Starting phenix.real_space_refine on Mon Jul 28 21:43:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymn_39400/07_2025/8ymn_39400_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymn_39400/07_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_39400/07_2025/8ymn_39400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymn_39400/07_2025/8ymn_39400.map" model { file = "/net/cci-nas-00/data/ceres_data/8ymn_39400/07_2025/8ymn_39400_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymn_39400/07_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-5711/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: 12.00, per 1000 atoms: 1.12 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: 2.40 Conformation dependent library (CDL) restraints added in 1.5 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: 1.01 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: 3.08 Time building geometry restraints manager: 2.89 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: 0.06 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: 18.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 31.240 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.350 ------------------------------------------------------------------------------- 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 : 1.537 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: 1.1021 time to fit residues: 622.8669 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 : 1.208 ------------------------------------------------------------------------------- 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 = 0.186943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113497 restraints weight = 10915.481| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.17 r_work: 0.3157 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 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 10.923 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 5.25838 ( 1908) covalent geometry : bond 0.00404 (11018) covalent geometry : angle 0.72396 (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 : 1.327 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: 0.6466 (OUTLIER) cc_final: 0.6067 (t80) REVERT: A 29 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6413 (ptm160) REVERT: A 78 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.6673 (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: 0.7299 (tt) REVERT: A 159 PHE cc_start: 0.6986 (OUTLIER) cc_final: 0.6484 (t80) REVERT: A 278 LYS cc_start: -0.0559 (OUTLIER) cc_final: -0.1335 (tptt) REVERT: A 352 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8190 (pt0) REVERT: A 353 TRP cc_start: 0.7517 (m100) cc_final: 0.6567 (t60) REVERT: A 372 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7338 (mp) REVERT: A 498 SER cc_start: 0.1846 (OUTLIER) cc_final: 0.1394 (p) REVERT: A 508 MET cc_start: -0.1136 (mtt) cc_final: -0.1462 (ppp) REVERT: A 676 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8137 (tpt90) REVERT: B 19 PHE cc_start: 0.6466 (OUTLIER) cc_final: 0.6063 (t80) REVERT: B 29 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6405 (ptm160) REVERT: B 78 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: B 114 MET cc_start: 0.7856 (mtp) cc_final: 0.7641 (mtm) REVERT: B 115 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7300 (tt) REVERT: B 159 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.6492 (t80) REVERT: B 278 LYS cc_start: -0.0559 (OUTLIER) cc_final: -0.1335 (tptt) REVERT: B 352 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8184 (pt0) REVERT: B 353 TRP cc_start: 0.7520 (m100) cc_final: 0.6561 (t60) REVERT: B 372 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7330 (mp) REVERT: B 498 SER cc_start: 0.1845 (OUTLIER) cc_final: 0.1390 (p) REVERT: B 508 MET cc_start: -0.1140 (mtt) cc_final: -0.1460 (ppp) REVERT: B 676 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8142 (tpt90) outliers start: 121 outliers final: 48 residues processed: 265 average time/residue: 1.0493 time to fit residues: 302.7600 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 : 1.145 ------------------------------------------------------------------------------- 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: 0.8980 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 49 optimal weight: 0.0870 chunk 80 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.186795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.112688 restraints weight = 11201.215| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.20 r_work: 0.3150 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11018 Z= 0.150 Angle : 0.649 15.109 14966 Z= 0.324 Chirality : 0.044 0.249 1678 Planarity : 0.005 0.044 1872 Dihedral : 10.573 76.424 1596 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.12 % Favored : 90.73 % Rotamer: Outliers : 8.45 % Allowed : 25.88 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.23), residues: 1316 helix: 0.88 (0.18), residues: 856 sheet: -3.11 (0.59), 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 0.003 0.001 HIS B 90 PHE 0.033 0.002 PHE A 478 TYR 0.017 0.001 TYR A 43 ARG 0.002 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 648) hydrogen bonds : angle 4.79536 ( 1908) covalent geometry : bond 0.00326 (11018) covalent geometry : angle 0.64945 (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 246 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 150 time to evaluate : 1.239 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: A 19 PHE cc_start: 0.6379 (OUTLIER) cc_final: 0.6007 (t80) REVERT: A 29 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6385 (ptm160) REVERT: A 78 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6631 (mp0) REVERT: A 85 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.5730 (mmm160) REVERT: A 86 GLU cc_start: 0.7773 (tt0) cc_final: 0.7263 (mt-10) REVERT: A 159 PHE cc_start: 0.7131 (OUTLIER) cc_final: 0.6553 (t80) REVERT: A 222 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: A 278 LYS cc_start: -0.0654 (OUTLIER) cc_final: -0.1375 (tptt) REVERT: A 352 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8179 (pt0) REVERT: A 353 TRP cc_start: 0.7361 (m100) cc_final: 0.6471 (t60) REVERT: A 498 SER cc_start: 0.1766 (OUTLIER) cc_final: 0.1406 (p) REVERT: A 508 MET cc_start: -0.1102 (mtt) cc_final: -0.1460 (ppp) REVERT: A 642 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7128 (mp) REVERT: A 676 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8093 (tpt90) REVERT: B 19 PHE cc_start: 0.6389 (OUTLIER) cc_final: 0.6040 (t80) REVERT: B 29 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6371 (ptm160) REVERT: B 78 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6651 (mp0) REVERT: B 85 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.5735 (mmm160) REVERT: B 86 GLU cc_start: 0.7771 (tt0) cc_final: 0.7264 (mt-10) REVERT: B 159 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6563 (t80) REVERT: B 222 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: B 278 LYS cc_start: -0.0654 (OUTLIER) cc_final: -0.1375 (tptt) REVERT: B 352 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8178 (pt0) REVERT: B 353 TRP cc_start: 0.7359 (m100) cc_final: 0.6468 (t60) REVERT: B 498 SER cc_start: 0.1766 (OUTLIER) cc_final: 0.1407 (p) REVERT: B 508 MET cc_start: -0.1101 (mtt) cc_final: -0.1454 (ppp) REVERT: B 642 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7124 (mp) REVERT: B 676 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8103 (tpt90) outliers start: 96 outliers final: 35 residues processed: 232 average time/residue: 1.0659 time to fit residues: 269.7996 Evaluate side-chains 195 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 138 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 222 GLU 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 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 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 222 GLU 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 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 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: 0.4980 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.184396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.109021 restraints weight = 11067.226| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.21 r_work: 0.3136 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4540 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= 0.157 Angle : 0.628 15.664 14966 Z= 0.314 Chirality : 0.044 0.269 1678 Planarity : 0.005 0.042 1872 Dihedral : 8.866 68.246 1542 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.60 % Favored : 92.10 % Rotamer: Outliers : 7.92 % Allowed : 24.91 % Favored : 67.17 % 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: -0.41 (0.23), residues: 1316 helix: 1.13 (0.18), residues: 836 sheet: -3.07 (0.60), residues: 42 loop : -2.87 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 625 HIS 0.003 0.001 HIS A 543 PHE 0.025 0.002 PHE B 19 TYR 0.010 0.001 TYR A 181 ARG 0.002 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 648) hydrogen bonds : angle 4.64651 ( 1908) covalent geometry : bond 0.00350 (11018) covalent geometry : angle 0.62758 (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 237 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 147 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6422 (OUTLIER) cc_final: 0.6034 (t80) REVERT: A 29 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6575 (ptm160) REVERT: A 78 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6665 (mp0) REVERT: A 86 GLU cc_start: 0.7884 (tt0) cc_final: 0.7406 (mt-10) REVERT: A 258 TRP cc_start: 0.5296 (OUTLIER) cc_final: 0.4580 (t60) REVERT: A 278 LYS cc_start: -0.0693 (OUTLIER) cc_final: -0.1521 (tmtm) REVERT: A 296 ILE cc_start: 0.6680 (OUTLIER) cc_final: 0.6221 (mm) REVERT: A 352 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8279 (pt0) REVERT: A 353 TRP cc_start: 0.7420 (m100) cc_final: 0.6516 (t60) REVERT: A 498 SER cc_start: 0.2032 (OUTLIER) cc_final: 0.1418 (m) REVERT: A 508 MET cc_start: -0.1087 (mtt) cc_final: -0.1535 (ppp) REVERT: A 642 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7223 (mp) REVERT: A 650 LYS cc_start: 0.6314 (OUTLIER) cc_final: 0.5984 (tmmt) REVERT: A 676 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8193 (tpt90) REVERT: B 19 PHE cc_start: 0.6427 (OUTLIER) cc_final: 0.6037 (t80) REVERT: B 29 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6564 (ptm160) REVERT: B 78 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: B 86 GLU cc_start: 0.7892 (tt0) cc_final: 0.7419 (mt-10) REVERT: B 258 TRP cc_start: 0.5293 (OUTLIER) cc_final: 0.4581 (t60) REVERT: B 278 LYS cc_start: -0.0689 (OUTLIER) cc_final: -0.1519 (tmtm) REVERT: B 296 ILE cc_start: 0.6675 (OUTLIER) cc_final: 0.6217 (mm) REVERT: B 352 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: B 353 TRP cc_start: 0.7412 (m100) cc_final: 0.6510 (t60) REVERT: B 498 SER cc_start: 0.2030 (OUTLIER) cc_final: 0.1421 (m) REVERT: B 508 MET cc_start: -0.1083 (mtt) cc_final: -0.1531 (ppp) REVERT: B 642 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7226 (mp) REVERT: B 650 LYS cc_start: 0.6311 (OUTLIER) cc_final: 0.5981 (tmmt) REVERT: B 676 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8201 (tpt90) outliers start: 90 outliers final: 33 residues processed: 227 average time/residue: 1.3659 time to fit residues: 336.0239 Evaluate side-chains 200 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 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 549 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 650 LYS 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 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 549 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 650 LYS 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: 0.9980 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.182724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107869 restraints weight = 11032.827| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.19 r_work: 0.3107 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11018 Z= 0.176 Angle : 0.634 15.964 14966 Z= 0.316 Chirality : 0.045 0.292 1678 Planarity : 0.005 0.040 1872 Dihedral : 7.825 58.845 1516 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.45 % Favored : 92.25 % Rotamer: Outliers : 6.87 % Allowed : 25.70 % Favored : 67.43 % 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: -0.34 (0.23), residues: 1316 helix: 1.16 (0.18), residues: 836 sheet: -3.05 (0.60), residues: 42 loop : -2.78 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 625 HIS 0.004 0.001 HIS B 90 PHE 0.025 0.002 PHE B 19 TYR 0.011 0.001 TYR A 181 ARG 0.001 0.000 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 648) hydrogen bonds : angle 4.59512 ( 1908) covalent geometry : bond 0.00405 (11018) covalent geometry : angle 0.63358 (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 232 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 154 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6411 (OUTLIER) cc_final: 0.6021 (t80) REVERT: A 29 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6631 (ptm160) REVERT: A 78 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6658 (mp0) REVERT: A 86 GLU cc_start: 0.7918 (tt0) cc_final: 0.7434 (mt-10) REVERT: A 258 TRP cc_start: 0.5336 (OUTLIER) cc_final: 0.4648 (t60) REVERT: A 278 LYS cc_start: -0.0759 (OUTLIER) cc_final: -0.1623 (tmtm) REVERT: A 296 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.6277 (mm) REVERT: A 305 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6720 (mt-10) REVERT: A 352 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8289 (pt0) REVERT: A 353 TRP cc_start: 0.7456 (m100) cc_final: 0.6533 (t60) REVERT: A 498 SER cc_start: 0.1467 (OUTLIER) cc_final: 0.1076 (p) REVERT: A 508 MET cc_start: -0.1422 (mtt) cc_final: -0.1761 (ppp) REVERT: A 642 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7248 (mp) REVERT: A 676 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8194 (tpt90) REVERT: B 19 PHE cc_start: 0.6407 (OUTLIER) cc_final: 0.6015 (t80) REVERT: B 29 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6618 (ptm160) REVERT: B 78 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: B 86 GLU cc_start: 0.7926 (tt0) cc_final: 0.7439 (mt-10) REVERT: B 258 TRP cc_start: 0.5337 (OUTLIER) cc_final: 0.4648 (t60) REVERT: B 278 LYS cc_start: -0.0757 (OUTLIER) cc_final: -0.1622 (tmtm) REVERT: B 296 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.6272 (mm) REVERT: B 305 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6710 (mt-10) REVERT: B 352 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8283 (pt0) REVERT: B 353 TRP cc_start: 0.7452 (m100) cc_final: 0.6526 (t60) REVERT: B 498 SER cc_start: 0.1465 (OUTLIER) cc_final: 0.1078 (p) REVERT: B 508 MET cc_start: -0.1422 (mtt) cc_final: -0.1762 (ppp) REVERT: B 642 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7243 (mp) REVERT: B 676 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8200 (tpt90) outliers start: 78 outliers final: 33 residues processed: 222 average time/residue: 1.1963 time to fit residues: 291.7549 Evaluate side-chains 197 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 1.495 ------------------------------------------------------------------------------- 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 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 549 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 641 LEU 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 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 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 549 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 642 LEU 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: 0.7980 chunk 98 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 53 optimal weight: 0.4980 chunk 117 optimal weight: 0.7980 chunk 112 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.184710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.108093 restraints weight = 11120.946| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.27 r_work: 0.3125 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4936 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= 0.145 Angle : 0.607 15.943 14966 Z= 0.301 Chirality : 0.043 0.309 1678 Planarity : 0.005 0.040 1872 Dihedral : 7.479 59.194 1514 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.90 % Favored : 91.95 % Rotamer: Outliers : 6.34 % Allowed : 26.14 % Favored : 67.52 % 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: -0.18 (0.23), residues: 1316 helix: 1.32 (0.18), residues: 836 sheet: -3.03 (0.61), residues: 42 loop : -2.78 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 625 HIS 0.003 0.001 HIS A 90 PHE 0.023 0.001 PHE A 19 TYR 0.010 0.001 TYR A 181 ARG 0.002 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 648) hydrogen bonds : angle 4.44939 ( 1908) covalent geometry : bond 0.00320 (11018) covalent geometry : angle 0.60725 (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 222 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 150 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6367 (OUTLIER) cc_final: 0.5982 (t80) REVERT: A 29 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6528 (ptm160) REVERT: A 78 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: A 81 LYS cc_start: 0.7943 (tptt) cc_final: 0.7665 (mptt) REVERT: A 86 GLU cc_start: 0.7836 (tt0) cc_final: 0.7342 (mt-10) REVERT: A 222 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: A 258 TRP cc_start: 0.5337 (OUTLIER) cc_final: 0.4674 (t60) REVERT: A 278 LYS cc_start: -0.0822 (OUTLIER) cc_final: -0.1708 (tmtm) REVERT: A 296 ILE cc_start: 0.6748 (OUTLIER) cc_final: 0.6366 (mm) REVERT: A 300 ASP cc_start: 0.6504 (OUTLIER) cc_final: 0.6174 (t70) REVERT: A 305 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6680 (mt-10) REVERT: A 352 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8268 (pt0) REVERT: A 353 TRP cc_start: 0.7353 (m100) cc_final: 0.6455 (t60) REVERT: A 498 SER cc_start: 0.1386 (OUTLIER) cc_final: 0.1041 (p) REVERT: A 508 MET cc_start: -0.1323 (mtt) cc_final: -0.1675 (ppp) REVERT: A 642 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7153 (mp) REVERT: A 676 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8204 (tpt90) REVERT: B 19 PHE cc_start: 0.6370 (OUTLIER) cc_final: 0.5982 (t80) REVERT: B 29 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6539 (ptm160) REVERT: B 78 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: B 81 LYS cc_start: 0.7945 (tptt) cc_final: 0.7667 (mptt) REVERT: B 86 GLU cc_start: 0.7851 (tt0) cc_final: 0.7361 (mt-10) REVERT: B 222 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: B 258 TRP cc_start: 0.5344 (OUTLIER) cc_final: 0.4682 (t60) REVERT: B 278 LYS cc_start: -0.0819 (OUTLIER) cc_final: -0.1707 (tmtm) REVERT: B 296 ILE cc_start: 0.6752 (OUTLIER) cc_final: 0.6368 (mm) REVERT: B 300 ASP cc_start: 0.6503 (OUTLIER) cc_final: 0.6173 (t70) REVERT: B 305 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6687 (mt-10) REVERT: B 352 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: B 353 TRP cc_start: 0.7345 (m100) cc_final: 0.6452 (t60) REVERT: B 498 SER cc_start: 0.1396 (OUTLIER) cc_final: 0.1050 (p) REVERT: B 508 MET cc_start: -0.1327 (mtt) cc_final: -0.1674 (ppp) REVERT: B 642 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7153 (mp) REVERT: B 676 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8207 (tpt90) outliers start: 72 outliers final: 27 residues processed: 214 average time/residue: 1.1416 time to fit residues: 267.1599 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 : 1.556 ------------------------------------------------------------------------------- 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 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 642 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 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 642 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: 0.7980 chunk 51 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.184960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.110162 restraints weight = 11251.992| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.22 r_work: 0.3133 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11018 Z= 0.135 Angle : 0.613 15.777 14966 Z= 0.300 Chirality : 0.044 0.327 1678 Planarity : 0.005 0.039 1872 Dihedral : 7.242 59.273 1512 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.37 % Favored : 92.48 % Rotamer: Outliers : 5.46 % Allowed : 26.14 % 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: -0.11 (0.23), residues: 1316 helix: 1.39 (0.18), residues: 836 sheet: -3.00 (0.61), residues: 42 loop : -2.78 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 625 HIS 0.003 0.001 HIS A 90 PHE 0.023 0.001 PHE B 494 TYR 0.010 0.001 TYR B 43 ARG 0.004 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 648) hydrogen bonds : angle 4.41083 ( 1908) covalent geometry : bond 0.00302 (11018) covalent geometry : angle 0.61339 (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 206 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 144 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6254 (OUTLIER) cc_final: 0.5869 (t80) REVERT: A 29 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6382 (ptm160) REVERT: A 78 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6617 (mp0) REVERT: A 81 LYS cc_start: 0.7842 (tptt) cc_final: 0.7580 (mptt) REVERT: A 86 GLU cc_start: 0.7759 (tt0) cc_final: 0.7247 (mt-10) REVERT: A 258 TRP cc_start: 0.5328 (OUTLIER) cc_final: 0.4685 (t60) REVERT: A 278 LYS cc_start: -0.0879 (OUTLIER) cc_final: -0.1749 (tmtm) REVERT: A 292 ILE cc_start: 0.0259 (OUTLIER) cc_final: 0.0003 (pp) REVERT: A 296 ILE cc_start: 0.6729 (OUTLIER) cc_final: 0.6369 (mm) REVERT: A 300 ASP cc_start: 0.6488 (OUTLIER) cc_final: 0.6146 (t70) REVERT: A 305 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6650 (mt-10) REVERT: A 352 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8220 (pt0) REVERT: A 353 TRP cc_start: 0.7253 (m100) cc_final: 0.6336 (t60) REVERT: A 498 SER cc_start: 0.1251 (OUTLIER) cc_final: 0.0908 (p) REVERT: A 508 MET cc_start: -0.1293 (mtt) cc_final: -0.1662 (ppp) REVERT: A 512 MET cc_start: 0.4762 (mmm) cc_final: 0.4416 (mmm) REVERT: A 532 GLU cc_start: 0.7654 (mm-30) cc_final: 0.6830 (tm-30) REVERT: A 676 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8142 (tpt90) REVERT: B 19 PHE cc_start: 0.6259 (OUTLIER) cc_final: 0.5875 (t80) REVERT: B 29 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6382 (ptm160) REVERT: B 78 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6608 (mp0) REVERT: B 81 LYS cc_start: 0.7834 (tptt) cc_final: 0.7572 (mptt) REVERT: B 86 GLU cc_start: 0.7775 (tt0) cc_final: 0.7263 (mt-10) REVERT: B 258 TRP cc_start: 0.5332 (OUTLIER) cc_final: 0.4687 (t60) REVERT: B 278 LYS cc_start: -0.0880 (OUTLIER) cc_final: -0.1750 (tmtm) REVERT: B 292 ILE cc_start: 0.0253 (OUTLIER) cc_final: -0.0003 (pp) REVERT: B 296 ILE cc_start: 0.6730 (OUTLIER) cc_final: 0.6370 (mm) REVERT: B 300 ASP cc_start: 0.6487 (OUTLIER) cc_final: 0.6144 (t70) REVERT: B 305 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6657 (mt-10) REVERT: B 352 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8215 (pt0) REVERT: B 353 TRP cc_start: 0.7246 (m100) cc_final: 0.6331 (t60) REVERT: B 498 SER cc_start: 0.1275 (OUTLIER) cc_final: 0.0929 (p) REVERT: B 508 MET cc_start: -0.1297 (mtt) cc_final: -0.1664 (ppp) REVERT: B 512 MET cc_start: 0.4761 (mmm) cc_final: 0.4416 (mmm) REVERT: B 532 GLU cc_start: 0.7649 (mm-30) cc_final: 0.6823 (tm-30) REVERT: B 676 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8146 (tpt90) outliers start: 62 outliers final: 29 residues processed: 198 average time/residue: 1.4086 time to fit residues: 302.4878 Evaluate side-chains 187 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 136 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 2 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 101 optimal weight: 0.0670 chunk 70 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 0.0870 chunk 80 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 0.5696 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.185755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.110007 restraints weight = 11038.387| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.24 r_work: 0.3132 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11018 Z= 0.133 Angle : 0.611 15.679 14966 Z= 0.297 Chirality : 0.044 0.315 1678 Planarity : 0.005 0.040 1872 Dihedral : 6.835 59.285 1508 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.29 % Favored : 92.55 % Rotamer: Outliers : 5.19 % Allowed : 26.58 % Favored : 68.22 % 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: -0.01 (0.23), residues: 1316 helix: 1.44 (0.18), residues: 838 sheet: -2.98 (0.62), residues: 42 loop : -2.71 (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 0.021 0.001 PHE A 19 TYR 0.009 0.001 TYR A 542 ARG 0.002 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 648) hydrogen bonds : angle 4.36654 ( 1908) covalent geometry : bond 0.00300 (11018) covalent geometry : angle 0.61099 (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 203 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 144 time to evaluate : 1.194 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: 0.6237 (OUTLIER) cc_final: 0.5853 (t80) REVERT: A 29 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6340 (ptm160) REVERT: A 64 LEU cc_start: 0.3830 (OUTLIER) cc_final: 0.3243 (pp) REVERT: A 78 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6565 (mp0) REVERT: A 81 LYS cc_start: 0.7812 (tptt) cc_final: 0.7559 (mptt) REVERT: A 258 TRP cc_start: 0.5307 (OUTLIER) cc_final: 0.4680 (t60) REVERT: A 278 LYS cc_start: -0.0961 (OUTLIER) cc_final: -0.1820 (tmtm) REVERT: A 292 ILE cc_start: 0.0322 (OUTLIER) cc_final: 0.0083 (pp) REVERT: A 296 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6383 (mm) REVERT: A 300 ASP cc_start: 0.6498 (OUTLIER) cc_final: 0.6150 (t70) REVERT: A 305 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6624 (mt-10) REVERT: A 352 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8215 (pt0) REVERT: A 353 TRP cc_start: 0.7243 (m100) cc_final: 0.6319 (t60) REVERT: A 498 SER cc_start: 0.1368 (OUTLIER) cc_final: 0.1031 (p) REVERT: A 508 MET cc_start: -0.1247 (mtt) cc_final: -0.1622 (ppp) REVERT: A 512 MET cc_start: 0.4689 (mmm) cc_final: 0.4348 (mmm) REVERT: A 532 GLU cc_start: 0.7635 (mm-30) cc_final: 0.6842 (tm-30) REVERT: A 642 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7020 (mp) REVERT: A 676 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8155 (tpt90) REVERT: B 19 PHE cc_start: 0.6233 (OUTLIER) cc_final: 0.5846 (t80) REVERT: B 29 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6338 (ptm160) REVERT: B 64 LEU cc_start: 0.3826 (OUTLIER) cc_final: 0.3241 (pp) REVERT: B 78 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6557 (mp0) REVERT: B 81 LYS cc_start: 0.7804 (tptt) cc_final: 0.7550 (mptt) REVERT: B 258 TRP cc_start: 0.5306 (OUTLIER) cc_final: 0.4675 (t60) REVERT: B 278 LYS cc_start: -0.0959 (OUTLIER) cc_final: -0.1818 (tmtm) REVERT: B 292 ILE cc_start: 0.0328 (OUTLIER) cc_final: 0.0087 (pp) REVERT: B 296 ILE cc_start: 0.6714 (OUTLIER) cc_final: 0.6383 (mm) REVERT: B 300 ASP cc_start: 0.6495 (OUTLIER) cc_final: 0.6144 (t70) REVERT: B 305 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6622 (mt-10) REVERT: B 352 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8217 (pt0) REVERT: B 353 TRP cc_start: 0.7240 (m100) cc_final: 0.6319 (t60) REVERT: B 498 SER cc_start: 0.1385 (OUTLIER) cc_final: 0.1047 (p) REVERT: B 508 MET cc_start: -0.1247 (mtt) cc_final: -0.1622 (ppp) REVERT: B 512 MET cc_start: 0.4681 (mmm) cc_final: 0.4344 (mmm) REVERT: B 532 GLU cc_start: 0.7625 (mm-30) cc_final: 0.6830 (tm-30) REVERT: B 642 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7019 (mp) REVERT: B 676 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8161 (tpt90) outliers start: 59 outliers final: 27 residues processed: 195 average time/residue: 1.0925 time to fit residues: 231.8387 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 : 1.230 ------------------------------------------------------------------------------- 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 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 86 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.183860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.107720 restraints weight = 11191.376| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.25 r_work: 0.3117 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5244 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= 0.150 Angle : 0.614 15.553 14966 Z= 0.300 Chirality : 0.044 0.278 1678 Planarity : 0.005 0.040 1872 Dihedral : 6.817 59.400 1508 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.45 % Favored : 92.40 % Rotamer: Outliers : 5.11 % Allowed : 26.85 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.23), residues: 1316 helix: 1.45 (0.18), residues: 836 sheet: -3.02 (0.62), residues: 42 loop : -2.68 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 625 HIS 0.004 0.001 HIS B 90 PHE 0.022 0.001 PHE A 384 TYR 0.009 0.001 TYR B 181 ARG 0.001 0.000 ARG B 468 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 648) hydrogen bonds : angle 4.38907 ( 1908) covalent geometry : bond 0.00345 (11018) covalent geometry : angle 0.61405 (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 198 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 140 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6247 (OUTLIER) cc_final: 0.5894 (t80) REVERT: A 29 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6450 (ptm160) REVERT: A 64 LEU cc_start: 0.3786 (OUTLIER) cc_final: 0.3185 (pp) REVERT: A 78 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6622 (mp0) REVERT: A 81 LYS cc_start: 0.7874 (tptt) cc_final: 0.7596 (mptt) REVERT: A 258 TRP cc_start: 0.5307 (OUTLIER) cc_final: 0.4675 (t60) REVERT: A 278 LYS cc_start: -0.0986 (OUTLIER) cc_final: -0.1868 (tmtm) REVERT: A 292 ILE cc_start: 0.0351 (OUTLIER) cc_final: 0.0111 (pp) REVERT: A 296 ILE cc_start: 0.6691 (OUTLIER) cc_final: 0.6399 (mm) REVERT: A 300 ASP cc_start: 0.6501 (OUTLIER) cc_final: 0.6149 (t70) REVERT: A 305 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6632 (mt-10) REVERT: A 352 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8222 (pt0) REVERT: A 353 TRP cc_start: 0.7344 (m100) cc_final: 0.6375 (t60) REVERT: A 498 SER cc_start: 0.1209 (OUTLIER) cc_final: 0.0874 (p) REVERT: A 508 MET cc_start: -0.1193 (mtt) cc_final: -0.1619 (ppp) REVERT: A 512 MET cc_start: 0.4634 (mmm) cc_final: 0.4344 (mmm) REVERT: A 532 GLU cc_start: 0.7661 (mm-30) cc_final: 0.6873 (tm-30) REVERT: A 642 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7081 (mp) REVERT: A 676 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8149 (tpt90) REVERT: B 19 PHE cc_start: 0.6258 (OUTLIER) cc_final: 0.5903 (t80) REVERT: B 29 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6450 (ptm160) REVERT: B 64 LEU cc_start: 0.3785 (OUTLIER) cc_final: 0.3187 (pp) REVERT: B 78 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: B 81 LYS cc_start: 0.7878 (tptt) cc_final: 0.7601 (mptt) REVERT: B 258 TRP cc_start: 0.5312 (OUTLIER) cc_final: 0.4677 (t60) REVERT: B 278 LYS cc_start: -0.0980 (OUTLIER) cc_final: -0.1865 (tmtm) REVERT: B 292 ILE cc_start: 0.0378 (OUTLIER) cc_final: 0.0135 (pp) REVERT: B 296 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.6405 (mm) REVERT: B 300 ASP cc_start: 0.6506 (OUTLIER) cc_final: 0.6152 (t70) REVERT: B 305 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6643 (mt-10) REVERT: B 352 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8222 (pt0) REVERT: B 353 TRP cc_start: 0.7344 (m100) cc_final: 0.6378 (t60) REVERT: B 498 SER cc_start: 0.1213 (OUTLIER) cc_final: 0.0877 (p) REVERT: B 508 MET cc_start: -0.1187 (mtt) cc_final: -0.1615 (ppp) REVERT: B 512 MET cc_start: 0.4634 (mmm) cc_final: 0.4346 (mmm) REVERT: B 532 GLU cc_start: 0.7660 (mm-30) cc_final: 0.6873 (tm-30) REVERT: B 642 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7077 (mp) REVERT: B 676 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8145 (tpt90) outliers start: 58 outliers final: 25 residues processed: 190 average time/residue: 1.5109 time to fit residues: 313.2488 Evaluate side-chains 191 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 140 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 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 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 639 SER 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 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 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 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 639 SER Chi-restraints excluded: chain B residue 642 LEU 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: 0.7980 chunk 74 optimal weight: 0.1980 chunk 87 optimal weight: 6.9990 chunk 114 optimal weight: 0.0870 chunk 97 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.184876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.110510 restraints weight = 11159.832| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.21 r_work: 0.3138 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11018 Z= 0.128 Angle : 0.599 15.483 14966 Z= 0.291 Chirality : 0.043 0.232 1678 Planarity : 0.005 0.040 1872 Dihedral : 6.663 59.558 1508 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.14 % Favored : 92.78 % Rotamer: Outliers : 4.67 % Allowed : 27.46 % Favored : 67.87 % 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: 0.10 (0.24), residues: 1316 helix: 1.53 (0.18), residues: 838 sheet: -3.00 (0.62), residues: 42 loop : -2.65 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 625 HIS 0.003 0.001 HIS B 90 PHE 0.020 0.001 PHE A 19 TYR 0.009 0.001 TYR B 713 ARG 0.005 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 648) hydrogen bonds : angle 4.30434 ( 1908) covalent geometry : bond 0.00286 (11018) covalent geometry : angle 0.59880 (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 196 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 143 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6225 (OUTLIER) cc_final: 0.5848 (t80) REVERT: A 29 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6315 (ptm160) REVERT: A 64 LEU cc_start: 0.3712 (OUTLIER) cc_final: 0.3135 (pp) REVERT: A 78 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6581 (mp0) REVERT: A 81 LYS cc_start: 0.7802 (tptt) cc_final: 0.7543 (mptt) REVERT: A 258 TRP cc_start: 0.5314 (OUTLIER) cc_final: 0.4704 (t60) REVERT: A 278 LYS cc_start: -0.0995 (OUTLIER) cc_final: -0.1870 (tmtm) REVERT: A 296 ILE cc_start: 0.6681 (OUTLIER) cc_final: 0.6393 (mm) REVERT: A 305 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6642 (mt-10) REVERT: A 352 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8211 (pt0) REVERT: A 353 TRP cc_start: 0.7210 (m100) cc_final: 0.6296 (t60) REVERT: A 498 SER cc_start: 0.1301 (OUTLIER) cc_final: 0.0962 (p) REVERT: A 508 MET cc_start: -0.1162 (mtt) cc_final: -0.1594 (ppp) REVERT: A 532 GLU cc_start: 0.7633 (mm-30) cc_final: 0.6874 (tm-30) REVERT: A 642 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7045 (mp) REVERT: A 676 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8156 (tpt90) REVERT: B 19 PHE cc_start: 0.6223 (OUTLIER) cc_final: 0.5843 (t80) REVERT: B 29 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6322 (ptm160) REVERT: B 64 LEU cc_start: 0.3710 (OUTLIER) cc_final: 0.3135 (pp) REVERT: B 78 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: B 81 LYS cc_start: 0.7798 (tptt) cc_final: 0.7541 (mptt) REVERT: B 258 TRP cc_start: 0.5314 (OUTLIER) cc_final: 0.4700 (t60) REVERT: B 278 LYS cc_start: -0.0989 (OUTLIER) cc_final: -0.1866 (tmtm) REVERT: B 296 ILE cc_start: 0.6668 (OUTLIER) cc_final: 0.6382 (mm) REVERT: B 305 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6642 (mt-10) REVERT: B 352 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8213 (pt0) REVERT: B 353 TRP cc_start: 0.7204 (m100) cc_final: 0.6293 (t60) REVERT: B 498 SER cc_start: 0.1308 (OUTLIER) cc_final: 0.0973 (p) REVERT: B 508 MET cc_start: -0.1157 (mtt) cc_final: -0.1592 (ppp) REVERT: B 532 GLU cc_start: 0.7627 (mm-30) cc_final: 0.6868 (tm-30) REVERT: B 642 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7050 (mp) REVERT: B 676 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8162 (tpt90) outliers start: 53 outliers final: 25 residues processed: 190 average time/residue: 1.3409 time to fit residues: 275.2265 Evaluate side-chains 184 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 129 optimal weight: 0.4980 chunk 100 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 162 HIS A 398 GLN B 34 ASN B 162 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.184188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.108397 restraints weight = 11014.678| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.24 r_work: 0.3116 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5399 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= 0.143 Angle : 0.606 15.400 14966 Z= 0.294 Chirality : 0.043 0.177 1678 Planarity : 0.005 0.041 1872 Dihedral : 6.655 59.457 1508 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 4.58 % Allowed : 28.26 % Favored : 67.17 % 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 (0.24), residues: 1316 helix: 1.55 (0.18), residues: 836 sheet: -3.00 (0.62), residues: 42 loop : -2.56 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 625 HIS 0.003 0.001 HIS A 90 PHE 0.024 0.001 PHE B 384 TYR 0.010 0.001 TYR B 542 ARG 0.004 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 648) hydrogen bonds : angle 4.32752 ( 1908) covalent geometry : bond 0.00327 (11018) covalent geometry : angle 0.60623 (14966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15584.93 seconds wall clock time: 280 minutes 48.55 seconds (16848.55 seconds total)