Starting phenix.real_space_refine on Tue Apr 29 11:04:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wru_37790/04_2025/8wru_37790.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wru_37790/04_2025/8wru_37790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wru_37790/04_2025/8wru_37790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wru_37790/04_2025/8wru_37790.map" model { file = "/net/cci-nas-00/data/ceres_data/8wru_37790/04_2025/8wru_37790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wru_37790/04_2025/8wru_37790.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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: 5 Type Number sf(0) Gaussians P 90 5.49 5 S 25 5.16 5 C 5133 2.51 5 N 1594 2.21 5 O 1844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8686 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6794 Classifications: {'peptide': 831} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 801} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1188 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p_pur': 21, 'rna3p_pyr': 27} Link IDs: {'rna2p': 8, 'rna3p': 47} Chain: "C" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 538 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 166 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Time building chain proxies: 5.79, per 1000 atoms: 0.67 Number of scatterers: 8686 At special positions: 0 Unit cell: (91.08, 103.62, 111.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 P 90 15.00 O 1844 8.00 N 1594 7.00 C 5133 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.1 seconds 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 48.7% alpha, 16.8% beta 25 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'A' and resid 15 through 41 Processing helix chain 'A' and resid 57 through 69 Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 100 through 103 Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.665A pdb=" N LEU A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 136 removed outlier: 3.793A pdb=" N GLU A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 150 removed outlier: 3.798A pdb=" N ALA A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 171 removed outlier: 3.611A pdb=" N ARG A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 185 Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 211 through 253 Processing helix chain 'A' and resid 256 through 259 removed outlier: 3.634A pdb=" N TYR A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 259' Processing helix chain 'A' and resid 260 through 273 removed outlier: 4.451A pdb=" N LYS A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.551A pdb=" N ARG A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 459 removed outlier: 3.531A pdb=" N LYS A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 552 removed outlier: 3.574A pdb=" N HIS A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 540 " --> pdb=" O CYS A 536 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS A 548 " --> pdb=" O ARG A 544 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 565 Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'A' and resid 579 through 606 removed outlier: 3.699A pdb=" N ARG A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 589 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 614 removed outlier: 3.964A pdb=" N ASP A 614 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 642 removed outlier: 3.650A pdb=" N LEU A 627 " --> pdb=" O TYR A 623 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 689 removed outlier: 3.689A pdb=" N HIS A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 736 Processing helix chain 'A' and resid 782 through 796 Processing helix chain 'A' and resid 820 through 831 removed outlier: 3.527A pdb=" N GLU A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 830 " --> pdb=" O TYR A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 899 removed outlier: 3.583A pdb=" N GLN A 894 " --> pdb=" O GLU A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 903 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 10 removed outlier: 3.627A pdb=" N SER A 7 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP A 438 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU A 423 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASN A 440 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL A 421 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4 through 10 removed outlier: 3.627A pdb=" N SER A 7 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP A 438 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU A 423 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASN A 440 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL A 421 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N THR A 408 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASN A 392 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.925A pdb=" N TYR A 44 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER A 45 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 365 Processing sheet with id=AA5, first strand: chain 'A' and resid 511 through 517 removed outlier: 7.128A pdb=" N PHE A 511 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR A 491 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A 513 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 485 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 697 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 479 " --> pdb=" O GLU A 697 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL A 694 " --> pdb=" O TRP A 741 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 743 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N MET A 696 " --> pdb=" O VAL A 743 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 501 through 503 removed outlier: 4.126A pdb=" N VAL A 503 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 760 through 761 Processing sheet with id=AA8, first strand: chain 'A' and resid 846 through 848 354 hydrogen bonds defined for protein. 1011 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 3.95 Time building geometry restraints manager: 2.85 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: 2023 1.33 - 1.45: 2312 1.45 - 1.57: 4492 1.57 - 1.69: 177 1.69 - 1.81: 39 Bond restraints: 9043 Sorted by residual: bond pdb=" C TYR A 643 " pdb=" N HIS A 644 " ideal model delta sigma weight residual 1.334 1.285 0.049 1.49e-02 4.50e+03 1.08e+01 bond pdb=" CA GLU A 659 " pdb=" CB GLU A 659 " ideal model delta sigma weight residual 1.527 1.491 0.036 1.38e-02 5.25e+03 6.82e+00 bond pdb=" C GLU A 659 " pdb=" N LEU A 660 " ideal model delta sigma weight residual 1.333 1.296 0.037 1.45e-02 4.76e+03 6.49e+00 bond pdb=" N GLU A 659 " pdb=" CA GLU A 659 " ideal model delta sigma weight residual 1.458 1.428 0.030 1.24e-02 6.50e+03 5.66e+00 bond pdb=" N HIS A 644 " pdb=" CA HIS A 644 " ideal model delta sigma weight residual 1.457 1.432 0.025 1.33e-02 5.65e+03 3.61e+00 ... (remaining 9038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 12412 2.24 - 4.47: 170 4.47 - 6.71: 17 6.71 - 8.95: 5 8.95 - 11.19: 2 Bond angle restraints: 12606 Sorted by residual: angle pdb=" N TYR A 4 " pdb=" CA TYR A 4 " pdb=" C TYR A 4 " ideal model delta sigma weight residual 108.69 118.92 -10.23 1.77e+00 3.19e-01 3.34e+01 angle pdb=" N TRP A 645 " pdb=" CA TRP A 645 " pdb=" C TRP A 645 " ideal model delta sigma weight residual 110.80 102.26 8.54 2.13e+00 2.20e-01 1.61e+01 angle pdb=" C TYR A 4 " pdb=" CA TYR A 4 " pdb=" CB TYR A 4 " ideal model delta sigma weight residual 109.65 102.69 6.96 1.75e+00 3.27e-01 1.58e+01 angle pdb=" CA PRO A 483 " pdb=" C PRO A 483 " pdb=" O PRO A 483 " ideal model delta sigma weight residual 123.07 117.70 5.37 1.38e+00 5.25e-01 1.51e+01 angle pdb=" CA THR A 646 " pdb=" C THR A 646 " pdb=" O THR A 646 " ideal model delta sigma weight residual 121.58 117.12 4.46 1.16e+00 7.43e-01 1.48e+01 ... (remaining 12601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 5124 35.00 - 69.99: 307 69.99 - 104.99: 29 104.99 - 139.99: 2 139.99 - 174.98: 1 Dihedral angle restraints: 5463 sinusoidal: 3038 harmonic: 2425 Sorted by residual: dihedral pdb=" O4' U B -32 " pdb=" C1' U B -32 " pdb=" N1 U B -32 " pdb=" C2 U B -32 " ideal model delta sinusoidal sigma weight residual -128.00 46.98 -174.98 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' A B -21 " pdb=" C1' A B -21 " pdb=" N9 A B -21 " pdb=" C4 A B -21 " ideal model delta sinusoidal sigma weight residual 70.00 -2.73 72.73 1 2.00e+01 2.50e-03 1.69e+01 dihedral pdb=" CA GLU A 559 " pdb=" C GLU A 559 " pdb=" N ALA A 560 " pdb=" CA ALA A 560 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 5460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1344 0.091 - 0.181: 55 0.181 - 0.272: 5 0.272 - 0.362: 1 0.362 - 0.453: 1 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CA GLU A 659 " pdb=" N GLU A 659 " pdb=" C GLU A 659 " pdb=" CB GLU A 659 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.13e+00 chirality pdb=" CA HIS A 747 " pdb=" N HIS A 747 " pdb=" C HIS A 747 " pdb=" CB HIS A 747 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA TRP A 645 " pdb=" N TRP A 645 " pdb=" C TRP A 645 " pdb=" CB TRP A 645 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1403 not shown) Planarity restraints: 1311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 643 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.06e+00 pdb=" C TYR A 643 " 0.046 2.00e-02 2.50e+03 pdb=" O TYR A 643 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS A 644 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 487 " -0.009 2.00e-02 2.50e+03 1.09e-02 2.06e+00 pdb=" CG PHE A 487 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 487 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 487 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 487 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 487 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 487 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 903 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO A 904 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 904 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 904 " -0.019 5.00e-02 4.00e+02 ... (remaining 1308 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 998 2.74 - 3.28: 8256 3.28 - 3.82: 15135 3.82 - 4.36: 18189 4.36 - 4.90: 28557 Nonbonded interactions: 71135 Sorted by model distance: nonbonded pdb=" OG1 THR A 338 " pdb=" OP1 A B 5 " model vdw 2.204 3.040 nonbonded pdb=" O LEU A 146 " pdb=" OG1 THR A 150 " model vdw 2.205 3.040 nonbonded pdb=" NZ LYS A 591 " pdb=" OP1 G B -17 " model vdw 2.216 3.120 nonbonded pdb=" OD1 ASP A 164 " pdb=" NH2 ARG A 167 " model vdw 2.251 3.120 nonbonded pdb=" OE2 GLU A 463 " pdb=" NE2 GLN A 821 " model vdw 2.256 3.120 ... (remaining 71130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.000 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.980 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 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 : 0.004 0.049 9043 Z= 0.218 Angle : 0.666 11.186 12606 Z= 0.368 Chirality : 0.044 0.453 1406 Planarity : 0.004 0.035 1311 Dihedral : 19.201 174.985 3895 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.56 % Allowed : 1.12 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.29), residues: 821 helix: 0.18 (0.26), residues: 378 sheet: -1.28 (0.43), residues: 136 loop : -1.88 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 720 HIS 0.010 0.002 HIS A 26 PHE 0.025 0.002 PHE A 487 TYR 0.019 0.002 TYR A 798 ARG 0.009 0.001 ARG A 561 Details of bonding type rmsd hydrogen bonds : bond 0.24449 ( 402) hydrogen bonds : angle 8.35854 ( 1119) covalent geometry : bond 0.00437 ( 9043) covalent geometry : angle 0.66649 (12606) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 214 time to evaluate : 0.799 Fit side-chains REVERT: A 79 ASP cc_start: 0.7135 (m-30) cc_final: 0.6911 (m-30) REVERT: A 99 LEU cc_start: 0.7770 (tt) cc_final: 0.7320 (tt) REVERT: A 391 TRP cc_start: 0.7462 (t-100) cc_final: 0.6127 (t-100) REVERT: A 564 GLU cc_start: 0.7281 (tp30) cc_final: 0.7033 (tp30) REVERT: A 568 ILE cc_start: 0.8275 (mm) cc_final: 0.8040 (mt) REVERT: A 613 ARG cc_start: 0.7557 (ttm110) cc_final: 0.7249 (ttm110) REVERT: A 688 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6778 (tm-30) REVERT: A 697 GLU cc_start: 0.6096 (pt0) cc_final: 0.5856 (pt0) REVERT: A 760 TYR cc_start: 0.6908 (t80) cc_final: 0.6194 (t80) REVERT: A 783 ASP cc_start: 0.6897 (m-30) cc_final: 0.6592 (m-30) REVERT: A 823 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7035 (tt0) outliers start: 4 outliers final: 2 residues processed: 218 average time/residue: 0.3066 time to fit residues: 83.6302 Evaluate side-chains 203 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 615 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.0870 chunk 81 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 HIS A 641 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.151278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.127414 restraints weight = 12743.087| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.73 r_work: 0.3427 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9043 Z= 0.192 Angle : 0.640 10.123 12606 Z= 0.335 Chirality : 0.041 0.176 1406 Planarity : 0.005 0.052 1311 Dihedral : 21.068 177.064 2196 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.81 % Allowed : 9.21 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.30), residues: 821 helix: 1.09 (0.27), residues: 385 sheet: -1.11 (0.42), residues: 140 loop : -1.56 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 645 HIS 0.007 0.002 HIS A 874 PHE 0.017 0.002 PHE A 435 TYR 0.022 0.002 TYR A 4 ARG 0.005 0.001 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.06204 ( 402) hydrogen bonds : angle 4.65900 ( 1119) covalent geometry : bond 0.00409 ( 9043) covalent geometry : angle 0.63972 (12606) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 219 time to evaluate : 0.827 Fit side-chains REVERT: A 99 LEU cc_start: 0.8077 (tt) cc_final: 0.7651 (tt) REVERT: A 100 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7160 (mm-30) REVERT: A 230 LEU cc_start: 0.8398 (tp) cc_final: 0.8113 (tp) REVERT: A 235 ARG cc_start: 0.7774 (ttp-170) cc_final: 0.7127 (ttp-170) REVERT: A 391 TRP cc_start: 0.7875 (t-100) cc_final: 0.6374 (t-100) REVERT: A 463 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7480 (mm-30) REVERT: A 559 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7331 (pt0) REVERT: A 564 GLU cc_start: 0.8142 (tp30) cc_final: 0.7913 (tp30) REVERT: A 613 ARG cc_start: 0.7763 (ttm110) cc_final: 0.7419 (ttm110) REVERT: A 650 ARG cc_start: 0.7612 (mtp85) cc_final: 0.7206 (mtp180) REVERT: A 760 TYR cc_start: 0.7145 (t80) cc_final: 0.6592 (t80) REVERT: A 783 ASP cc_start: 0.7364 (m-30) cc_final: 0.7134 (m-30) REVERT: A 823 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7380 (tt0) REVERT: A 882 GLU cc_start: 0.7242 (mp0) cc_final: 0.6933 (mp0) outliers start: 13 outliers final: 6 residues processed: 224 average time/residue: 0.2993 time to fit residues: 83.5992 Evaluate side-chains 214 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 207 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 886 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 25 optimal weight: 10.0000 chunk 72 optimal weight: 0.5980 chunk 56 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN A 735 ASN A 894 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.151940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127891 restraints weight = 12898.120| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.73 r_work: 0.3430 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9043 Z= 0.158 Angle : 0.579 7.687 12606 Z= 0.305 Chirality : 0.039 0.156 1406 Planarity : 0.005 0.087 1311 Dihedral : 21.008 176.451 2192 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.21 % Allowed : 12.41 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.31), residues: 821 helix: 1.47 (0.27), residues: 382 sheet: -1.06 (0.42), residues: 140 loop : -1.37 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 328 HIS 0.006 0.001 HIS A 747 PHE 0.014 0.002 PHE A 64 TYR 0.016 0.001 TYR A 4 ARG 0.005 0.000 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.05375 ( 402) hydrogen bonds : angle 4.24863 ( 1119) covalent geometry : bond 0.00335 ( 9043) covalent geometry : angle 0.57937 (12606) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.810 Fit side-chains REVERT: A 100 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7220 (mm-30) REVERT: A 230 LEU cc_start: 0.8315 (tp) cc_final: 0.8099 (tp) REVERT: A 391 TRP cc_start: 0.7853 (t-100) cc_final: 0.6304 (t-100) REVERT: A 410 ARG cc_start: 0.7728 (mtm180) cc_final: 0.7180 (mtm180) REVERT: A 463 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7347 (mm-30) REVERT: A 559 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7454 (pt0) REVERT: A 564 GLU cc_start: 0.8136 (tp30) cc_final: 0.7884 (tp30) REVERT: A 608 TYR cc_start: 0.7687 (m-10) cc_final: 0.7413 (m-10) REVERT: A 618 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7509 (tt) REVERT: A 650 ARG cc_start: 0.7539 (mtp85) cc_final: 0.7110 (mtp180) REVERT: A 688 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7176 (tm-30) REVERT: A 736 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6816 (mm-30) REVERT: A 760 TYR cc_start: 0.7139 (t80) cc_final: 0.6412 (t80) REVERT: A 783 ASP cc_start: 0.7403 (m-30) cc_final: 0.7113 (m-30) REVERT: A 817 ASN cc_start: 0.7680 (t0) cc_final: 0.7473 (t0) REVERT: A 823 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7454 (tt0) REVERT: A 882 GLU cc_start: 0.7276 (mp0) cc_final: 0.6930 (mp0) outliers start: 23 outliers final: 12 residues processed: 210 average time/residue: 0.3240 time to fit residues: 84.4325 Evaluate side-chains 220 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 886 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 GLN A 735 ASN A 894 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.151085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.127091 restraints weight = 12662.284| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.72 r_work: 0.3419 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9043 Z= 0.186 Angle : 0.587 8.677 12606 Z= 0.309 Chirality : 0.039 0.167 1406 Planarity : 0.004 0.036 1311 Dihedral : 21.040 177.365 2192 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.93 % Allowed : 15.76 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.31), residues: 821 helix: 1.46 (0.27), residues: 387 sheet: -1.09 (0.42), residues: 140 loop : -1.38 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 645 HIS 0.006 0.002 HIS A 874 PHE 0.013 0.002 PHE A 485 TYR 0.018 0.002 TYR A 605 ARG 0.008 0.000 ARG A 642 Details of bonding type rmsd hydrogen bonds : bond 0.05154 ( 402) hydrogen bonds : angle 4.17554 ( 1119) covalent geometry : bond 0.00398 ( 9043) covalent geometry : angle 0.58724 (12606) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.760 Fit side-chains REVERT: A 48 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.6496 (mpt) REVERT: A 230 LEU cc_start: 0.8332 (tp) cc_final: 0.8094 (tp) REVERT: A 391 TRP cc_start: 0.7895 (t-100) cc_final: 0.6320 (t-100) REVERT: A 410 ARG cc_start: 0.7706 (mtm180) cc_final: 0.6583 (mtm180) REVERT: A 463 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7376 (mm-30) REVERT: A 564 GLU cc_start: 0.8151 (tp30) cc_final: 0.7878 (tp30) REVERT: A 613 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.7269 (ttm110) REVERT: A 618 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7508 (tp) REVERT: A 643 TYR cc_start: 0.8140 (t80) cc_final: 0.7666 (t80) REVERT: A 650 ARG cc_start: 0.7541 (mtp85) cc_final: 0.7004 (mtp180) REVERT: A 760 TYR cc_start: 0.7121 (t80) cc_final: 0.6397 (t80) REVERT: A 783 ASP cc_start: 0.7370 (m-30) cc_final: 0.7157 (m-30) REVERT: A 823 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7474 (tt0) REVERT: A 848 LEU cc_start: 0.7817 (mt) cc_final: 0.7605 (mt) REVERT: A 882 GLU cc_start: 0.7280 (mp0) cc_final: 0.6967 (mp0) outliers start: 21 outliers final: 13 residues processed: 211 average time/residue: 0.3158 time to fit residues: 82.6200 Evaluate side-chains 217 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 896 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 79 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 73 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 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 894 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.151011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.127083 restraints weight = 12755.901| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.74 r_work: 0.3411 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9043 Z= 0.187 Angle : 0.586 8.421 12606 Z= 0.307 Chirality : 0.039 0.169 1406 Planarity : 0.004 0.037 1311 Dihedral : 21.035 177.145 2192 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.49 % Allowed : 16.04 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.31), residues: 821 helix: 1.53 (0.27), residues: 387 sheet: -1.14 (0.43), residues: 140 loop : -1.33 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 645 HIS 0.006 0.001 HIS A 874 PHE 0.013 0.002 PHE A 64 TYR 0.018 0.002 TYR A 605 ARG 0.004 0.000 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.05041 ( 402) hydrogen bonds : angle 4.10610 ( 1119) covalent geometry : bond 0.00400 ( 9043) covalent geometry : angle 0.58589 (12606) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.867 Fit side-chains REVERT: A 26 HIS cc_start: 0.8132 (OUTLIER) cc_final: 0.7926 (m90) REVERT: A 99 LEU cc_start: 0.8046 (tt) cc_final: 0.7845 (tt) REVERT: A 230 LEU cc_start: 0.8350 (tp) cc_final: 0.8106 (tp) REVERT: A 410 ARG cc_start: 0.7672 (mtm180) cc_final: 0.6468 (mtm180) REVERT: A 463 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7341 (mm-30) REVERT: A 564 GLU cc_start: 0.8152 (tp30) cc_final: 0.7854 (tp30) REVERT: A 613 ARG cc_start: 0.7627 (ttm-80) cc_final: 0.7283 (ttm110) REVERT: A 618 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7496 (tt) REVERT: A 643 TYR cc_start: 0.8145 (t80) cc_final: 0.7734 (t80) REVERT: A 650 ARG cc_start: 0.7519 (mtp85) cc_final: 0.6937 (mtp180) REVERT: A 760 TYR cc_start: 0.7122 (t80) cc_final: 0.6389 (t80) REVERT: A 783 ASP cc_start: 0.7328 (m-30) cc_final: 0.7059 (m-30) REVERT: A 823 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7519 (tt0) REVERT: A 848 LEU cc_start: 0.7804 (mt) cc_final: 0.7601 (mt) REVERT: A 882 GLU cc_start: 0.7292 (mp0) cc_final: 0.6981 (mp0) outliers start: 25 outliers final: 16 residues processed: 216 average time/residue: 0.3031 time to fit residues: 82.2690 Evaluate side-chains 223 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 886 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 56 optimal weight: 0.0020 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN A 894 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.151749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127814 restraints weight = 12614.552| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.72 r_work: 0.3429 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9043 Z= 0.158 Angle : 0.574 10.566 12606 Z= 0.299 Chirality : 0.039 0.231 1406 Planarity : 0.004 0.037 1311 Dihedral : 20.972 176.458 2192 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.77 % Allowed : 16.88 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.31), residues: 821 helix: 1.59 (0.27), residues: 385 sheet: -1.16 (0.43), residues: 140 loop : -1.26 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 645 HIS 0.005 0.001 HIS A 526 PHE 0.013 0.001 PHE A 64 TYR 0.014 0.001 TYR A 605 ARG 0.004 0.000 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.04883 ( 402) hydrogen bonds : angle 4.01361 ( 1119) covalent geometry : bond 0.00337 ( 9043) covalent geometry : angle 0.57429 (12606) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.749 Fit side-chains REVERT: A 99 LEU cc_start: 0.8025 (tt) cc_final: 0.7821 (tt) REVERT: A 230 LEU cc_start: 0.8338 (tp) cc_final: 0.8097 (tp) REVERT: A 410 ARG cc_start: 0.7640 (mtm180) cc_final: 0.6942 (mtm180) REVERT: A 463 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7305 (mm-30) REVERT: A 564 GLU cc_start: 0.8139 (tp30) cc_final: 0.7849 (tp30) REVERT: A 608 TYR cc_start: 0.7741 (m-80) cc_final: 0.7483 (m-10) REVERT: A 618 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7502 (tp) REVERT: A 643 TYR cc_start: 0.8122 (t80) cc_final: 0.7741 (t80) REVERT: A 650 ARG cc_start: 0.7484 (mtp85) cc_final: 0.6993 (mtp180) REVERT: A 739 LEU cc_start: 0.8030 (mt) cc_final: 0.7717 (mt) REVERT: A 760 TYR cc_start: 0.7109 (t80) cc_final: 0.6372 (t80) REVERT: A 823 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7531 (tt0) REVERT: A 882 GLU cc_start: 0.7295 (mp0) cc_final: 0.6978 (mp0) outliers start: 27 outliers final: 18 residues processed: 217 average time/residue: 0.3167 time to fit residues: 85.4479 Evaluate side-chains 231 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 212 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 896 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS A 92 ASN A 641 ASN A 894 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.150777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126654 restraints weight = 12813.526| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.75 r_work: 0.3405 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9043 Z= 0.205 Angle : 0.599 10.454 12606 Z= 0.313 Chirality : 0.041 0.247 1406 Planarity : 0.004 0.039 1311 Dihedral : 21.013 177.463 2192 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.91 % Allowed : 16.74 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.31), residues: 821 helix: 1.54 (0.27), residues: 385 sheet: -1.20 (0.42), residues: 140 loop : -1.29 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 645 HIS 0.006 0.002 HIS A 874 PHE 0.013 0.002 PHE A 485 TYR 0.020 0.002 TYR A 605 ARG 0.004 0.000 ARG A 544 Details of bonding type rmsd hydrogen bonds : bond 0.05051 ( 402) hydrogen bonds : angle 4.07444 ( 1119) covalent geometry : bond 0.00440 ( 9043) covalent geometry : angle 0.59904 (12606) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8355 (tp) cc_final: 0.8110 (tp) REVERT: A 463 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7363 (mm-30) REVERT: A 564 GLU cc_start: 0.8165 (tp30) cc_final: 0.7901 (tp30) REVERT: A 608 TYR cc_start: 0.7786 (m-80) cc_final: 0.7578 (m-10) REVERT: A 613 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.7257 (ttm110) REVERT: A 618 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7495 (tt) REVERT: A 643 TYR cc_start: 0.8136 (t80) cc_final: 0.7788 (t80) REVERT: A 650 ARG cc_start: 0.7503 (mtp85) cc_final: 0.6965 (mtp180) REVERT: A 688 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7320 (tm-30) REVERT: A 760 TYR cc_start: 0.7113 (t80) cc_final: 0.6376 (t80) REVERT: A 823 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7537 (tt0) REVERT: A 882 GLU cc_start: 0.7324 (mp0) cc_final: 0.6998 (mp0) outliers start: 28 outliers final: 17 residues processed: 219 average time/residue: 0.3227 time to fit residues: 88.0911 Evaluate side-chains 231 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 896 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS A 92 ASN A 894 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.151012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.127055 restraints weight = 12788.264| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.74 r_work: 0.3416 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9043 Z= 0.206 Angle : 0.604 9.118 12606 Z= 0.316 Chirality : 0.040 0.178 1406 Planarity : 0.004 0.055 1311 Dihedral : 21.015 177.133 2192 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.35 % Allowed : 17.71 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.31), residues: 821 helix: 1.51 (0.27), residues: 385 sheet: -1.17 (0.42), residues: 140 loop : -1.29 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 645 HIS 0.006 0.001 HIS A 874 PHE 0.012 0.002 PHE A 485 TYR 0.020 0.002 TYR A 605 ARG 0.004 0.000 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.05059 ( 402) hydrogen bonds : angle 4.11043 ( 1119) covalent geometry : bond 0.00442 ( 9043) covalent geometry : angle 0.60431 (12606) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8361 (tp) cc_final: 0.8133 (tp) REVERT: A 463 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7328 (mm-30) REVERT: A 564 GLU cc_start: 0.8125 (tp30) cc_final: 0.7845 (tp30) REVERT: A 613 ARG cc_start: 0.7653 (ttm-80) cc_final: 0.7251 (ttm110) REVERT: A 618 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7493 (tt) REVERT: A 643 TYR cc_start: 0.8136 (t80) cc_final: 0.7766 (t80) REVERT: A 650 ARG cc_start: 0.7515 (mtp85) cc_final: 0.6898 (mtp180) REVERT: A 688 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7319 (tm-30) REVERT: A 760 TYR cc_start: 0.7102 (t80) cc_final: 0.6367 (t80) REVERT: A 823 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7555 (tt0) REVERT: A 882 GLU cc_start: 0.7317 (mp0) cc_final: 0.7011 (mp0) outliers start: 24 outliers final: 19 residues processed: 209 average time/residue: 0.3191 time to fit residues: 83.9333 Evaluate side-chains 219 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 886 GLU Chi-restraints excluded: chain A residue 896 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 68 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 75 optimal weight: 0.0370 chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 82 optimal weight: 0.0670 chunk 41 optimal weight: 0.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS A 894 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.152476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.128650 restraints weight = 12686.893| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.72 r_work: 0.3437 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9043 Z= 0.137 Angle : 0.566 8.769 12606 Z= 0.296 Chirality : 0.038 0.153 1406 Planarity : 0.004 0.059 1311 Dihedral : 20.940 175.241 2192 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.93 % Allowed : 18.55 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.31), residues: 821 helix: 1.63 (0.27), residues: 386 sheet: -1.10 (0.43), residues: 140 loop : -1.33 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 645 HIS 0.004 0.001 HIS A 526 PHE 0.017 0.001 PHE A 64 TYR 0.010 0.001 TYR A 605 ARG 0.009 0.000 ARG A 588 Details of bonding type rmsd hydrogen bonds : bond 0.04754 ( 402) hydrogen bonds : angle 4.00539 ( 1119) covalent geometry : bond 0.00295 ( 9043) covalent geometry : angle 0.56640 (12606) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8345 (tp) cc_final: 0.8137 (tp) REVERT: A 463 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7270 (mm-30) REVERT: A 564 GLU cc_start: 0.8119 (tp30) cc_final: 0.7826 (tp30) REVERT: A 608 TYR cc_start: 0.7743 (m-80) cc_final: 0.7507 (m-10) REVERT: A 613 ARG cc_start: 0.7567 (ttm-80) cc_final: 0.7261 (ttm110) REVERT: A 618 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7478 (tt) REVERT: A 744 ASP cc_start: 0.7604 (t0) cc_final: 0.7286 (t0) REVERT: A 760 TYR cc_start: 0.7087 (t80) cc_final: 0.6349 (t80) REVERT: A 823 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7602 (tt0) REVERT: A 882 GLU cc_start: 0.7252 (mp0) cc_final: 0.6937 (mp0) outliers start: 21 outliers final: 16 residues processed: 211 average time/residue: 0.3090 time to fit residues: 81.5665 Evaluate side-chains 220 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 886 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 41 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 65 optimal weight: 0.0770 chunk 17 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS A 641 ASN A 894 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.152675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128816 restraints weight = 12761.438| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.72 r_work: 0.3437 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9043 Z= 0.142 Angle : 0.560 8.608 12606 Z= 0.294 Chirality : 0.038 0.202 1406 Planarity : 0.004 0.052 1311 Dihedral : 20.886 175.941 2192 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.79 % Allowed : 18.69 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.31), residues: 821 helix: 1.64 (0.27), residues: 387 sheet: -1.07 (0.44), residues: 140 loop : -1.29 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 645 HIS 0.004 0.001 HIS A 526 PHE 0.016 0.001 PHE A 64 TYR 0.011 0.001 TYR A 605 ARG 0.008 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.04711 ( 402) hydrogen bonds : angle 3.96062 ( 1119) covalent geometry : bond 0.00305 ( 9043) covalent geometry : angle 0.56039 (12606) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8340 (tp) cc_final: 0.8117 (tp) REVERT: A 434 TYR cc_start: 0.7966 (m-80) cc_final: 0.7554 (m-80) REVERT: A 463 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7279 (mm-30) REVERT: A 545 LEU cc_start: 0.8053 (mp) cc_final: 0.7805 (mt) REVERT: A 564 GLU cc_start: 0.8143 (tp30) cc_final: 0.7855 (tp30) REVERT: A 608 TYR cc_start: 0.7727 (m-80) cc_final: 0.7430 (m-10) REVERT: A 618 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7508 (tt) REVERT: A 643 TYR cc_start: 0.8045 (t80) cc_final: 0.7797 (t80) REVERT: A 744 ASP cc_start: 0.7631 (t0) cc_final: 0.7318 (t0) REVERT: A 760 TYR cc_start: 0.7097 (t80) cc_final: 0.6360 (t80) REVERT: A 817 ASN cc_start: 0.7614 (t0) cc_final: 0.7372 (t0) REVERT: A 823 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7657 (tt0) REVERT: A 882 GLU cc_start: 0.7279 (mp0) cc_final: 0.6947 (mp0) outliers start: 20 outliers final: 17 residues processed: 212 average time/residue: 0.3336 time to fit residues: 88.4472 Evaluate side-chains 222 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 886 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 56 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS A 92 ASN A 641 ASN A 803 GLN A 894 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.149228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.125274 restraints weight = 12521.967| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.74 r_work: 0.3390 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 9043 Z= 0.331 Angle : 0.709 9.876 12606 Z= 0.370 Chirality : 0.047 0.238 1406 Planarity : 0.005 0.055 1311 Dihedral : 21.117 179.119 2192 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.07 % Allowed : 19.25 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.30), residues: 821 helix: 1.14 (0.26), residues: 385 sheet: -1.30 (0.43), residues: 134 loop : -1.50 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 645 HIS 0.009 0.002 HIS A 874 PHE 0.025 0.002 PHE A 31 TYR 0.032 0.003 TYR A 605 ARG 0.008 0.001 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.05646 ( 402) hydrogen bonds : angle 4.32329 ( 1119) covalent geometry : bond 0.00716 ( 9043) covalent geometry : angle 0.70869 (12606) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6321.40 seconds wall clock time: 109 minutes 28.79 seconds (6568.79 seconds total)