Sorted by residual: 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 -135.13 13.13 0 2.50e+00 1.60e-01 2.76e+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 -135.13 13.13 0 2.50e+00 1.60e-01 2.76e+01 dihedral pdb=" C VAL A 559 " pdb=" N VAL A 559 " pdb=" CA VAL A 559 " pdb=" CB VAL A 559 " ideal model delta harmonic sigma weight residual -122.00 -134.25 12.25 0 2.50e+00 1.60e-01 2.40e+01 ... (remaining 6431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1301 0.110 - 0.220: 325 0.220 - 0.330: 62 0.330 - 0.440: 26 0.440 - 0.550: 8 Chirality restraints: 1722 Sorted by residual: 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 7.57e+00 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 7.57e+00 chirality pdb=" CA LEU B 103 " pdb=" N LEU B 103 " pdb=" C LEU B 103 " pdb=" CB LEU B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.18e+00 ... (remaining 1719 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 107 " -0.123 5.00e-02 4.00e+02 1.86e-01 5.51e+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 107 " 0.123 5.00e-02 4.00e+02 1.86e-01 5.51e+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 498 " 0.121 5.00e-02 4.00e+02 1.81e-01 5.26e+01 pdb=" N PRO B 499 " -0.313 5.00e-02 4.00e+02 pdb=" CA PRO B 499 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO B 499 " 0.105 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.94: 10 1.94 - 2.68: 835 2.68 - 3.42: 15682 3.42 - 4.16: 27148 4.16 - 4.90: 46423 Nonbonded interactions: 90098 Sorted by model distance: nonbonded pdb=" CZ2 TRP B 240 " pdb=" CE LYS B 294 " model vdw 1.194 3.740 nonbonded pdb=" CZ2 TRP A 240 " pdb=" CE LYS A 294 " model vdw 1.194 3.740 nonbonded pdb=" NE1 TRP B 240 " pdb=" NZ LYS B 294 " model vdw 1.408 3.200 nonbonded pdb=" NE1 TRP A 240 " pdb=" NZ LYS A 294 " model vdw 1.408 3.200 nonbonded pdb=" CE2 TRP A 240 " pdb=" NZ LYS A 294 " model vdw 1.446 3.340 ... (remaining 90093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 28.300 Find NCS groups from input model: 0.290 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 0.104 10906 Z= 0.822 Angle : 1.667 14.669 14824 Z= 1.149 Chirality : 0.111 0.550 1722 Planarity : 0.014 0.186 1808 Dihedral : 25.245 87.304 3902 Min Nonbonded Distance : 1.194 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 6.62 % Allowed : 16.29 % Favored : 77.09 % Rotamer: Outliers : 41.49 % Allowed : 13.11 % Favored : 45.40 % Cbeta Deviations : 1.34 % 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: -2.60 (0.13), residues: 876 sheet: -6.27 (0.42), residues: 24 loop : -4.95 (0.25), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 548 HIS 0.005 0.001 HIS A 617 PHE 0.030 0.002 PHE A 513 TYR 0.010 0.002 TYR B 555 ARG 0.001 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 777 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 478 poor density : 299 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5703 (tt0) REVERT: A 104 PRO cc_start: 0.7192 (OUTLIER) cc_final: 0.5730 (Cg_exo) REVERT: A 144 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6699 (mtmm) REVERT: A 153 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7634 (tp) REVERT: A 187 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8193 (t) REVERT: A 229 VAL cc_start: 0.6806 (OUTLIER) cc_final: 0.6550 (t) REVERT: A 236 VAL cc_start: 0.4525 (OUTLIER) cc_final: 0.4252 (t) REVERT: A 287 LEU cc_start: 0.5414 (OUTLIER) cc_final: 0.4398 (mp) REVERT: A 363 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.6279 (mt0) REVERT: A 466 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.6823 (mt) REVERT: A 492 ASN cc_start: 0.3974 (OUTLIER) cc_final: 0.3700 (t0) REVERT: A 513 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6231 (t80) REVERT: A 545 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7328 (mmtm) REVERT: A 595 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6946 (ttt90) REVERT: A 641 PHE cc_start: 0.4896 (OUTLIER) cc_final: 0.4302 (m-10) REVERT: A 680 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7580 (mt) REVERT: B 2 GLU cc_start: 0.6199 (OUTLIER) cc_final: 0.5779 (tt0) REVERT: B 104 PRO cc_start: 0.7174 (OUTLIER) cc_final: 0.5705 (Cg_exo) REVERT: B 144 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6685 (mtmm) REVERT: B 187 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8180 (t) REVERT: B 229 VAL cc_start: 0.6785 (OUTLIER) cc_final: 0.6536 (t) REVERT: B 236 VAL cc_start: 0.4539 (OUTLIER) cc_final: 0.4251 (t) REVERT: B 287 LEU cc_start: 0.5414 (OUTLIER) cc_final: 0.4380 (mp) REVERT: B 363 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6329 (mt0) REVERT: B 400 ILE cc_start: 0.6313 (OUTLIER) cc_final: 0.6060 (tt) REVERT: B 466 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.6825 (mt) REVERT: B 492 ASN cc_start: 0.4013 (OUTLIER) cc_final: 0.3710 (t0) REVERT: B 499 PRO cc_start: 0.8688 (OUTLIER) cc_final: 0.8478 (Cg_exo) REVERT: B 513 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6214 (t80) REVERT: B 545 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7323 (mmtm) REVERT: B 595 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6967 (ttt90) REVERT: B 641 PHE cc_start: 0.4862 (OUTLIER) cc_final: 0.4295 (m-10) REVERT: B 680 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7571 (mt) outliers start: 478 outliers final: 120 residues processed: 642 average time/residue: 0.2571 time to fit residues: 224.5095 Evaluate side-chains 337 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 184 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 52 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 104 PRO Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 ASP 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 144 LYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 411 THR 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 484 ASN Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 104 PRO Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 ASP 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 144 LYS Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 411 THR 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 478 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 499 PRO Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 545 LYS Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 653 SER Chi-restraints excluded: chain B residue 680 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 40 ASN A 208 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 HIS A 628 GLN A 662 GLN B 33 ASN B 40 ASN B 208 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 HIS B 617 HIS B 628 GLN B 662 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10906 Z= 0.319 Angle : 0.915 12.305 14824 Z= 0.478 Chirality : 0.049 0.178 1722 Planarity : 0.007 0.087 1808 Dihedral : 14.852 80.473 1743 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 1.22 % Allowed : 13.09 % Favored : 85.69 % Rotamer: Outliers : 12.76 % Allowed : 23.78 % Favored : 63.45 % 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: -3.05 (0.22), residues: 1314 helix: -0.73 (0.16), residues: 890 sheet: -6.58 (0.29), residues: 24 loop : -4.70 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 613 HIS 0.008 0.001 HIS A 329 PHE 0.022 0.002 PHE A 224 TYR 0.018 0.002 TYR B 215 ARG 0.006 0.001 ARG A 395 *********************** 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 380 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 233 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.5442 (tt0) REVERT: A 103 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7831 (mp) REVERT: A 236 VAL cc_start: 0.4538 (OUTLIER) cc_final: 0.3712 (t) REVERT: A 487 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7095 (mp) REVERT: A 513 PHE cc_start: 0.6995 (OUTLIER) cc_final: 0.6244 (t80) REVERT: A 581 ILE cc_start: 0.9008 (tt) cc_final: 0.8729 (tt) REVERT: A 641 PHE cc_start: 0.4756 (OUTLIER) cc_final: 0.4038 (m-80) REVERT: B 2 GLU cc_start: 0.6003 (OUTLIER) cc_final: 0.5565 (tt0) REVERT: B 103 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7820 (mp) REVERT: B 236 VAL cc_start: 0.4599 (OUTLIER) cc_final: 0.3760 (t) REVERT: B 392 ASN cc_start: 0.6452 (t0) cc_final: 0.6234 (t0) REVERT: B 400 ILE cc_start: 0.5619 (OUTLIER) cc_final: 0.5323 (pp) REVERT: B 513 PHE cc_start: 0.6997 (OUTLIER) cc_final: 0.6220 (t80) REVERT: B 581 ILE cc_start: 0.9014 (tt) cc_final: 0.8729 (tt) REVERT: B 641 PHE cc_start: 0.4791 (OUTLIER) cc_final: 0.4070 (m-80) outliers start: 147 outliers final: 66 residues processed: 336 average time/residue: 0.1925 time to fit residues: 95.8883 Evaluate side-chains 259 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 181 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 ASN 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 183 MET Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 ASN 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 183 MET Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 ILE 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 407 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 691 ARG 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: 0.9980 chunk 81 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 96 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 206 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN B 206 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 ASN ** B 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10906 Z= 0.256 Angle : 0.803 8.907 14824 Z= 0.416 Chirality : 0.046 0.198 1722 Planarity : 0.007 0.080 1808 Dihedral : 11.008 57.928 1526 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.68 % Allowed : 12.48 % Favored : 86.83 % Rotamer: Outliers : 8.51 % Allowed : 27.78 % Favored : 63.72 % 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: -2.01 (0.23), residues: 1314 helix: -0.08 (0.17), residues: 912 sheet: -5.73 (0.74), residues: 10 loop : -4.31 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 613 HIS 0.006 0.001 HIS B 329 PHE 0.018 0.001 PHE B 224 TYR 0.015 0.001 TYR B 215 ARG 0.005 0.001 ARG A 395 *********************** 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 310 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 212 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 SER cc_start: 0.7100 (OUTLIER) cc_final: 0.6643 (p) REVERT: A 171 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.8443 (t80) REVERT: A 236 VAL cc_start: 0.4396 (OUTLIER) cc_final: 0.2352 (t) REVERT: A 581 ILE cc_start: 0.9033 (tt) cc_final: 0.8799 (tt) REVERT: A 612 MET cc_start: 0.7999 (tpt) cc_final: 0.7757 (tpt) REVERT: A 641 PHE cc_start: 0.4827 (OUTLIER) cc_final: 0.4105 (m-80) REVERT: B 69 SER cc_start: 0.7143 (OUTLIER) cc_final: 0.6633 (p) REVERT: B 171 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.8445 (t80) REVERT: B 236 VAL cc_start: 0.4417 (OUTLIER) cc_final: 0.2330 (t) REVERT: B 392 ASN cc_start: 0.6403 (t0) cc_final: 0.6125 (t0) REVERT: B 400 ILE cc_start: 0.5571 (OUTLIER) cc_final: 0.5273 (pp) REVERT: B 545 LYS cc_start: 0.7604 (mmtm) cc_final: 0.7285 (mmtt) REVERT: B 581 ILE cc_start: 0.9037 (tt) cc_final: 0.8789 (tt) REVERT: B 612 MET cc_start: 0.8007 (tpt) cc_final: 0.7748 (tpt) REVERT: B 641 PHE cc_start: 0.4800 (OUTLIER) cc_final: 0.4086 (m-80) outliers start: 98 outliers final: 55 residues processed: 281 average time/residue: 0.2123 time to fit residues: 86.5548 Evaluate side-chains 236 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 172 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 ASN 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 171 TYR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 491 ILE 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 563 MET Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 ASN 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 183 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 ILE 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 407 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 487 LEU 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 563 MET Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.0670 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 106 optimal weight: 0.0020 overall best weight: 0.5728 ------------------------------------------------------------------------------- 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 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN A 662 GLN A 670 HIS ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 662 GLN B 670 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10906 Z= 0.227 Angle : 0.757 9.085 14824 Z= 0.387 Chirality : 0.045 0.241 1722 Planarity : 0.006 0.074 1808 Dihedral : 9.555 58.141 1492 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.61 % Allowed : 11.64 % Favored : 87.75 % Rotamer: Outliers : 6.86 % Allowed : 28.47 % 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: -1.47 (0.24), residues: 1314 helix: 0.28 (0.17), residues: 920 sheet: -4.92 (0.85), residues: 20 loop : -4.01 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 240 HIS 0.002 0.001 HIS A 670 PHE 0.021 0.001 PHE A 224 TYR 0.016 0.001 TYR B 215 ARG 0.004 0.001 ARG B 226 *********************** 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 280 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 201 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.8400 (t80) REVERT: A 236 VAL cc_start: 0.4501 (OUTLIER) cc_final: 0.3656 (m) REVERT: A 563 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7429 (mtt) REVERT: A 581 ILE cc_start: 0.9128 (tt) cc_final: 0.8763 (tt) REVERT: A 641 PHE cc_start: 0.4863 (OUTLIER) cc_final: 0.4366 (m-80) REVERT: B 171 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8387 (t80) REVERT: B 236 VAL cc_start: 0.4524 (OUTLIER) cc_final: 0.3677 (m) REVERT: B 400 ILE cc_start: 0.5486 (OUTLIER) cc_final: 0.5213 (pp) REVERT: B 563 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7444 (mtt) REVERT: B 581 ILE cc_start: 0.9127 (tt) cc_final: 0.8770 (tt) REVERT: B 639 THR cc_start: 0.5765 (OUTLIER) cc_final: 0.5509 (m) REVERT: B 641 PHE cc_start: 0.4832 (OUTLIER) cc_final: 0.4313 (m-80) outliers start: 79 outliers final: 41 residues processed: 264 average time/residue: 0.1935 time to fit residues: 75.8339 Evaluate side-chains 221 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LEU 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 153 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU 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 236 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 691 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 0.0470 chunk 108 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 HIS A 662 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 HIS B 662 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10906 Z= 0.219 Angle : 0.755 11.006 14824 Z= 0.383 Chirality : 0.044 0.204 1722 Planarity : 0.006 0.070 1808 Dihedral : 8.847 58.057 1480 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.46 % Allowed : 12.48 % Favored : 87.06 % Rotamer: Outliers : 6.94 % Allowed : 29.08 % Favored : 63.98 % 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: -1.07 (0.24), residues: 1314 helix: 0.62 (0.17), residues: 900 sheet: -4.53 (1.11), residues: 20 loop : -3.74 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 613 HIS 0.002 0.001 HIS A 329 PHE 0.019 0.001 PHE A 224 TYR 0.019 0.001 TYR B 215 ARG 0.005 0.001 ARG A 226 *********************** 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 275 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 195 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8339 (t80) REVERT: A 236 VAL cc_start: 0.4144 (OUTLIER) cc_final: 0.3712 (m) REVERT: A 581 ILE cc_start: 0.9110 (tt) cc_final: 0.8859 (tt) REVERT: A 641 PHE cc_start: 0.4914 (OUTLIER) cc_final: 0.4528 (m-80) REVERT: B 171 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.8347 (t80) REVERT: B 236 VAL cc_start: 0.4190 (OUTLIER) cc_final: 0.3749 (m) REVERT: B 392 ASN cc_start: 0.6391 (t0) cc_final: 0.6087 (t0) REVERT: B 400 ILE cc_start: 0.5537 (OUTLIER) cc_final: 0.5267 (pp) REVERT: B 581 ILE cc_start: 0.9111 (tt) cc_final: 0.8852 (tt) REVERT: B 641 PHE cc_start: 0.4875 (OUTLIER) cc_final: 0.4512 (m-80) outliers start: 80 outliers final: 50 residues processed: 251 average time/residue: 0.2091 time to fit residues: 76.6850 Evaluate side-chains 234 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 177 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 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 183 MET Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 107 LEU 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 171 TYR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 74 optimal weight: 0.5980 chunk 31 optimal weight: 0.0070 chunk 127 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 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: 0.7253 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10906 Z= 0.227 Angle : 0.753 10.036 14824 Z= 0.382 Chirality : 0.044 0.204 1722 Planarity : 0.006 0.068 1808 Dihedral : 8.167 59.739 1468 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.95 % Favored : 87.75 % Rotamer: Outliers : 6.08 % Allowed : 29.51 % Favored : 64.41 % 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: -0.88 (0.24), residues: 1314 helix: 0.71 (0.17), residues: 906 sheet: -4.08 (1.23), residues: 20 loop : -3.62 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 240 HIS 0.002 0.001 HIS B 329 PHE 0.021 0.001 PHE A 690 TYR 0.016 0.001 TYR A 215 ARG 0.005 0.001 ARG A 29 *********************** 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 255 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 185 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LEU cc_start: 0.6289 (OUTLIER) cc_final: 0.5787 (tp) REVERT: A 171 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8316 (t80) REVERT: A 545 LYS cc_start: 0.7442 (mmmm) cc_final: 0.7239 (mmmm) REVERT: A 581 ILE cc_start: 0.9115 (tt) cc_final: 0.8867 (tt) REVERT: A 641 PHE cc_start: 0.5007 (OUTLIER) cc_final: 0.4668 (m-80) REVERT: B 69 SER cc_start: 0.7282 (OUTLIER) cc_final: 0.6750 (p) REVERT: B 107 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5661 (tp) REVERT: B 171 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.8315 (t80) REVERT: B 400 ILE cc_start: 0.5603 (OUTLIER) cc_final: 0.5308 (pp) REVERT: B 581 ILE cc_start: 0.9115 (tt) cc_final: 0.8862 (tt) REVERT: B 641 PHE cc_start: 0.4906 (OUTLIER) cc_final: 0.4538 (m-80) outliers start: 70 outliers final: 45 residues processed: 231 average time/residue: 0.2023 time to fit residues: 69.7629 Evaluate side-chains 228 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 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 183 MET Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 107 LEU 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 171 TYR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS 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: 3.9990 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 127 optimal weight: 0.0570 chunk 79 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- 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 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 HIS A 682 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.6054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10906 Z= 0.273 Angle : 0.767 8.291 14824 Z= 0.392 Chirality : 0.045 0.187 1722 Planarity : 0.006 0.065 1808 Dihedral : 7.993 59.571 1464 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.64 % Favored : 88.05 % Rotamer: Outliers : 6.51 % Allowed : 28.73 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1314 helix: 0.84 (0.18), residues: 900 sheet: -3.88 (1.18), residues: 20 loop : -3.44 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 240 HIS 0.002 0.001 HIS A 173 PHE 0.017 0.001 PHE A 513 TYR 0.013 0.001 TYR B 215 ARG 0.003 0.000 ARG A 29 *********************** 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 258 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 183 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5717 (tp) REVERT: A 171 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.8330 (t80) REVERT: A 581 ILE cc_start: 0.9146 (tt) cc_final: 0.8895 (tt) REVERT: A 641 PHE cc_start: 0.5007 (OUTLIER) cc_final: 0.4592 (m-80) REVERT: B 69 SER cc_start: 0.7480 (OUTLIER) cc_final: 0.7083 (p) REVERT: B 107 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5733 (tp) REVERT: B 171 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.8298 (t80) REVERT: B 400 ILE cc_start: 0.5720 (OUTLIER) cc_final: 0.5410 (pp) REVERT: B 581 ILE cc_start: 0.9137 (tt) cc_final: 0.8888 (tt) REVERT: B 641 PHE cc_start: 0.4966 (OUTLIER) cc_final: 0.4613 (m-80) outliers start: 75 outliers final: 47 residues processed: 232 average time/residue: 0.2000 time to fit residues: 69.1369 Evaluate side-chains 234 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 179 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 103 LEU 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 183 MET Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 107 LEU 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 171 TYR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 86 optimal weight: 0.0670 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 115 optimal weight: 0.0270 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.5376 ------------------------------------------------------------------------------- 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 476 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: 0.7255 moved from start: 0.6266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10906 Z= 0.221 Angle : 0.755 9.313 14824 Z= 0.383 Chirality : 0.044 0.190 1722 Planarity : 0.006 0.063 1808 Dihedral : 7.606 59.821 1456 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.11 % Favored : 88.58 % Rotamer: Outliers : 4.95 % Allowed : 30.30 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.25), residues: 1314 helix: 0.89 (0.18), residues: 898 sheet: -3.58 (1.11), residues: 20 loop : -3.38 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 240 HIS 0.002 0.000 HIS B 531 PHE 0.020 0.001 PHE B 690 TYR 0.013 0.001 TYR A 215 ARG 0.005 0.001 ARG B 226 *********************** 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 252 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 195 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7231 (tp) REVERT: A 171 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8319 (t80) REVERT: A 573 SER cc_start: 0.8591 (t) cc_final: 0.8125 (m) REVERT: A 581 ILE cc_start: 0.9096 (tt) cc_final: 0.8835 (tt) REVERT: A 641 PHE cc_start: 0.5034 (OUTLIER) cc_final: 0.4506 (m-80) REVERT: A 694 ILE cc_start: 0.7163 (mm) cc_final: 0.6910 (mm) REVERT: B 69 SER cc_start: 0.7327 (OUTLIER) cc_final: 0.6720 (p) REVERT: B 101 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7195 (tp) REVERT: B 171 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8317 (t80) REVERT: B 392 ASN cc_start: 0.6356 (t0) cc_final: 0.6021 (t0) REVERT: B 400 ILE cc_start: 0.5581 (OUTLIER) cc_final: 0.5294 (pp) REVERT: B 570 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7082 (t80) REVERT: B 573 SER cc_start: 0.8506 (t) cc_final: 0.8139 (m) REVERT: B 581 ILE cc_start: 0.9092 (tt) cc_final: 0.8825 (tt) REVERT: B 641 PHE cc_start: 0.4957 (OUTLIER) cc_final: 0.4550 (m-80) outliers start: 57 outliers final: 43 residues processed: 233 average time/residue: 0.2124 time to fit residues: 74.4402 Evaluate side-chains 238 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 103 LEU Chi-restraints excluded: chain A residue 114 ASN 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 183 MET Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 114 ASN 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 171 TYR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 476 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: 0.7284 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10906 Z= 0.245 Angle : 0.761 9.347 14824 Z= 0.385 Chirality : 0.044 0.199 1722 Planarity : 0.006 0.063 1808 Dihedral : 7.595 59.788 1456 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.80 % Favored : 87.90 % Rotamer: Outliers : 5.12 % Allowed : 30.73 % Favored : 64.15 % 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: -0.55 (0.25), residues: 1314 helix: 0.97 (0.18), residues: 886 sheet: -3.17 (1.14), residues: 20 loop : -3.35 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 240 HIS 0.002 0.001 HIS A 670 PHE 0.018 0.001 PHE B 690 TYR 0.013 0.001 TYR B 215 ARG 0.007 0.001 ARG B 226 *********************** 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 246 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 187 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8225 (t80) REVERT: A 573 SER cc_start: 0.8584 (t) cc_final: 0.8160 (m) REVERT: A 581 ILE cc_start: 0.9089 (tt) cc_final: 0.8869 (tt) REVERT: A 641 PHE cc_start: 0.5019 (OUTLIER) cc_final: 0.4468 (m-80) REVERT: A 694 ILE cc_start: 0.7170 (mm) cc_final: 0.6908 (mm) REVERT: B 69 SER cc_start: 0.7182 (OUTLIER) cc_final: 0.6834 (p) REVERT: B 107 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.5510 (tp) REVERT: B 171 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.8342 (t80) REVERT: B 190 GLU cc_start: 0.6575 (pp20) cc_final: 0.6239 (pp20) REVERT: B 392 ASN cc_start: 0.6449 (t0) cc_final: 0.6106 (t0) REVERT: B 400 ILE cc_start: 0.5623 (OUTLIER) cc_final: 0.5333 (pp) REVERT: B 570 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7181 (t80) REVERT: B 573 SER cc_start: 0.8547 (t) cc_final: 0.8195 (m) REVERT: B 581 ILE cc_start: 0.9071 (tt) cc_final: 0.8828 (tt) REVERT: B 641 PHE cc_start: 0.5010 (OUTLIER) cc_final: 0.4437 (m-80) REVERT: B 694 ILE cc_start: 0.7217 (mm) cc_final: 0.6965 (mm) outliers start: 59 outliers final: 46 residues processed: 227 average time/residue: 0.2019 time to fit residues: 69.4687 Evaluate side-chains 229 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 175 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 103 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 183 MET Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 107 LEU 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 171 TYR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10906 Z= 0.235 Angle : 0.778 9.966 14824 Z= 0.392 Chirality : 0.044 0.207 1722 Planarity : 0.006 0.062 1808 Dihedral : 7.552 59.286 1456 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.19 % Favored : 88.51 % Rotamer: Outliers : 4.69 % Allowed : 31.77 % Favored : 63.54 % 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: -0.53 (0.25), residues: 1314 helix: 0.98 (0.18), residues: 888 sheet: -3.03 (1.17), residues: 20 loop : -3.36 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 349 HIS 0.003 0.001 HIS B 531 PHE 0.024 0.001 PHE A 690 TYR 0.012 0.001 TYR B 215 ARG 0.006 0.001 ARG B 226 ********************** 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 242 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 188 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.5439 (tp) REVERT: A 171 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8276 (t80) REVERT: A 573 SER cc_start: 0.8535 (t) cc_final: 0.8131 (m) REVERT: A 581 ILE cc_start: 0.9070 (tt) cc_final: 0.8846 (tt) REVERT: A 641 PHE cc_start: 0.4920 (OUTLIER) cc_final: 0.4280 (m-80) REVERT: A 694 ILE cc_start: 0.7086 (mm) cc_final: 0.6885 (mm) REVERT: B 69 SER cc_start: 0.7167 (OUTLIER) cc_final: 0.6747 (p) REVERT: B 107 LEU cc_start: 0.5904 (OUTLIER) cc_final: 0.5448 (tp) REVERT: B 171 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8333 (t80) REVERT: B 392 ASN cc_start: 0.6489 (t0) cc_final: 0.6154 (t0) REVERT: B 400 ILE cc_start: 0.5535 (OUTLIER) cc_final: 0.5246 (pp) REVERT: B 570 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7214 (t80) REVERT: B 573 SER cc_start: 0.8529 (t) cc_final: 0.8179 (m) REVERT: B 581 ILE cc_start: 0.9061 (tt) cc_final: 0.8839 (tt) REVERT: B 641 PHE cc_start: 0.4902 (OUTLIER) cc_final: 0.4284 (m-80) REVERT: B 694 ILE cc_start: 0.7175 (mm) cc_final: 0.6965 (mm) outliers start: 54 outliers final: 42 residues processed: 222 average time/residue: 0.1997 time to fit residues: 66.6536 Evaluate side-chains 234 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 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 191 GLN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 69 SER 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 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 191 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 641 PHE Chi-restraints excluded: chain B residue 660 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 5 optimal weight: 0.0870 chunk 75 optimal weight: 0.1980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 191 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.144321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.113895 restraints weight = 17501.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.117489 restraints weight = 7624.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.119737 restraints weight = 4751.108| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.6521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10906 Z= 0.218 Angle : 0.766 11.580 14824 Z= 0.386 Chirality : 0.044 0.209 1722 Planarity : 0.006 0.062 1808 Dihedral : 7.446 58.179 1456 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.34 % Favored : 88.36 % Rotamer: Outliers : 4.77 % Allowed : 32.12 % Favored : 63.11 % 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: 0.96 (0.18), residues: 888 sheet: -3.04 (1.16), residues: 20 loop : -3.27 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 240 HIS 0.003 0.001 HIS B 531 PHE 0.019 0.001 PHE B 690 TYR 0.013 0.001 TYR B 215 ARG 0.006 0.001 ARG B 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2542.97 seconds wall clock time: 47 minutes 56.07 seconds (2876.07 seconds total)