Starting phenix.real_space_refine on Sat Oct 11 01:57:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymn_39400/10_2025/8ymn_39400_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymn_39400/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ymn_39400/10_2025/8ymn_39400_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymn_39400/10_2025/8ymn_39400_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ymn_39400/10_2025/8ymn_39400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymn_39400/10_2025/8ymn_39400.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.59, per 1000 atoms: 0.24 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: 1.20 Conformation dependent library (CDL) restraints added in 556.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.31 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: 1.73 Time building geometry restraints manager: 1.52 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: 0.02 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: 33.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.750 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.540 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.300 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 36 TYR 0.008 0.001 TYR B 295 PHE 0.013 0.002 PHE A 494 TRP 0.017 0.002 TRP A 625 HIS 0.005 0.001 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00695 (11018) covalent geometry : angle 1.18243 (14966) hydrogen bonds : bond 0.17944 ( 648) hydrogen bonds : angle 7.21827 ( 1908) *********************** 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 : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7547 (tptm) REVERT: A 212 ASP cc_start: 0.4981 (t70) cc_final: 0.4440 (t0) REVERT: A 278 LYS cc_start: 0.0266 (OUTLIER) cc_final: -0.0768 (tmtm) REVERT: A 353 TRP cc_start: 0.5971 (m100) cc_final: 0.5708 (t60) REVERT: A 498 SER cc_start: 0.0567 (OUTLIER) cc_final: 0.0319 (p) REVERT: A 501 GLN cc_start: 0.1000 (OUTLIER) cc_final: 0.0092 (mm110) REVERT: A 502 ILE cc_start: 0.0533 (OUTLIER) cc_final: -0.0040 (mm) REVERT: A 508 MET cc_start: 0.0544 (mtt) cc_final: -0.0401 (ppp) REVERT: A 521 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.7175 (mt) REVERT: A 651 HIS cc_start: 0.1757 (OUTLIER) cc_final: 0.0726 (m90) REVERT: A 676 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7590 (tpt90) REVERT: A 692 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7045 (tttt) REVERT: B 41 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7549 (tptm) REVERT: B 212 ASP cc_start: 0.4998 (t70) cc_final: 0.4406 (t0) REVERT: B 278 LYS cc_start: 0.0252 (OUTLIER) cc_final: -0.0800 (tmtm) REVERT: B 353 TRP cc_start: 0.5983 (m100) cc_final: 0.5696 (t60) REVERT: B 498 SER cc_start: 0.0578 (OUTLIER) cc_final: 0.0322 (p) REVERT: B 501 GLN cc_start: 0.0992 (OUTLIER) cc_final: 0.0075 (mm110) REVERT: B 502 ILE cc_start: 0.0545 (OUTLIER) cc_final: -0.0014 (mm) REVERT: B 508 MET cc_start: 0.0500 (mtt) cc_final: -0.0452 (ppp) REVERT: B 521 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.7190 (mt) REVERT: B 651 HIS cc_start: 0.1779 (OUTLIER) cc_final: 0.0707 (m90) REVERT: B 676 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7601 (tpt90) REVERT: B 692 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7038 (tttt) outliers start: 392 outliers final: 48 residues processed: 518 average time/residue: 0.4978 time to fit residues: 280.4211 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 : 0.399 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 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 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 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: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.187504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.114337 restraints weight = 10948.396| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.16 r_work: 0.3167 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11018 Z= 0.183 Angle : 0.721 11.012 14966 Z= 0.368 Chirality : 0.047 0.260 1678 Planarity : 0.006 0.047 1872 Dihedral : 12.486 75.979 1632 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.90 % Favored : 91.95 % Rotamer: Outliers : 10.39 % Allowed : 24.21 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.23), residues: 1316 helix: 0.36 (0.17), residues: 842 sheet: -3.23 (0.61), residues: 42 loop : -3.19 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 556 TYR 0.016 0.002 TYR B 43 PHE 0.037 0.002 PHE B 19 TRP 0.028 0.002 TRP A 625 HIS 0.008 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00410 (11018) covalent geometry : angle 0.72134 (14966) hydrogen bonds : bond 0.04779 ( 648) hydrogen bonds : angle 5.23847 ( 1908) *********************** 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 272 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 154 time to evaluate : 0.429 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: 0.6442 (OUTLIER) cc_final: 0.6040 (t80) REVERT: A 29 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6414 (ptm160) REVERT: A 114 MET cc_start: 0.7846 (mtp) cc_final: 0.7628 (mtm) REVERT: A 115 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7318 (tt) REVERT: A 159 PHE cc_start: 0.6976 (OUTLIER) cc_final: 0.6398 (t80) REVERT: A 278 LYS cc_start: -0.0562 (OUTLIER) cc_final: -0.1338 (tptt) REVERT: A 352 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8190 (pt0) REVERT: A 353 TRP cc_start: 0.7475 (m100) cc_final: 0.6553 (t60) REVERT: A 372 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7332 (mp) REVERT: A 498 SER cc_start: 0.1928 (OUTLIER) cc_final: 0.1480 (p) REVERT: A 508 MET cc_start: -0.1111 (mtt) cc_final: -0.1444 (ppp) REVERT: A 676 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8138 (tpt90) REVERT: B 19 PHE cc_start: 0.6446 (OUTLIER) cc_final: 0.6037 (t80) REVERT: B 29 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6411 (ptm160) REVERT: B 114 MET cc_start: 0.7848 (mtp) cc_final: 0.7629 (mtm) REVERT: B 115 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7313 (tt) REVERT: B 159 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6407 (t80) REVERT: B 278 LYS cc_start: -0.0560 (OUTLIER) cc_final: -0.1336 (tptt) REVERT: B 352 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8185 (pt0) REVERT: B 353 TRP cc_start: 0.7475 (m100) cc_final: 0.6548 (t60) REVERT: B 372 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7326 (mp) REVERT: B 498 SER cc_start: 0.1923 (OUTLIER) cc_final: 0.1474 (p) REVERT: B 508 MET cc_start: -0.1115 (mtt) cc_final: -0.1443 (ppp) REVERT: B 676 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8148 (tpt90) outliers start: 118 outliers final: 46 residues processed: 262 average time/residue: 0.5166 time to fit residues: 147.1049 Evaluate side-chains 212 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 148 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 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 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 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 55 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 78 optimal weight: 0.0470 chunk 7 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 45 optimal weight: 30.0000 chunk 60 optimal weight: 8.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 492 ASN A 501 GLN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 ASN B 492 ASN B 501 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.186273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113188 restraints weight = 11172.518| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.17 r_work: 0.3150 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11018 Z= 0.161 Angle : 0.663 15.374 14966 Z= 0.330 Chirality : 0.045 0.256 1678 Planarity : 0.005 0.044 1872 Dihedral : 10.680 75.134 1592 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.81 % Favored : 91.03 % Rotamer: Outliers : 8.54 % Allowed : 25.35 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.23), residues: 1316 helix: 0.86 (0.18), residues: 856 sheet: -3.14 (0.60), residues: 42 loop : -3.15 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 67 TYR 0.009 0.001 TYR B 261 PHE 0.040 0.002 PHE A 494 TRP 0.021 0.001 TRP A 625 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00350 (11018) covalent geometry : angle 0.66326 (14966) hydrogen bonds : bond 0.04356 ( 648) hydrogen bonds : angle 4.86364 ( 1908) *********************** 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 251 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 154 time to evaluate : 0.510 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: 0.6388 (OUTLIER) cc_final: 0.6015 (t80) REVERT: A 29 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6408 (ptm160) REVERT: A 78 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6658 (mp0) REVERT: A 85 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.5716 (mmm160) REVERT: A 86 GLU cc_start: 0.7766 (tt0) cc_final: 0.7257 (mt-10) REVERT: A 159 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6550 (t80) REVERT: A 222 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: A 278 LYS cc_start: -0.0614 (OUTLIER) cc_final: -0.1368 (tptt) REVERT: A 352 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8175 (pt0) REVERT: A 353 TRP cc_start: 0.7385 (m100) cc_final: 0.6484 (t60) REVERT: A 498 SER cc_start: 0.1843 (OUTLIER) cc_final: 0.1412 (p) REVERT: A 508 MET cc_start: -0.1113 (mtt) cc_final: -0.1568 (ppp) REVERT: A 642 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7134 (mp) REVERT: A 676 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8076 (tpt90) REVERT: B 19 PHE cc_start: 0.6399 (OUTLIER) cc_final: 0.6021 (t80) REVERT: B 29 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6391 (ptm160) REVERT: B 78 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: B 85 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.5714 (mmm160) REVERT: B 86 GLU cc_start: 0.7758 (tt0) cc_final: 0.7255 (mt-10) REVERT: B 159 PHE cc_start: 0.7105 (OUTLIER) cc_final: 0.6564 (t80) REVERT: B 222 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: B 278 LYS cc_start: -0.0614 (OUTLIER) cc_final: -0.1369 (tptt) REVERT: B 352 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8172 (pt0) REVERT: B 353 TRP cc_start: 0.7381 (m100) cc_final: 0.6477 (t60) REVERT: B 498 SER cc_start: 0.1839 (OUTLIER) cc_final: 0.1411 (p) REVERT: B 508 MET cc_start: -0.1121 (mtt) cc_final: -0.1566 (ppp) REVERT: B 642 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7129 (mp) REVERT: B 676 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8084 (tpt90) outliers start: 97 outliers final: 34 residues processed: 237 average time/residue: 0.5238 time to fit residues: 135.1331 Evaluate side-chains 198 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 142 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 250 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 272 GLN 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 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 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 250 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 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 6 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 43 optimal weight: 0.0040 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN A 315 ASN A 398 GLN B 272 GLN B 315 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.184736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.110637 restraints weight = 11201.721| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.18 r_work: 0.3141 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4596 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= 0.154 Angle : 0.630 15.797 14966 Z= 0.316 Chirality : 0.045 0.272 1678 Planarity : 0.005 0.041 1872 Dihedral : 8.833 76.735 1534 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.05 % Favored : 91.64 % Rotamer: Outliers : 8.54 % Allowed : 24.21 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.23), residues: 1316 helix: 1.10 (0.18), residues: 836 sheet: -3.05 (0.59), residues: 42 loop : -2.85 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 67 TYR 0.011 0.001 TYR B 43 PHE 0.049 0.002 PHE A 494 TRP 0.020 0.001 TRP B 625 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00332 (11018) covalent geometry : angle 0.62964 (14966) hydrogen bonds : bond 0.04060 ( 648) hydrogen bonds : angle 4.68878 ( 1908) *********************** 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 243 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 146 time to evaluate : 0.416 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: 0.6425 (OUTLIER) cc_final: 0.6058 (t80) REVERT: A 29 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6540 (ptm160) REVERT: A 78 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: A 86 GLU cc_start: 0.7863 (tt0) cc_final: 0.7393 (mt-10) REVERT: A 258 TRP cc_start: 0.5277 (OUTLIER) cc_final: 0.4577 (t60) REVERT: A 278 LYS cc_start: -0.0697 (OUTLIER) cc_final: -0.1525 (tmtm) REVERT: A 296 ILE cc_start: 0.6635 (OUTLIER) cc_final: 0.6206 (mm) REVERT: A 352 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8262 (pt0) REVERT: A 353 TRP cc_start: 0.7390 (m100) cc_final: 0.6501 (t60) REVERT: A 498 SER cc_start: 0.1471 (OUTLIER) cc_final: 0.1070 (p) REVERT: A 508 MET cc_start: -0.1338 (mtt) cc_final: -0.1706 (ppp) REVERT: A 642 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7195 (mp) REVERT: A 676 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8182 (tpt90) REVERT: B 19 PHE cc_start: 0.6427 (OUTLIER) cc_final: 0.6058 (t80) REVERT: B 29 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6530 (ptm160) REVERT: B 78 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: B 86 GLU cc_start: 0.7866 (tt0) cc_final: 0.7400 (mt-10) REVERT: B 258 TRP cc_start: 0.5270 (OUTLIER) cc_final: 0.4575 (t60) REVERT: B 278 LYS cc_start: -0.0693 (OUTLIER) cc_final: -0.1524 (tmtm) REVERT: B 296 ILE cc_start: 0.6636 (OUTLIER) cc_final: 0.6207 (mm) REVERT: B 352 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8263 (pt0) REVERT: B 353 TRP cc_start: 0.7384 (m100) cc_final: 0.6492 (t60) REVERT: B 498 SER cc_start: 0.1480 (OUTLIER) cc_final: 0.1080 (p) REVERT: B 508 MET cc_start: -0.1338 (mtt) cc_final: -0.1704 (ppp) REVERT: B 642 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7205 (mp) REVERT: B 676 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8195 (tpt90) outliers start: 97 outliers final: 34 residues processed: 235 average time/residue: 0.5483 time to fit residues: 139.2793 Evaluate side-chains 194 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 140 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 288 LYS 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 498 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 702 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.183806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.109488 restraints weight = 11125.657| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.18 r_work: 0.3126 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4822 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= 0.155 Angle : 0.635 16.101 14966 Z= 0.314 Chirality : 0.045 0.289 1678 Planarity : 0.005 0.040 1872 Dihedral : 7.694 58.895 1524 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.45 % Favored : 92.25 % Rotamer: Outliers : 6.60 % Allowed : 25.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.23), residues: 1316 helix: 1.17 (0.18), residues: 836 sheet: -3.00 (0.61), residues: 42 loop : -2.74 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 67 TYR 0.010 0.001 TYR A 181 PHE 0.038 0.002 PHE A 494 TRP 0.019 0.001 TRP A 625 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00346 (11018) covalent geometry : angle 0.63527 (14966) hydrogen bonds : bond 0.04031 ( 648) hydrogen bonds : angle 4.54868 ( 1908) *********************** 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 233 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 158 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6396 (OUTLIER) cc_final: 0.6007 (t80) REVERT: A 29 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6555 (ptm160) REVERT: A 78 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: A 86 GLU cc_start: 0.7897 (tt0) cc_final: 0.7416 (mt-10) REVERT: A 258 TRP cc_start: 0.5348 (OUTLIER) cc_final: 0.4674 (t60) REVERT: A 278 LYS cc_start: -0.0751 (OUTLIER) cc_final: -0.1618 (tmtm) REVERT: A 296 ILE cc_start: 0.6677 (OUTLIER) cc_final: 0.6247 (mm) REVERT: A 305 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6693 (mt-10) REVERT: A 352 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8277 (pt0) REVERT: A 353 TRP cc_start: 0.7409 (m100) cc_final: 0.6502 (t60) REVERT: A 498 SER cc_start: 0.1462 (OUTLIER) cc_final: 0.1105 (p) REVERT: A 508 MET cc_start: -0.1295 (mtt) cc_final: -0.1653 (ppp) REVERT: A 676 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8191 (tpt90) REVERT: B 19 PHE cc_start: 0.6399 (OUTLIER) cc_final: 0.6006 (t80) REVERT: B 29 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6549 (ptm160) REVERT: B 78 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: B 86 GLU cc_start: 0.7901 (tt0) cc_final: 0.7423 (mt-10) REVERT: B 258 TRP cc_start: 0.5345 (OUTLIER) cc_final: 0.4674 (t60) REVERT: B 278 LYS cc_start: -0.0746 (OUTLIER) cc_final: -0.1617 (tmtm) REVERT: B 296 ILE cc_start: 0.6671 (OUTLIER) cc_final: 0.6241 (mm) REVERT: B 305 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6691 (mt-10) REVERT: B 352 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8276 (pt0) REVERT: B 353 TRP cc_start: 0.7407 (m100) cc_final: 0.6499 (t60) REVERT: B 498 SER cc_start: 0.1469 (OUTLIER) cc_final: 0.1115 (p) REVERT: B 508 MET cc_start: -0.1298 (mtt) cc_final: -0.1653 (ppp) REVERT: B 676 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8196 (tpt90) outliers start: 75 outliers final: 32 residues processed: 223 average time/residue: 0.5352 time to fit residues: 129.7594 Evaluate side-chains 194 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 144 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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 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 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 659 LEU Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 702 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.0570 chunk 101 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 83 optimal weight: 0.0050 chunk 20 optimal weight: 6.9990 overall best weight: 0.5512 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.184732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110390 restraints weight = 11121.232| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.19 r_work: 0.3135 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5006 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= 0.136 Angle : 0.616 16.048 14966 Z= 0.302 Chirality : 0.044 0.306 1678 Planarity : 0.005 0.040 1872 Dihedral : 7.392 59.232 1514 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.90 % Favored : 91.79 % Rotamer: Outliers : 6.25 % Allowed : 25.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.23), residues: 1316 helix: 1.29 (0.18), residues: 838 sheet: -2.97 (0.61), residues: 42 loop : -2.78 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 45 TYR 0.009 0.001 TYR A 713 PHE 0.032 0.001 PHE B 494 TRP 0.020 0.001 TRP A 625 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00300 (11018) covalent geometry : angle 0.61628 (14966) hydrogen bonds : bond 0.03742 ( 648) hydrogen bonds : angle 4.45886 ( 1908) *********************** 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 223 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 152 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6300 (OUTLIER) cc_final: 0.5943 (t80) REVERT: A 29 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6341 (ptm160) REVERT: A 78 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6579 (mp0) REVERT: A 81 LYS cc_start: 0.7859 (tptt) cc_final: 0.7599 (mptt) REVERT: A 86 GLU cc_start: 0.7770 (tt0) cc_final: 0.7281 (mt-10) REVERT: A 222 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: A 258 TRP cc_start: 0.5340 (OUTLIER) cc_final: 0.4685 (t60) REVERT: A 278 LYS cc_start: -0.0805 (OUTLIER) cc_final: -0.1684 (tmtm) REVERT: A 296 ILE cc_start: 0.6713 (OUTLIER) cc_final: 0.6314 (mm) REVERT: A 305 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6633 (mt-10) REVERT: A 352 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8214 (pt0) REVERT: A 353 TRP cc_start: 0.7271 (m100) cc_final: 0.6361 (t60) REVERT: A 498 SER cc_start: 0.1448 (OUTLIER) cc_final: 0.1109 (p) REVERT: A 508 MET cc_start: -0.1272 (mtt) cc_final: -0.1652 (ppp) REVERT: A 512 MET cc_start: 0.4815 (mmm) cc_final: 0.4446 (mmm) REVERT: A 532 GLU cc_start: 0.7687 (mm-30) cc_final: 0.6863 (tm-30) REVERT: A 676 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8132 (tpt90) REVERT: B 19 PHE cc_start: 0.6311 (OUTLIER) cc_final: 0.5953 (t80) REVERT: B 29 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6353 (ptm160) REVERT: B 78 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6583 (mp0) REVERT: B 81 LYS cc_start: 0.7861 (tptt) cc_final: 0.7601 (mptt) REVERT: B 86 GLU cc_start: 0.7752 (tt0) cc_final: 0.7262 (mt-10) REVERT: B 222 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: B 258 TRP cc_start: 0.5342 (OUTLIER) cc_final: 0.4687 (t60) REVERT: B 278 LYS cc_start: -0.0806 (OUTLIER) cc_final: -0.1683 (tmtm) REVERT: B 296 ILE cc_start: 0.6717 (OUTLIER) cc_final: 0.6317 (mm) REVERT: B 305 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6635 (mt-10) REVERT: B 352 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8194 (pt0) REVERT: B 353 TRP cc_start: 0.7261 (m100) cc_final: 0.6352 (t60) REVERT: B 498 SER cc_start: 0.1443 (OUTLIER) cc_final: 0.1106 (p) REVERT: B 508 MET cc_start: -0.1272 (mtt) cc_final: -0.1653 (ppp) REVERT: B 512 MET cc_start: 0.4820 (mmm) cc_final: 0.4453 (mmm) REVERT: B 532 GLU cc_start: 0.7674 (mm-30) cc_final: 0.6849 (tm-30) REVERT: B 676 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8130 (tpt90) outliers start: 71 outliers final: 26 residues processed: 213 average time/residue: 0.5218 time to fit residues: 121.0969 Evaluate side-chains 186 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 222 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 31 optimal weight: 0.9980 chunk 131 optimal weight: 0.0670 chunk 18 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.184930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.110219 restraints weight = 11090.668| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.17 r_work: 0.3136 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11018 Z= 0.135 Angle : 0.605 15.867 14966 Z= 0.298 Chirality : 0.044 0.320 1678 Planarity : 0.005 0.041 1872 Dihedral : 7.107 59.269 1512 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.60 % Favored : 92.25 % Rotamer: Outliers : 6.07 % Allowed : 25.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.23), residues: 1316 helix: 1.38 (0.18), residues: 838 sheet: -2.99 (0.61), residues: 42 loop : -2.70 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 60 TYR 0.009 0.001 TYR B 261 PHE 0.031 0.001 PHE B 494 TRP 0.018 0.001 TRP B 625 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00306 (11018) covalent geometry : angle 0.60513 (14966) hydrogen bonds : bond 0.03713 ( 648) hydrogen bonds : angle 4.37954 ( 1908) *********************** 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 221 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 152 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6073 (OUTLIER) cc_final: 0.5722 (t80) REVERT: A 29 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.6156 (ptm160) REVERT: A 78 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6390 (mp0) REVERT: A 81 LYS cc_start: 0.7659 (tptt) cc_final: 0.7394 (mptt) REVERT: A 222 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: A 258 TRP cc_start: 0.5325 (OUTLIER) cc_final: 0.4677 (t60) REVERT: A 278 LYS cc_start: -0.0936 (OUTLIER) cc_final: -0.1783 (tmtm) REVERT: A 292 ILE cc_start: 0.0197 (OUTLIER) cc_final: -0.0059 (pp) REVERT: A 296 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.6234 (mm) REVERT: A 300 ASP cc_start: 0.6428 (OUTLIER) cc_final: 0.6082 (t70) REVERT: A 305 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6519 (mt-10) REVERT: A 352 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8083 (pt0) REVERT: A 353 TRP cc_start: 0.7167 (m100) cc_final: 0.6166 (t60) REVERT: A 498 SER cc_start: 0.1359 (OUTLIER) cc_final: 0.1035 (p) REVERT: A 508 MET cc_start: -0.1245 (mtt) cc_final: -0.1637 (ppp) REVERT: A 532 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6704 (tm-30) REVERT: A 676 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7930 (tpt90) REVERT: B 19 PHE cc_start: 0.6076 (OUTLIER) cc_final: 0.5724 (t80) REVERT: B 29 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6151 (ptm160) REVERT: B 78 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6382 (mp0) REVERT: B 81 LYS cc_start: 0.7652 (tptt) cc_final: 0.7387 (mptt) REVERT: B 222 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: B 258 TRP cc_start: 0.5325 (OUTLIER) cc_final: 0.4677 (t60) REVERT: B 278 LYS cc_start: -0.0932 (OUTLIER) cc_final: -0.1780 (tmtm) REVERT: B 292 ILE cc_start: 0.0200 (OUTLIER) cc_final: -0.0053 (pp) REVERT: B 296 ILE cc_start: 0.6577 (OUTLIER) cc_final: 0.6233 (mm) REVERT: B 300 ASP cc_start: 0.6423 (OUTLIER) cc_final: 0.6074 (t70) REVERT: B 305 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6511 (mt-10) REVERT: B 352 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8080 (pt0) REVERT: B 353 TRP cc_start: 0.7171 (m100) cc_final: 0.6169 (t60) REVERT: B 498 SER cc_start: 0.1361 (OUTLIER) cc_final: 0.1038 (p) REVERT: B 508 MET cc_start: -0.1240 (mtt) cc_final: -0.1636 (ppp) REVERT: B 532 GLU cc_start: 0.7511 (mm-30) cc_final: 0.6705 (tm-30) REVERT: B 676 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7931 (tpt90) outliers start: 69 outliers final: 30 residues processed: 211 average time/residue: 0.4983 time to fit residues: 114.3869 Evaluate side-chains 196 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 142 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 222 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 SER 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 222 GLU Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 493 SER 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 124 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN A 398 GLN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.184604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.108835 restraints weight = 11093.014| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.23 r_work: 0.3124 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11018 Z= 0.149 Angle : 0.622 15.774 14966 Z= 0.304 Chirality : 0.045 0.322 1678 Planarity : 0.005 0.041 1872 Dihedral : 6.850 59.346 1508 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.60 % Favored : 92.25 % Rotamer: Outliers : 5.37 % Allowed : 25.70 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.23), residues: 1316 helix: 1.37 (0.18), residues: 838 sheet: -2.99 (0.61), residues: 42 loop : -2.69 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 60 TYR 0.010 0.001 TYR B 542 PHE 0.031 0.002 PHE A 494 TRP 0.018 0.001 TRP B 625 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00343 (11018) covalent geometry : angle 0.62215 (14966) hydrogen bonds : bond 0.03830 ( 648) hydrogen bonds : angle 4.41442 ( 1908) *********************** 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 205 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 144 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6308 (OUTLIER) cc_final: 0.5949 (t80) REVERT: A 29 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6471 (ptm160) REVERT: A 64 LEU cc_start: 0.3838 (OUTLIER) cc_final: 0.3236 (pp) REVERT: A 78 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6592 (mp0) REVERT: A 81 LYS cc_start: 0.7911 (tptt) cc_final: 0.7642 (mptt) REVERT: A 258 TRP cc_start: 0.5363 (OUTLIER) cc_final: 0.4741 (t60) REVERT: A 278 LYS cc_start: -0.0950 (OUTLIER) cc_final: -0.1831 (tmtm) REVERT: A 292 ILE cc_start: 0.0425 (OUTLIER) cc_final: 0.0163 (pp) REVERT: A 296 ILE cc_start: 0.6691 (OUTLIER) cc_final: 0.6362 (mm) REVERT: A 300 ASP cc_start: 0.6501 (OUTLIER) cc_final: 0.6149 (t70) REVERT: A 305 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6653 (mt-10) REVERT: A 352 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8240 (pt0) REVERT: A 353 TRP cc_start: 0.7311 (m100) cc_final: 0.6379 (t60) REVERT: A 498 SER cc_start: 0.1485 (OUTLIER) cc_final: 0.1150 (p) REVERT: A 508 MET cc_start: -0.1175 (mtt) cc_final: -0.1638 (ppp) REVERT: A 512 MET cc_start: 0.4717 (mmm) cc_final: 0.4266 (mmm) REVERT: A 532 GLU cc_start: 0.7683 (mm-30) cc_final: 0.6910 (tm-30) REVERT: A 642 LEU cc_start: 0.7477 (mp) cc_final: 0.7136 (mp) REVERT: A 676 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8158 (tpt90) REVERT: B 19 PHE cc_start: 0.6317 (OUTLIER) cc_final: 0.5958 (t80) REVERT: B 29 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6472 (ptm160) REVERT: B 64 LEU cc_start: 0.3842 (OUTLIER) cc_final: 0.3240 (pp) REVERT: B 78 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6591 (mp0) REVERT: B 81 LYS cc_start: 0.7905 (tptt) cc_final: 0.7634 (mptt) REVERT: B 258 TRP cc_start: 0.5368 (OUTLIER) cc_final: 0.4747 (t60) REVERT: B 278 LYS cc_start: -0.0955 (OUTLIER) cc_final: -0.1834 (tmtm) REVERT: B 292 ILE cc_start: 0.0462 (OUTLIER) cc_final: 0.0199 (pp) REVERT: B 296 ILE cc_start: 0.6702 (OUTLIER) cc_final: 0.6371 (mm) REVERT: B 300 ASP cc_start: 0.6502 (OUTLIER) cc_final: 0.6147 (t70) REVERT: B 305 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6661 (mt-10) REVERT: B 352 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8231 (pt0) REVERT: B 353 TRP cc_start: 0.7308 (m100) cc_final: 0.6375 (t60) REVERT: B 498 SER cc_start: 0.1492 (OUTLIER) cc_final: 0.1158 (p) REVERT: B 508 MET cc_start: -0.1175 (mtt) cc_final: -0.1638 (ppp) REVERT: B 512 MET cc_start: 0.4707 (mmm) cc_final: 0.4259 (mmm) REVERT: B 532 GLU cc_start: 0.7679 (mm-30) cc_final: 0.6902 (tm-30) REVERT: B 642 LEU cc_start: 0.7473 (mp) cc_final: 0.7131 (mp) REVERT: B 676 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8157 (tpt90) outliers start: 61 outliers final: 26 residues processed: 197 average time/residue: 0.5245 time to fit residues: 112.4210 Evaluate side-chains 192 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 142 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 491 LEU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 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 491 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 702 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 67 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 131 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 40 optimal weight: 0.0980 chunk 20 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 111 optimal weight: 0.0970 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.186045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.111533 restraints weight = 11107.825| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.18 r_work: 0.3152 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5401 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= 0.124 Angle : 0.603 15.611 14966 Z= 0.293 Chirality : 0.043 0.288 1678 Planarity : 0.005 0.039 1872 Dihedral : 6.633 59.774 1508 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.14 % Favored : 92.71 % Rotamer: Outliers : 4.67 % Allowed : 27.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.24), residues: 1316 helix: 1.51 (0.18), residues: 836 sheet: -2.99 (0.61), residues: 42 loop : -2.63 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 60 TYR 0.009 0.001 TYR A 713 PHE 0.029 0.001 PHE A 494 TRP 0.021 0.001 TRP A 625 HIS 0.002 0.000 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00276 (11018) covalent geometry : angle 0.60309 (14966) hydrogen bonds : bond 0.03492 ( 648) hydrogen bonds : angle 4.26948 ( 1908) *********************** 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: 53 poor density : 145 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6021 (OUTLIER) cc_final: 0.5652 (t80) REVERT: A 64 LEU cc_start: 0.3755 (OUTLIER) cc_final: 0.3195 (pp) REVERT: A 78 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6393 (mp0) REVERT: A 81 LYS cc_start: 0.7593 (tptt) cc_final: 0.7342 (mptt) REVERT: A 258 TRP cc_start: 0.5261 (OUTLIER) cc_final: 0.4626 (t60) REVERT: A 278 LYS cc_start: -0.1013 (OUTLIER) cc_final: -0.1871 (tmtm) REVERT: A 296 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.6288 (mm) REVERT: A 300 ASP cc_start: 0.6453 (OUTLIER) cc_final: 0.6091 (t0) REVERT: A 305 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6501 (mt-10) REVERT: A 353 TRP cc_start: 0.7071 (m100) cc_final: 0.6082 (t60) REVERT: A 376 ARG cc_start: 0.6584 (mtt90) cc_final: 0.6381 (mpt180) REVERT: A 498 SER cc_start: 0.1178 (OUTLIER) cc_final: 0.0875 (p) REVERT: A 508 MET cc_start: -0.1161 (mtt) cc_final: -0.1630 (ppp) REVERT: A 512 MET cc_start: 0.4481 (mmm) cc_final: 0.4048 (mmm) REVERT: A 532 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6630 (tm-30) REVERT: A 642 LEU cc_start: 0.7170 (mp) cc_final: 0.6785 (mp) REVERT: A 676 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7934 (tpt90) REVERT: B 19 PHE cc_start: 0.6029 (OUTLIER) cc_final: 0.5659 (t80) REVERT: B 64 LEU cc_start: 0.3752 (OUTLIER) cc_final: 0.3195 (pp) REVERT: B 78 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6386 (mp0) REVERT: B 81 LYS cc_start: 0.7584 (tptt) cc_final: 0.7333 (mptt) REVERT: B 258 TRP cc_start: 0.5258 (OUTLIER) cc_final: 0.4623 (t60) REVERT: B 278 LYS cc_start: -0.1010 (OUTLIER) cc_final: -0.1869 (tmtm) REVERT: B 296 ILE cc_start: 0.6541 (OUTLIER) cc_final: 0.6283 (mm) REVERT: B 300 ASP cc_start: 0.6444 (OUTLIER) cc_final: 0.6083 (t0) REVERT: B 305 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6493 (mt-10) REVERT: B 353 TRP cc_start: 0.7073 (m100) cc_final: 0.6085 (t60) REVERT: B 498 SER cc_start: 0.1182 (OUTLIER) cc_final: 0.0877 (p) REVERT: B 508 MET cc_start: -0.1160 (mtt) cc_final: -0.1630 (ppp) REVERT: B 512 MET cc_start: 0.4478 (mmm) cc_final: 0.4047 (mmm) REVERT: B 532 GLU cc_start: 0.7462 (mm-30) cc_final: 0.6623 (tm-30) REVERT: B 642 LEU cc_start: 0.7175 (mp) cc_final: 0.6792 (mp) REVERT: B 676 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7929 (tpt90) outliers start: 53 outliers final: 22 residues processed: 192 average time/residue: 0.5258 time to fit residues: 109.5043 Evaluate side-chains 181 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 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 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 392 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 19 PHE 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 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 392 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 30.0000 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 A 615 ASN B 34 ASN B 162 HIS B 615 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.184319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.108312 restraints weight = 11039.061| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.23 r_work: 0.3113 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11018 Z= 0.150 Angle : 0.619 15.580 14966 Z= 0.301 Chirality : 0.044 0.230 1678 Planarity : 0.005 0.040 1872 Dihedral : 6.433 59.505 1500 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.45 % Favored : 92.40 % Rotamer: Outliers : 4.49 % Allowed : 27.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.24), residues: 1316 helix: 1.49 (0.18), residues: 836 sheet: -3.02 (0.61), residues: 42 loop : -2.56 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 60 TYR 0.010 0.001 TYR B 542 PHE 0.030 0.002 PHE A 494 TRP 0.016 0.001 TRP B 625 HIS 0.003 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00344 (11018) covalent geometry : angle 0.61929 (14966) hydrogen bonds : bond 0.03828 ( 648) hydrogen bonds : angle 4.34482 ( 1908) ********************** 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 191 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 140 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6234 (OUTLIER) cc_final: 0.5875 (t80) REVERT: A 64 LEU cc_start: 0.3698 (OUTLIER) cc_final: 0.3126 (pp) REVERT: A 78 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6603 (mp0) REVERT: A 81 LYS cc_start: 0.7858 (tptt) cc_final: 0.7587 (mptt) REVERT: A 258 TRP cc_start: 0.5334 (OUTLIER) cc_final: 0.4722 (t60) REVERT: A 278 LYS cc_start: -0.1024 (OUTLIER) cc_final: -0.1899 (tmtm) REVERT: A 296 ILE cc_start: 0.6657 (OUTLIER) cc_final: 0.6415 (mm) REVERT: A 300 ASP cc_start: 0.6497 (OUTLIER) cc_final: 0.6132 (t0) REVERT: A 305 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6634 (mt-10) REVERT: A 353 TRP cc_start: 0.7311 (m100) cc_final: 0.6349 (t60) REVERT: A 498 SER cc_start: 0.1276 (OUTLIER) cc_final: 0.0972 (p) REVERT: A 508 MET cc_start: -0.1120 (mtt) cc_final: -0.1597 (ppp) REVERT: A 512 MET cc_start: 0.4525 (mmm) cc_final: 0.4134 (mmm) REVERT: A 532 GLU cc_start: 0.7646 (mm-30) cc_final: 0.6873 (tm-30) REVERT: A 676 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8133 (tpt90) REVERT: B 19 PHE cc_start: 0.6237 (OUTLIER) cc_final: 0.5877 (t80) REVERT: B 64 LEU cc_start: 0.3700 (OUTLIER) cc_final: 0.3128 (pp) REVERT: B 78 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6603 (mp0) REVERT: B 81 LYS cc_start: 0.7859 (tptt) cc_final: 0.7591 (mptt) REVERT: B 258 TRP cc_start: 0.5333 (OUTLIER) cc_final: 0.4716 (t60) REVERT: B 278 LYS cc_start: -0.1020 (OUTLIER) cc_final: -0.1896 (tmtm) REVERT: B 296 ILE cc_start: 0.6654 (OUTLIER) cc_final: 0.6411 (mm) REVERT: B 300 ASP cc_start: 0.6486 (OUTLIER) cc_final: 0.6123 (t0) REVERT: B 305 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6620 (mt-10) REVERT: B 353 TRP cc_start: 0.7304 (m100) cc_final: 0.6349 (t60) REVERT: B 498 SER cc_start: 0.1285 (OUTLIER) cc_final: 0.0981 (p) REVERT: B 508 MET cc_start: -0.1115 (mtt) cc_final: -0.1595 (ppp) REVERT: B 512 MET cc_start: 0.4526 (mmm) cc_final: 0.4138 (mmm) REVERT: B 532 GLU cc_start: 0.7638 (mm-30) cc_final: 0.6864 (tm-30) REVERT: B 676 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8137 (tpt90) outliers start: 51 outliers final: 22 residues processed: 183 average time/residue: 0.5185 time to fit residues: 103.2612 Evaluate side-chains 178 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 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 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 296 ILE Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 491 LEU 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 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 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 296 ILE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 702 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 87 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 0.2980 chunk 120 optimal weight: 3.9990 chunk 60 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN A 497 GLN B 162 HIS B 497 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.185458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.110715 restraints weight = 11122.308| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.18 r_work: 0.3143 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5549 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= 0.127 Angle : 0.604 15.508 14966 Z= 0.290 Chirality : 0.043 0.191 1678 Planarity : 0.005 0.040 1872 Dihedral : 6.126 59.940 1496 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 4.49 % Allowed : 27.90 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.24), residues: 1316 helix: 1.60 (0.18), residues: 836 sheet: -2.99 (0.62), residues: 42 loop : -2.51 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 60 TYR 0.009 0.001 TYR A 713 PHE 0.031 0.001 PHE A 494 TRP 0.021 0.001 TRP B 625 HIS 0.002 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00283 (11018) covalent geometry : angle 0.60410 (14966) hydrogen bonds : bond 0.03522 ( 648) hydrogen bonds : angle 4.24351 ( 1908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6921.44 seconds wall clock time: 118 minutes 21.14 seconds (7101.14 seconds total)