Starting phenix.real_space_refine on Tue May 13 16:07:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymn_39400/05_2025/8ymn_39400_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymn_39400/05_2025/8ymn_39400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ymn_39400/05_2025/8ymn_39400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymn_39400/05_2025/8ymn_39400.map" model { file = "/net/cci-nas-00/data/ceres_data/8ymn_39400/05_2025/8ymn_39400_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymn_39400/05_2025/8ymn_39400_neut.cif" } resolution = 2.5 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= 0.000 sd= 0.008 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 52 5.16 5 C 7088 2.51 5 N 1758 2.21 5 O 1830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10728 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5346 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 35, 'TRANS': 628} Chain breaks: 2 Chain: "B" Number of atoms: 5346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5346 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 35, 'TRANS': 628} Chain breaks: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-1': 2, 'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-1': 2, 'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 12.57, per 1000 atoms: 1.17 Number of scatterers: 10728 At special positions: 0 Unit cell: (149.45, 82.25, 88.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1830 8.00 N 1758 7.00 C 7088 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: 2.63 Conformation dependent library (CDL) restraints added in 1.4 seconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2524 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 2 sheets defined 68.8% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 3 through 31 removed outlier: 3.505A pdb=" N GLN A 31 " --> pdb=" O PHE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 38 Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 92 through 119 removed outlier: 3.975A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 160 through 195 Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 242 through 257 Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 295 through 315 removed outlier: 3.895A pdb=" N VAL A 299 " --> pdb=" O TYR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.614A pdb=" N ALA A 366 " --> pdb=" O PRO A 363 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 367 " --> pdb=" O ASN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 388 removed outlier: 3.793A pdb=" N THR A 373 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 407 removed outlier: 3.577A pdb=" N GLU A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 454 Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 457 through 477 Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 513 through 525 removed outlier: 3.703A pdb=" N PHE A 517 " --> pdb=" O LYS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 535 removed outlier: 3.532A pdb=" N LEU A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 547 Processing helix chain 'A' and resid 566 through 585 Proline residue: A 572 - end of helix Processing helix chain 'A' and resid 590 through 613 removed outlier: 4.518A pdb=" N PHE A 594 " --> pdb=" O MET A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 647 Processing helix chain 'A' and resid 655 through 677 Proline residue: A 663 - end of helix Processing helix chain 'A' and resid 678 through 683 removed outlier: 3.552A pdb=" N VAL A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 700 Processing helix chain 'A' and resid 704 through 711 removed outlier: 3.732A pdb=" N TYR A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP A 711 " --> pdb=" O GLY A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'B' and resid 3 through 31 removed outlier: 3.505A pdb=" N GLN B 31 " --> pdb=" O PHE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 38 Processing helix chain 'B' and resid 39 through 45 Processing helix chain 'B' and resid 74 through 80 Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 92 through 119 removed outlier: 3.975A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 160 through 195 Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 216 through 228 Processing helix chain 'B' and resid 242 through 257 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 295 through 315 removed outlier: 3.895A pdb=" N VAL B 299 " --> pdb=" O TYR B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 339 Processing helix chain 'B' and resid 361 through 367 removed outlier: 3.614A pdb=" N ALA B 366 " --> pdb=" O PRO B 363 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 367 " --> pdb=" O ASN B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 388 removed outlier: 3.793A pdb=" N THR B 373 " --> pdb=" O TYR B 369 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 407 removed outlier: 3.577A pdb=" N GLU B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 454 Proline residue: B 443 - end of helix Processing helix chain 'B' and resid 457 through 477 Processing helix chain 'B' and resid 488 through 496 Processing helix chain 'B' and resid 501 through 510 Processing helix chain 'B' and resid 513 through 525 removed outlier: 3.703A pdb=" N PHE B 517 " --> pdb=" O LYS B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 535 removed outlier: 3.532A pdb=" N LEU B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 547 Processing helix chain 'B' and resid 566 through 585 Proline residue: B 572 - end of helix Processing helix chain 'B' and resid 590 through 613 removed outlier: 4.518A pdb=" N PHE B 594 " --> pdb=" O MET B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 647 Processing helix chain 'B' and resid 655 through 677 Proline residue: B 663 - end of helix Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.552A pdb=" N VAL B 682 " --> pdb=" O GLU B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 700 Processing helix chain 'B' and resid 704 through 711 removed outlier: 3.732A pdb=" N TYR B 708 " --> pdb=" O ASN B 704 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP B 711 " --> pdb=" O GLY B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 714 No H-bonds generated for 'chain 'B' and resid 712 through 714' Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 240 removed outlier: 5.218A pdb=" N ALA A 323 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 240 removed outlier: 5.218A pdb=" N ALA B 323 " --> pdb=" O VAL B 239 " (cutoff:3.500A) 648 hydrogen bonds defined for protein. 1908 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: 3.30 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3118 1.33 - 1.45: 1734 1.45 - 1.57: 6074 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 11018 Sorted by residual: bond pdb=" CA ILE B 392 " pdb=" CB ILE B 392 " ideal model delta sigma weight residual 1.539 1.558 -0.019 5.40e-03 3.43e+04 1.30e+01 bond pdb=" CA ILE A 392 " pdb=" CB ILE A 392 " ideal model delta sigma weight residual 1.539 1.558 -0.019 5.40e-03 3.43e+04 1.30e+01 bond pdb=" C LYS B 537 " pdb=" N PRO B 538 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.36e-02 5.41e+03 1.19e+01 bond pdb=" C LYS A 537 " pdb=" N PRO A 538 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.36e-02 5.41e+03 1.19e+01 bond pdb=" CA LYS A 537 " pdb=" C LYS A 537 " ideal model delta sigma weight residual 1.520 1.560 -0.040 1.23e-02 6.61e+03 1.05e+01 ... (remaining 11013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 14259 2.37 - 4.75: 559 4.75 - 7.12: 106 7.12 - 9.49: 36 9.49 - 11.86: 6 Bond angle restraints: 14966 Sorted by residual: angle pdb=" N VAL B 477 " pdb=" CA VAL B 477 " pdb=" C VAL B 477 " ideal model delta sigma weight residual 112.96 106.53 6.43 1.00e+00 1.00e+00 4.13e+01 angle pdb=" N VAL A 477 " pdb=" CA VAL A 477 " pdb=" C VAL A 477 " ideal model delta sigma weight residual 112.96 106.53 6.43 1.00e+00 1.00e+00 4.13e+01 angle pdb=" N LYS B 318 " pdb=" CA LYS B 318 " pdb=" C LYS B 318 " ideal model delta sigma weight residual 113.72 105.49 8.23 1.30e+00 5.92e-01 4.01e+01 angle pdb=" N LYS A 318 " pdb=" CA LYS A 318 " pdb=" C LYS A 318 " ideal model delta sigma weight residual 113.72 105.49 8.23 1.30e+00 5.92e-01 4.01e+01 angle pdb=" N ASN B 476 " pdb=" CA ASN B 476 " pdb=" C ASN B 476 " ideal model delta sigma weight residual 113.18 120.65 -7.47 1.21e+00 6.83e-01 3.81e+01 ... (remaining 14961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 5080 16.68 - 33.35: 652 33.35 - 50.03: 481 50.03 - 66.70: 257 66.70 - 83.37: 28 Dihedral angle restraints: 6498 sinusoidal: 2596 harmonic: 3902 Sorted by residual: dihedral pdb=" C VAL A 121 " pdb=" N VAL A 121 " pdb=" CA VAL A 121 " pdb=" CB VAL A 121 " ideal model delta harmonic sigma weight residual -122.00 -133.06 11.06 0 2.50e+00 1.60e-01 1.96e+01 dihedral pdb=" C VAL B 121 " pdb=" N VAL B 121 " pdb=" CA VAL B 121 " pdb=" CB VAL B 121 " ideal model delta harmonic sigma weight residual -122.00 -133.06 11.06 0 2.50e+00 1.60e-01 1.96e+01 dihedral pdb=" C ILE B 392 " pdb=" N ILE B 392 " pdb=" CA ILE B 392 " pdb=" CB ILE B 392 " ideal model delta harmonic sigma weight residual -122.00 -132.90 10.90 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 6495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1343 0.090 - 0.179: 265 0.179 - 0.269: 54 0.269 - 0.358: 12 0.358 - 0.447: 4 Chirality restraints: 1678 Sorted by residual: chirality pdb=" CA TRP A 625 " pdb=" N TRP A 625 " pdb=" C TRP A 625 " pdb=" CB TRP A 625 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CA TRP B 625 " pdb=" N TRP B 625 " pdb=" C TRP B 625 " pdb=" CB TRP B 625 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CA ASN B 476 " pdb=" N ASN B 476 " pdb=" C ASN B 476 " pdb=" CB ASN B 476 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 1675 not shown) Planarity restraints: 1872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 50 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO B 51 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 50 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO A 51 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 51 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 51 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 392 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO B 393 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 393 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 393 " -0.033 5.00e-02 4.00e+02 ... (remaining 1869 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 13 2.50 - 3.10: 7740 3.10 - 3.70: 18261 3.70 - 4.30: 27851 4.30 - 4.90: 42460 Nonbonded interactions: 96325 Sorted by model distance: nonbonded pdb=" CD1 LEU B 255 " pdb=" OE1 GLU B 298 " model vdw 1.898 3.460 nonbonded pdb=" CD1 LEU A 255 " pdb=" OE1 GLU A 298 " model vdw 1.898 3.460 nonbonded pdb=" CB ILE B 483 " pdb=" CG2 ILE B 510 " model vdw 2.094 3.890 nonbonded pdb=" CB ILE A 483 " pdb=" CG2 ILE A 510 " model vdw 2.094 3.890 nonbonded pdb=" NH2 ARG A 344 " pdb=" OE2 GLU B 688 " model vdw 2.214 3.120 ... (remaining 96320 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 37.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.930 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.990 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 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 : 0.007 0.047 11018 Z= 0.524 Angle : 1.182 11.862 14966 Z= 0.787 Chirality : 0.079 0.447 1678 Planarity : 0.006 0.057 1872 Dihedral : 24.058 83.374 3974 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 1.06 % Allowed : 11.09 % Favored : 87.84 % Rotamer: Outliers : 34.51 % Allowed : 13.38 % Favored : 52.11 % Cbeta Deviations : 0.32 % 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: -2.94 (0.21), residues: 1316 helix: -1.08 (0.16), residues: 824 sheet: -2.86 (0.68), residues: 46 loop : -3.43 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 625 HIS 0.005 0.001 HIS A 715 PHE 0.013 0.002 PHE A 494 TYR 0.008 0.001 TYR B 295 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.17944 ( 648) hydrogen bonds : angle 7.21827 ( 1908) covalent geometry : bond 0.00695 (11018) covalent geometry : angle 1.18243 (14966) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 392 poor density : 230 time to evaluate : 1.176 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7547 (tptm) REVERT: A 212 ASP cc_start: 0.4981 (t70) cc_final: 0.4440 (t0) REVERT: A 278 LYS cc_start: 0.0266 (OUTLIER) cc_final: -0.0768 (tmtm) REVERT: A 353 TRP cc_start: 0.5971 (m100) cc_final: 0.5708 (t60) REVERT: A 498 SER cc_start: 0.0567 (OUTLIER) cc_final: 0.0319 (p) REVERT: A 501 GLN cc_start: 0.1000 (OUTLIER) cc_final: 0.0092 (mm110) REVERT: A 502 ILE cc_start: 0.0533 (OUTLIER) cc_final: -0.0040 (mm) REVERT: A 508 MET cc_start: 0.0544 (mtt) cc_final: -0.0401 (ppp) REVERT: A 521 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.7175 (mt) REVERT: A 651 HIS cc_start: 0.1757 (OUTLIER) cc_final: 0.0726 (m90) REVERT: A 676 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7590 (tpt90) REVERT: A 692 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7045 (tttt) REVERT: B 41 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7549 (tptm) REVERT: B 212 ASP cc_start: 0.4998 (t70) cc_final: 0.4406 (t0) REVERT: B 278 LYS cc_start: 0.0252 (OUTLIER) cc_final: -0.0800 (tmtm) REVERT: B 353 TRP cc_start: 0.5983 (m100) cc_final: 0.5696 (t60) REVERT: B 498 SER cc_start: 0.0578 (OUTLIER) cc_final: 0.0322 (p) REVERT: B 501 GLN cc_start: 0.0992 (OUTLIER) cc_final: 0.0075 (mm110) REVERT: B 502 ILE cc_start: 0.0545 (OUTLIER) cc_final: -0.0014 (mm) REVERT: B 508 MET cc_start: 0.0500 (mtt) cc_final: -0.0452 (ppp) REVERT: B 521 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.7190 (mt) REVERT: B 651 HIS cc_start: 0.1779 (OUTLIER) cc_final: 0.0707 (m90) REVERT: B 676 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7601 (tpt90) REVERT: B 692 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7038 (tttt) outliers start: 392 outliers final: 48 residues processed: 518 average time/residue: 0.9967 time to fit residues: 563.2631 Evaluate side-chains 214 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 148 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 692 LYS Chi-restraints excluded: chain B residue 702 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 30.0000 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 90 HIS A 208 ASN A 228 ASN A 315 ASN A 339 GLN A 398 GLN A 476 ASN A 490 GLN A 501 GLN A 546 ASN A 573 GLN A 609 GLN A 616 GLN A 651 HIS A 687 GLN A 715 HIS B 63 ASN B 90 HIS B 208 ASN B 228 ASN B 315 ASN B 339 GLN B 476 ASN B 490 GLN B 501 GLN B 546 ASN B 573 GLN B 609 GLN B 616 GLN B 651 HIS B 687 GLN B 715 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.186942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113493 restraints weight = 10915.370| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.17 r_work: 0.3154 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11018 Z= 0.184 Angle : 0.724 10.922 14966 Z= 0.370 Chirality : 0.047 0.261 1678 Planarity : 0.006 0.047 1872 Dihedral : 12.580 76.078 1632 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.21 % Favored : 91.64 % Rotamer: Outliers : 10.65 % Allowed : 24.12 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.23), residues: 1316 helix: 0.34 (0.17), residues: 838 sheet: -3.22 (0.61), residues: 42 loop : -3.10 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 625 HIS 0.008 0.002 HIS A 74 PHE 0.039 0.002 PHE B 19 TYR 0.017 0.002 TYR B 43 ARG 0.003 0.001 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.05040 ( 648) hydrogen bonds : angle 5.25839 ( 1908) covalent geometry : bond 0.00404 (11018) covalent geometry : angle 0.72397 (14966) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 152 time to evaluate : 1.280 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6467 (OUTLIER) cc_final: 0.6069 (t80) REVERT: A 29 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6413 (ptm160) REVERT: A 78 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6676 (mp0) REVERT: A 114 MET cc_start: 0.7851 (mtp) cc_final: 0.7636 (mtm) REVERT: A 115 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7300 (tt) REVERT: A 159 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6484 (t80) REVERT: A 278 LYS cc_start: -0.0559 (OUTLIER) cc_final: -0.1336 (tptt) REVERT: A 352 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8192 (pt0) REVERT: A 353 TRP cc_start: 0.7519 (m100) cc_final: 0.6568 (t60) REVERT: A 372 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7339 (mp) REVERT: A 498 SER cc_start: 0.1848 (OUTLIER) cc_final: 0.1397 (p) REVERT: A 508 MET cc_start: -0.1135 (mtt) cc_final: -0.1462 (ppp) REVERT: A 676 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8138 (tpt90) REVERT: B 19 PHE cc_start: 0.6467 (OUTLIER) cc_final: 0.6063 (t80) REVERT: B 29 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6406 (ptm160) REVERT: B 78 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: B 114 MET cc_start: 0.7857 (mtp) cc_final: 0.7642 (mtm) REVERT: B 115 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7301 (tt) REVERT: B 159 PHE cc_start: 0.6994 (OUTLIER) cc_final: 0.6493 (t80) REVERT: B 278 LYS cc_start: -0.0559 (OUTLIER) cc_final: -0.1336 (tptt) REVERT: B 352 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: B 353 TRP cc_start: 0.7521 (m100) cc_final: 0.6563 (t60) REVERT: B 372 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7332 (mp) REVERT: B 498 SER cc_start: 0.1848 (OUTLIER) cc_final: 0.1393 (p) REVERT: B 508 MET cc_start: -0.1140 (mtt) cc_final: -0.1460 (ppp) REVERT: B 676 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8144 (tpt90) outliers start: 121 outliers final: 48 residues processed: 265 average time/residue: 1.0167 time to fit residues: 293.4963 Evaluate side-chains 213 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 145 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 702 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 124 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 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 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN A 398 GLN A 497 GLN A 501 GLN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 ASN B 497 GLN B 501 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.185590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.112301 restraints weight = 11211.681| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.18 r_work: 0.3135 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11018 Z= 0.161 Angle : 0.657 15.565 14966 Z= 0.328 Chirality : 0.045 0.251 1678 Planarity : 0.005 0.044 1872 Dihedral : 10.616 76.465 1596 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.66 % Favored : 91.19 % Rotamer: Outliers : 8.27 % Allowed : 25.70 % Favored : 66.02 % 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: -0.72 (0.23), residues: 1316 helix: 0.87 (0.18), residues: 856 sheet: -3.12 (0.60), residues: 42 loop : -3.13 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 625 HIS 0.004 0.001 HIS B 90 PHE 0.030 0.002 PHE A 478 TYR 0.014 0.001 TYR B 43 ARG 0.002 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.04412 ( 648) hydrogen bonds : angle 4.82317 ( 1908) covalent geometry : bond 0.00357 (11018) covalent geometry : angle 0.65693 (14966) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 150 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6380 (OUTLIER) cc_final: 0.6010 (t80) REVERT: A 29 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6404 (ptm160) REVERT: A 78 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: A 86 GLU cc_start: 0.7785 (tt0) cc_final: 0.7305 (mt-10) REVERT: A 159 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6520 (t80) REVERT: A 278 LYS cc_start: -0.0637 (OUTLIER) cc_final: -0.1365 (tptt) REVERT: A 352 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8198 (pt0) REVERT: A 353 TRP cc_start: 0.7412 (m100) cc_final: 0.6497 (t60) REVERT: A 498 SER cc_start: 0.1817 (OUTLIER) cc_final: 0.1403 (p) REVERT: A 508 MET cc_start: -0.1105 (mtt) cc_final: -0.1456 (ppp) REVERT: A 642 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7149 (mp) REVERT: A 676 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8096 (tpt90) REVERT: B 19 PHE cc_start: 0.6388 (OUTLIER) cc_final: 0.6016 (t80) REVERT: B 29 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6390 (ptm160) REVERT: B 78 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6653 (mp0) REVERT: B 86 GLU cc_start: 0.7784 (tt0) cc_final: 0.7307 (mt-10) REVERT: B 159 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6533 (t80) REVERT: B 278 LYS cc_start: -0.0636 (OUTLIER) cc_final: -0.1365 (tptt) REVERT: B 352 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8194 (pt0) REVERT: B 353 TRP cc_start: 0.7410 (m100) cc_final: 0.6491 (t60) REVERT: B 498 SER cc_start: 0.1814 (OUTLIER) cc_final: 0.1402 (p) REVERT: B 508 MET cc_start: -0.1107 (mtt) cc_final: -0.1454 (ppp) REVERT: B 642 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7144 (mp) REVERT: B 676 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8100 (tpt90) outliers start: 94 outliers final: 35 residues processed: 232 average time/residue: 0.9952 time to fit residues: 252.1010 Evaluate side-chains 191 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 138 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 50 optimal weight: 0.0970 chunk 104 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN A 398 GLN A 615 ASN B 315 ASN B 615 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.184131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110188 restraints weight = 11083.790| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.18 r_work: 0.3144 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11018 Z= 0.153 Angle : 0.629 15.779 14966 Z= 0.316 Chirality : 0.044 0.270 1678 Planarity : 0.005 0.041 1872 Dihedral : 8.506 58.664 1536 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.90 % Favored : 91.79 % Rotamer: Outliers : 7.92 % Allowed : 25.09 % Favored : 66.99 % 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: -0.42 (0.23), residues: 1316 helix: 1.12 (0.18), residues: 836 sheet: -3.03 (0.60), residues: 42 loop : -2.86 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 625 HIS 0.002 0.001 HIS B 90 PHE 0.025 0.002 PHE B 19 TYR 0.009 0.001 TYR A 181 ARG 0.002 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 648) hydrogen bonds : angle 4.68212 ( 1908) covalent geometry : bond 0.00335 (11018) covalent geometry : angle 0.62853 (14966) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 151 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6410 (OUTLIER) cc_final: 0.6022 (t80) REVERT: A 29 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6563 (ptm160) REVERT: A 78 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: A 86 GLU cc_start: 0.7875 (tt0) cc_final: 0.7397 (mt-10) REVERT: A 222 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8312 (tt0) REVERT: A 258 TRP cc_start: 0.5308 (OUTLIER) cc_final: 0.4593 (t60) REVERT: A 278 LYS cc_start: -0.0718 (OUTLIER) cc_final: -0.1544 (tmtm) REVERT: A 296 ILE cc_start: 0.6691 (OUTLIER) cc_final: 0.6231 (mm) REVERT: A 305 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6721 (mt-10) REVERT: A 352 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8269 (pt0) REVERT: A 353 TRP cc_start: 0.7394 (m100) cc_final: 0.6505 (t60) REVERT: A 498 SER cc_start: 0.1518 (OUTLIER) cc_final: 0.1125 (p) REVERT: A 508 MET cc_start: -0.1154 (mtt) cc_final: -0.1535 (ppp) REVERT: A 642 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7219 (mp) REVERT: A 676 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8201 (tpt90) REVERT: B 19 PHE cc_start: 0.6413 (OUTLIER) cc_final: 0.6024 (t80) REVERT: B 29 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6554 (ptm160) REVERT: B 78 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: B 86 GLU cc_start: 0.7885 (tt0) cc_final: 0.7409 (mt-10) REVERT: B 222 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: B 258 TRP cc_start: 0.5301 (OUTLIER) cc_final: 0.4592 (t60) REVERT: B 278 LYS cc_start: -0.0718 (OUTLIER) cc_final: -0.1544 (tmtm) REVERT: B 296 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6228 (mm) REVERT: B 305 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6726 (mt-10) REVERT: B 352 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: B 353 TRP cc_start: 0.7390 (m100) cc_final: 0.6500 (t60) REVERT: B 498 SER cc_start: 0.1518 (OUTLIER) cc_final: 0.1127 (p) REVERT: B 508 MET cc_start: -0.1154 (mtt) cc_final: -0.1532 (ppp) REVERT: B 642 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7220 (mp) REVERT: B 676 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8206 (tpt90) outliers start: 90 outliers final: 35 residues processed: 231 average time/residue: 1.0739 time to fit residues: 269.6333 Evaluate side-chains 204 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 147 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 702 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 69 optimal weight: 0.5980 chunk 53 optimal weight: 0.0870 chunk 114 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN A 398 GLN B 315 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.185374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109728 restraints weight = 11038.813| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.24 r_work: 0.3145 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11018 Z= 0.140 Angle : 0.607 16.064 14966 Z= 0.300 Chirality : 0.043 0.271 1678 Planarity : 0.005 0.040 1872 Dihedral : 7.727 58.861 1524 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.29 % Favored : 92.40 % Rotamer: Outliers : 7.04 % Allowed : 25.00 % Favored : 67.96 % 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: -0.26 (0.23), residues: 1316 helix: 1.25 (0.18), residues: 838 sheet: -2.99 (0.60), residues: 42 loop : -2.82 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 625 HIS 0.002 0.001 HIS B 90 PHE 0.023 0.001 PHE B 19 TYR 0.009 0.001 TYR A 181 ARG 0.001 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 648) hydrogen bonds : angle 4.46491 ( 1908) covalent geometry : bond 0.00308 (11018) covalent geometry : angle 0.60749 (14966) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 155 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6372 (OUTLIER) cc_final: 0.5984 (t80) REVERT: A 29 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6531 (ptm160) REVERT: A 78 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6676 (mp0) REVERT: A 86 GLU cc_start: 0.7886 (tt0) cc_final: 0.7398 (mt-10) REVERT: A 222 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: A 258 TRP cc_start: 0.5314 (OUTLIER) cc_final: 0.4647 (t60) REVERT: A 278 LYS cc_start: -0.0790 (OUTLIER) cc_final: -0.1634 (tmtm) REVERT: A 296 ILE cc_start: 0.6699 (OUTLIER) cc_final: 0.6273 (mm) REVERT: A 305 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6717 (mt-10) REVERT: A 352 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8267 (pt0) REVERT: A 353 TRP cc_start: 0.7346 (m100) cc_final: 0.6464 (t60) REVERT: A 498 SER cc_start: 0.1448 (OUTLIER) cc_final: 0.1095 (p) REVERT: A 508 MET cc_start: -0.1141 (mtt) cc_final: -0.1551 (ppp) REVERT: A 532 GLU cc_start: 0.7728 (mm-30) cc_final: 0.6991 (tm-30) REVERT: A 676 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8198 (tpt90) REVERT: B 19 PHE cc_start: 0.6372 (OUTLIER) cc_final: 0.5986 (t80) REVERT: B 29 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6535 (ptm160) REVERT: B 78 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: B 86 GLU cc_start: 0.7886 (tt0) cc_final: 0.7401 (mt-10) REVERT: B 222 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: B 258 TRP cc_start: 0.5308 (OUTLIER) cc_final: 0.4640 (t60) REVERT: B 278 LYS cc_start: -0.0789 (OUTLIER) cc_final: -0.1633 (tmtm) REVERT: B 296 ILE cc_start: 0.6689 (OUTLIER) cc_final: 0.6265 (mm) REVERT: B 305 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6713 (mt-10) REVERT: B 352 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8261 (pt0) REVERT: B 353 TRP cc_start: 0.7341 (m100) cc_final: 0.6459 (t60) REVERT: B 498 SER cc_start: 0.1455 (OUTLIER) cc_final: 0.1103 (p) REVERT: B 508 MET cc_start: -0.1144 (mtt) cc_final: -0.1551 (ppp) REVERT: B 532 GLU cc_start: 0.7720 (mm-30) cc_final: 0.6985 (tm-30) REVERT: B 676 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8203 (tpt90) outliers start: 80 outliers final: 33 residues processed: 219 average time/residue: 1.0698 time to fit residues: 254.8529 Evaluate side-chains 194 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 141 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 39 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 117 optimal weight: 0.0060 chunk 112 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN A 398 GLN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.184690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.110051 restraints weight = 11089.744| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.19 r_work: 0.3136 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11018 Z= 0.141 Angle : 0.611 15.913 14966 Z= 0.299 Chirality : 0.043 0.302 1678 Planarity : 0.005 0.040 1872 Dihedral : 7.490 59.004 1522 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.14 % Favored : 92.71 % Rotamer: Outliers : 6.69 % Allowed : 24.91 % Favored : 68.40 % 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: -0.16 (0.23), residues: 1316 helix: 1.33 (0.18), residues: 840 sheet: -3.02 (0.60), residues: 42 loop : -2.79 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 625 HIS 0.003 0.001 HIS A 90 PHE 0.022 0.001 PHE A 19 TYR 0.008 0.001 TYR B 713 ARG 0.002 0.000 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 648) hydrogen bonds : angle 4.42609 ( 1908) covalent geometry : bond 0.00315 (11018) covalent geometry : angle 0.61086 (14966) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 150 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6282 (OUTLIER) cc_final: 0.5902 (t80) REVERT: A 29 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6421 (ptm160) REVERT: A 78 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: A 81 LYS cc_start: 0.7873 (tptt) cc_final: 0.7606 (mptt) REVERT: A 86 GLU cc_start: 0.7765 (tt0) cc_final: 0.7257 (mt-10) REVERT: A 222 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: A 258 TRP cc_start: 0.5312 (OUTLIER) cc_final: 0.4652 (t60) REVERT: A 278 LYS cc_start: -0.0830 (OUTLIER) cc_final: -0.1703 (tmtm) REVERT: A 296 ILE cc_start: 0.6750 (OUTLIER) cc_final: 0.6374 (mm) REVERT: A 300 ASP cc_start: 0.6476 (OUTLIER) cc_final: 0.6127 (t70) REVERT: A 305 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6625 (mt-10) REVERT: A 352 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8220 (pt0) REVERT: A 353 TRP cc_start: 0.7324 (m100) cc_final: 0.6396 (t60) REVERT: A 498 SER cc_start: 0.1318 (OUTLIER) cc_final: 0.0971 (p) REVERT: A 508 MET cc_start: -0.1065 (mtt) cc_final: -0.1498 (ppp) REVERT: A 512 MET cc_start: 0.4813 (mmm) cc_final: 0.4462 (mmm) REVERT: A 532 GLU cc_start: 0.7636 (mm-30) cc_final: 0.6824 (tm-30) REVERT: A 676 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8133 (tpt90) REVERT: B 19 PHE cc_start: 0.6279 (OUTLIER) cc_final: 0.5900 (t80) REVERT: B 29 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6415 (ptm160) REVERT: B 78 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6577 (mp0) REVERT: B 81 LYS cc_start: 0.7871 (tptt) cc_final: 0.7604 (mptt) REVERT: B 86 GLU cc_start: 0.7781 (tt0) cc_final: 0.7277 (mt-10) REVERT: B 222 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: B 258 TRP cc_start: 0.5317 (OUTLIER) cc_final: 0.4656 (t60) REVERT: B 278 LYS cc_start: -0.0826 (OUTLIER) cc_final: -0.1702 (tmtm) REVERT: B 296 ILE cc_start: 0.6754 (OUTLIER) cc_final: 0.6377 (mm) REVERT: B 300 ASP cc_start: 0.6476 (OUTLIER) cc_final: 0.6125 (t70) REVERT: B 305 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6634 (mt-10) REVERT: B 352 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8217 (pt0) REVERT: B 353 TRP cc_start: 0.7316 (m100) cc_final: 0.6387 (t60) REVERT: B 498 SER cc_start: 0.1329 (OUTLIER) cc_final: 0.0982 (p) REVERT: B 508 MET cc_start: -0.1067 (mtt) cc_final: -0.1499 (ppp) REVERT: B 512 MET cc_start: 0.4814 (mmm) cc_final: 0.4462 (mmm) REVERT: B 532 GLU cc_start: 0.7633 (mm-30) cc_final: 0.6822 (tm-30) REVERT: B 676 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8142 (tpt90) outliers start: 76 outliers final: 29 residues processed: 216 average time/residue: 1.0192 time to fit residues: 240.1456 Evaluate side-chains 189 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 138 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 55 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 37 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.183598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.109339 restraints weight = 11247.423| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.18 r_work: 0.3130 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11018 Z= 0.149 Angle : 0.614 15.771 14966 Z= 0.303 Chirality : 0.044 0.321 1678 Planarity : 0.005 0.042 1872 Dihedral : 7.130 59.250 1512 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.75 % Favored : 92.10 % Rotamer: Outliers : 5.46 % Allowed : 25.18 % Favored : 69.37 % 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: -0.13 (0.23), residues: 1316 helix: 1.35 (0.18), residues: 838 sheet: -3.00 (0.61), residues: 42 loop : -2.75 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 625 HIS 0.004 0.001 HIS A 90 PHE 0.024 0.001 PHE B 494 TYR 0.008 0.001 TYR B 713 ARG 0.003 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 648) hydrogen bonds : angle 4.43614 ( 1908) covalent geometry : bond 0.00340 (11018) covalent geometry : angle 0.61402 (14966) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 142 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6303 (OUTLIER) cc_final: 0.5920 (t80) REVERT: A 29 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6463 (ptm160) REVERT: A 78 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: A 81 LYS cc_start: 0.7912 (tptt) cc_final: 0.7638 (mptt) REVERT: A 222 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: A 258 TRP cc_start: 0.5341 (OUTLIER) cc_final: 0.4697 (t60) REVERT: A 278 LYS cc_start: -0.0914 (OUTLIER) cc_final: -0.1763 (tmtm) REVERT: A 292 ILE cc_start: 0.0296 (OUTLIER) cc_final: 0.0054 (pp) REVERT: A 296 ILE cc_start: 0.6742 (OUTLIER) cc_final: 0.6373 (mm) REVERT: A 305 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6665 (mt-10) REVERT: A 352 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8235 (pt0) REVERT: A 353 TRP cc_start: 0.7349 (m100) cc_final: 0.6433 (t60) REVERT: A 498 SER cc_start: 0.1335 (OUTLIER) cc_final: 0.0982 (p) REVERT: A 508 MET cc_start: -0.1025 (mtt) cc_final: -0.1474 (ppp) REVERT: A 532 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6888 (tm-30) REVERT: A 676 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8161 (tpt90) REVERT: B 19 PHE cc_start: 0.6308 (OUTLIER) cc_final: 0.5924 (t80) REVERT: B 29 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6459 (ptm160) REVERT: B 78 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.6633 (mp0) REVERT: B 81 LYS cc_start: 0.7908 (tptt) cc_final: 0.7633 (mptt) REVERT: B 222 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: B 258 TRP cc_start: 0.5344 (OUTLIER) cc_final: 0.4698 (t60) REVERT: B 278 LYS cc_start: -0.0912 (OUTLIER) cc_final: -0.1763 (tmtm) REVERT: B 292 ILE cc_start: 0.0307 (OUTLIER) cc_final: 0.0064 (pp) REVERT: B 296 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6379 (mm) REVERT: B 305 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6673 (mt-10) REVERT: B 352 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8233 (pt0) REVERT: B 353 TRP cc_start: 0.7342 (m100) cc_final: 0.6426 (t60) REVERT: B 498 SER cc_start: 0.1347 (OUTLIER) cc_final: 0.0993 (p) REVERT: B 508 MET cc_start: -0.1029 (mtt) cc_final: -0.1476 (ppp) REVERT: B 532 GLU cc_start: 0.7670 (mm-30) cc_final: 0.6890 (tm-30) REVERT: B 676 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8161 (tpt90) outliers start: 62 outliers final: 33 residues processed: 196 average time/residue: 1.0667 time to fit residues: 227.7776 Evaluate side-chains 189 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 134 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 702 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 2 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 chunk 70 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN A 398 GLN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.183873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108969 restraints weight = 11014.698| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.19 r_work: 0.3123 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11018 Z= 0.147 Angle : 0.608 15.634 14966 Z= 0.297 Chirality : 0.044 0.315 1678 Planarity : 0.005 0.041 1872 Dihedral : 7.043 59.435 1512 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.60 % Favored : 92.25 % Rotamer: Outliers : 5.81 % Allowed : 25.26 % Favored : 68.93 % 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: -0.06 (0.23), residues: 1316 helix: 1.37 (0.18), residues: 838 sheet: -3.02 (0.61), residues: 42 loop : -2.66 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 625 HIS 0.003 0.001 HIS A 90 PHE 0.022 0.002 PHE A 19 TYR 0.008 0.001 TYR B 713 ARG 0.002 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 648) hydrogen bonds : angle 4.38856 ( 1908) covalent geometry : bond 0.00338 (11018) covalent geometry : angle 0.60767 (14966) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 144 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6236 (OUTLIER) cc_final: 0.5884 (t80) REVERT: A 29 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6437 (ptm160) REVERT: A 64 LEU cc_start: 0.3781 (OUTLIER) cc_final: 0.3214 (pp) REVERT: A 78 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6627 (mp0) REVERT: A 81 LYS cc_start: 0.7864 (tptt) cc_final: 0.7579 (mptt) REVERT: A 222 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: A 258 TRP cc_start: 0.5315 (OUTLIER) cc_final: 0.4690 (t60) REVERT: A 278 LYS cc_start: -0.0961 (OUTLIER) cc_final: -0.1838 (tmtm) REVERT: A 292 ILE cc_start: 0.0358 (OUTLIER) cc_final: 0.0121 (pp) REVERT: A 296 ILE cc_start: 0.6754 (OUTLIER) cc_final: 0.6436 (mm) REVERT: A 300 ASP cc_start: 0.6489 (OUTLIER) cc_final: 0.6142 (t70) REVERT: A 305 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6641 (mt-10) REVERT: A 352 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: A 353 TRP cc_start: 0.7336 (m100) cc_final: 0.6391 (t60) REVERT: A 498 SER cc_start: 0.1366 (OUTLIER) cc_final: 0.1018 (p) REVERT: A 508 MET cc_start: -0.1038 (mtt) cc_final: -0.1496 (ppp) REVERT: A 512 MET cc_start: 0.4644 (mmm) cc_final: 0.4098 (mmm) REVERT: A 532 GLU cc_start: 0.7635 (mm-30) cc_final: 0.6877 (tm-30) REVERT: A 642 LEU cc_start: 0.7431 (mp) cc_final: 0.7106 (mp) REVERT: A 676 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8122 (tpt90) REVERT: B 19 PHE cc_start: 0.6256 (OUTLIER) cc_final: 0.5903 (t80) REVERT: B 29 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6431 (ptm160) REVERT: B 64 LEU cc_start: 0.3780 (OUTLIER) cc_final: 0.3215 (pp) REVERT: B 78 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6627 (mp0) REVERT: B 81 LYS cc_start: 0.7865 (tptt) cc_final: 0.7580 (mptt) REVERT: B 222 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: B 258 TRP cc_start: 0.5316 (OUTLIER) cc_final: 0.4691 (t60) REVERT: B 278 LYS cc_start: -0.0958 (OUTLIER) cc_final: -0.1838 (tmtm) REVERT: B 292 ILE cc_start: 0.0371 (OUTLIER) cc_final: 0.0132 (pp) REVERT: B 296 ILE cc_start: 0.6757 (OUTLIER) cc_final: 0.6439 (mm) REVERT: B 300 ASP cc_start: 0.6491 (OUTLIER) cc_final: 0.6142 (t70) REVERT: B 305 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6650 (mt-10) REVERT: B 352 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8225 (pt0) REVERT: B 353 TRP cc_start: 0.7332 (m100) cc_final: 0.6391 (t60) REVERT: B 498 SER cc_start: 0.1366 (OUTLIER) cc_final: 0.1018 (p) REVERT: B 508 MET cc_start: -0.1031 (mtt) cc_final: -0.1495 (ppp) REVERT: B 512 MET cc_start: 0.4643 (mmm) cc_final: 0.4102 (mmm) REVERT: B 532 GLU cc_start: 0.7632 (mm-30) cc_final: 0.6874 (tm-30) REVERT: B 642 LEU cc_start: 0.7415 (mp) cc_final: 0.7092 (mp) REVERT: B 676 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8121 (tpt90) outliers start: 66 outliers final: 27 residues processed: 202 average time/residue: 1.1080 time to fit residues: 243.4643 Evaluate side-chains 189 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 136 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 702 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 86 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 131 optimal weight: 0.0670 chunk 16 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 398 GLN ** B 34 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 = 0.4102 r_free = 0.4102 target = 0.183622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.107435 restraints weight = 11208.722| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.26 r_work: 0.3113 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11018 Z= 0.152 Angle : 0.614 15.517 14966 Z= 0.301 Chirality : 0.044 0.285 1678 Planarity : 0.005 0.041 1872 Dihedral : 6.809 59.620 1508 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.45 % Favored : 92.40 % Rotamer: Outliers : 5.28 % Allowed : 26.32 % Favored : 68.40 % 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: -0.05 (0.23), residues: 1316 helix: 1.41 (0.18), residues: 836 sheet: -3.01 (0.61), residues: 42 loop : -2.69 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 625 HIS 0.004 0.001 HIS A 90 PHE 0.021 0.001 PHE A 19 TYR 0.014 0.001 TYR B 542 ARG 0.002 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 648) hydrogen bonds : angle 4.39342 ( 1908) covalent geometry : bond 0.00352 (11018) covalent geometry : angle 0.61388 (14966) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 136 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6263 (OUTLIER) cc_final: 0.5888 (t80) REVERT: A 29 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6450 (ptm160) REVERT: A 64 LEU cc_start: 0.3745 (OUTLIER) cc_final: 0.3162 (pp) REVERT: A 78 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: A 81 LYS cc_start: 0.7889 (tptt) cc_final: 0.7600 (mptt) REVERT: A 222 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: A 258 TRP cc_start: 0.5331 (OUTLIER) cc_final: 0.4707 (t60) REVERT: A 278 LYS cc_start: -0.0964 (OUTLIER) cc_final: -0.1860 (tmtm) REVERT: A 296 ILE cc_start: 0.6727 (OUTLIER) cc_final: 0.6442 (mm) REVERT: A 300 ASP cc_start: 0.6502 (OUTLIER) cc_final: 0.6157 (t70) REVERT: A 305 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6634 (mt-10) REVERT: A 352 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8238 (pt0) REVERT: A 353 TRP cc_start: 0.7359 (m100) cc_final: 0.6411 (t60) REVERT: A 498 SER cc_start: 0.1333 (OUTLIER) cc_final: 0.0989 (p) REVERT: A 508 MET cc_start: -0.1014 (mtt) cc_final: -0.1483 (ppp) REVERT: A 512 MET cc_start: 0.4580 (mmm) cc_final: 0.4050 (mmm) REVERT: A 532 GLU cc_start: 0.7652 (mm-30) cc_final: 0.6882 (tm-30) REVERT: A 676 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8129 (tpt90) REVERT: B 19 PHE cc_start: 0.6277 (OUTLIER) cc_final: 0.5900 (t80) REVERT: B 29 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6450 (ptm160) REVERT: B 64 LEU cc_start: 0.3745 (OUTLIER) cc_final: 0.3163 (pp) REVERT: B 78 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: B 81 LYS cc_start: 0.7892 (tptt) cc_final: 0.7604 (mptt) REVERT: B 222 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: B 258 TRP cc_start: 0.5337 (OUTLIER) cc_final: 0.4713 (t60) REVERT: B 278 LYS cc_start: -0.0962 (OUTLIER) cc_final: -0.1859 (tmtm) REVERT: B 296 ILE cc_start: 0.6730 (OUTLIER) cc_final: 0.6444 (mm) REVERT: B 300 ASP cc_start: 0.6509 (OUTLIER) cc_final: 0.6161 (t70) REVERT: B 305 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6644 (mt-10) REVERT: B 352 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8234 (pt0) REVERT: B 353 TRP cc_start: 0.7358 (m100) cc_final: 0.6412 (t60) REVERT: B 498 SER cc_start: 0.1344 (OUTLIER) cc_final: 0.0998 (p) REVERT: B 508 MET cc_start: -0.1015 (mtt) cc_final: -0.1483 (ppp) REVERT: B 512 MET cc_start: 0.4576 (mmm) cc_final: 0.4052 (mmm) REVERT: B 532 GLU cc_start: 0.7655 (mm-30) cc_final: 0.6884 (tm-30) REVERT: B 676 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8120 (tpt90) outliers start: 60 outliers final: 25 residues processed: 190 average time/residue: 1.0919 time to fit residues: 225.3362 Evaluate side-chains 183 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 134 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 79 optimal weight: 0.9990 chunk 74 optimal weight: 0.3980 chunk 87 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 97 optimal weight: 0.0670 chunk 89 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.185330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.109640 restraints weight = 11164.252| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.26 r_work: 0.3129 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11018 Z= 0.130 Angle : 0.596 15.435 14966 Z= 0.290 Chirality : 0.043 0.223 1678 Planarity : 0.005 0.040 1872 Dihedral : 6.668 59.689 1508 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.22 % Favored : 92.71 % Rotamer: Outliers : 4.58 % Allowed : 26.85 % Favored : 68.57 % 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: 0.07 (0.24), residues: 1316 helix: 1.49 (0.18), residues: 838 sheet: -3.02 (0.62), residues: 42 loop : -2.63 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 625 HIS 0.003 0.001 HIS A 90 PHE 0.021 0.001 PHE A 384 TYR 0.009 0.001 TYR B 713 ARG 0.001 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 648) hydrogen bonds : angle 4.30235 ( 1908) covalent geometry : bond 0.00295 (11018) covalent geometry : angle 0.59572 (14966) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6212 (OUTLIER) cc_final: 0.5857 (t80) REVERT: A 29 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6320 (ptm160) REVERT: A 64 LEU cc_start: 0.3663 (OUTLIER) cc_final: 0.3102 (pp) REVERT: A 78 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.6623 (mp0) REVERT: A 81 LYS cc_start: 0.7806 (tptt) cc_final: 0.7543 (mptt) REVERT: A 222 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: A 258 TRP cc_start: 0.5338 (OUTLIER) cc_final: 0.4718 (t60) REVERT: A 278 LYS cc_start: -0.1001 (OUTLIER) cc_final: -0.1881 (tmtm) REVERT: A 296 ILE cc_start: 0.6669 (OUTLIER) cc_final: 0.6411 (mm) REVERT: A 300 ASP cc_start: 0.6480 (OUTLIER) cc_final: 0.6121 (t70) REVERT: A 305 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6620 (mt-10) REVERT: A 352 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8224 (pt0) REVERT: A 353 TRP cc_start: 0.7225 (m100) cc_final: 0.6316 (t60) REVERT: A 498 SER cc_start: 0.1334 (OUTLIER) cc_final: 0.0987 (p) REVERT: A 508 MET cc_start: -0.0986 (mtt) cc_final: -0.1457 (ppp) REVERT: A 512 MET cc_start: 0.4525 (mmm) cc_final: 0.4017 (mmm) REVERT: A 532 GLU cc_start: 0.7624 (mm-30) cc_final: 0.6866 (tm-30) REVERT: A 676 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8131 (tpt90) REVERT: B 19 PHE cc_start: 0.6227 (OUTLIER) cc_final: 0.5870 (t80) REVERT: B 29 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6326 (ptm160) REVERT: B 64 LEU cc_start: 0.3663 (OUTLIER) cc_final: 0.3104 (pp) REVERT: B 78 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: B 81 LYS cc_start: 0.7799 (tptt) cc_final: 0.7537 (mptt) REVERT: B 222 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: B 258 TRP cc_start: 0.5335 (OUTLIER) cc_final: 0.4712 (t60) REVERT: B 278 LYS cc_start: -0.0997 (OUTLIER) cc_final: -0.1880 (tmtm) REVERT: B 296 ILE cc_start: 0.6655 (OUTLIER) cc_final: 0.6398 (mm) REVERT: B 300 ASP cc_start: 0.6477 (OUTLIER) cc_final: 0.6115 (t70) REVERT: B 305 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6620 (mt-10) REVERT: B 352 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8232 (pt0) REVERT: B 353 TRP cc_start: 0.7223 (m100) cc_final: 0.6315 (t60) REVERT: B 498 SER cc_start: 0.1348 (OUTLIER) cc_final: 0.1000 (p) REVERT: B 508 MET cc_start: -0.0982 (mtt) cc_final: -0.1456 (ppp) REVERT: B 532 GLU cc_start: 0.7620 (mm-30) cc_final: 0.6862 (tm-30) REVERT: B 676 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8135 (tpt90) outliers start: 52 outliers final: 25 residues processed: 185 average time/residue: 1.1224 time to fit residues: 225.2768 Evaluate side-chains 183 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 134 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 702 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 129 optimal weight: 0.0570 chunk 100 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 95 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.184523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.109409 restraints weight = 11028.788| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.23 r_work: 0.3122 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11018 Z= 0.135 Angle : 0.602 15.389 14966 Z= 0.291 Chirality : 0.043 0.181 1678 Planarity : 0.005 0.040 1872 Dihedral : 6.616 59.632 1508 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.58 % Allowed : 26.94 % Favored : 68.49 % 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: 0.15 (0.24), residues: 1316 helix: 1.52 (0.18), residues: 838 sheet: -2.97 (0.62), residues: 42 loop : -2.52 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 625 HIS 0.003 0.001 HIS B 90 PHE 0.019 0.001 PHE B 19 TYR 0.009 0.001 TYR A 542 ARG 0.004 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 648) hydrogen bonds : angle 4.29293 ( 1908) covalent geometry : bond 0.00307 (11018) covalent geometry : angle 0.60187 (14966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12688.57 seconds wall clock time: 220 minutes 8.03 seconds (13208.03 seconds total)