Starting phenix.real_space_refine on Sun Apr 27 12:16:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8phw_17677/04_2025/8phw_17677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8phw_17677/04_2025/8phw_17677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8phw_17677/04_2025/8phw_17677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8phw_17677/04_2025/8phw_17677.map" model { file = "/net/cci-nas-00/data/ceres_data/8phw_17677/04_2025/8phw_17677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8phw_17677/04_2025/8phw_17677.cif" } resolution = 3.6 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 3500 2.51 5 N 847 2.21 5 O 976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5359 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3528 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 15, 'TRANS': 438} Chain breaks: 7 Chain: "H" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 972 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 800 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'FY5': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.85, per 1000 atoms: 0.91 Number of scatterers: 5359 At special positions: 0 Unit cell: (87.72, 94.86, 104.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 976 8.00 N 847 7.00 C 3500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 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: 1.29 Conformation dependent library (CDL) restraints added in 699.1 milliseconds 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1246 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 6 sheets defined 46.4% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 27 through 52 removed outlier: 3.742A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.860A pdb=" N PHE A 68 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 77 " --> pdb=" O PHE A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 117 removed outlier: 4.217A pdb=" N GLY A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N CYS A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Proline residue: A 114 - end of helix removed outlier: 3.612A pdb=" N PHE A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 removed outlier: 3.718A pdb=" N GLY A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 removed outlier: 3.743A pdb=" N LEU A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.891A pdb=" N MET A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 231 removed outlier: 4.153A pdb=" N ILE A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 257 through 274 removed outlier: 4.055A pdb=" N ASN A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 340 through 366 removed outlier: 3.595A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N SER A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.875A pdb=" N GLY A 394 " --> pdb=" O MET A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 423 removed outlier: 3.522A pdb=" N ALA A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 527 through 559 removed outlier: 3.685A pdb=" N THR A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 559 " --> pdb=" O HIS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 597 Proline residue: A 588 - end of helix Processing helix chain 'A' and resid 617 through 646 removed outlier: 3.665A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 434 through 435 removed outlier: 7.052A pdb=" N SER A 434 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS A 520 " --> pdb=" O CYS A 474 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 6 through 10 removed outlier: 4.208A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 48 through 54 removed outlier: 6.837A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.777A pdb=" N SER L 54 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.777A pdb=" N SER L 54 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 750 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: 1.40 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: 1.20 - 1.32: 822 1.32 - 1.45: 1624 1.45 - 1.57: 2991 1.57 - 1.70: 1 1.70 - 1.82: 53 Bond restraints: 5491 Sorted by residual: bond pdb=" O20 FY5 A 701 " pdb=" S21 FY5 A 701 " ideal model delta sigma weight residual 1.673 1.603 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C THR A 186 " pdb=" N PRO A 187 " ideal model delta sigma weight residual 1.331 1.351 -0.020 7.90e-03 1.60e+04 6.28e+00 bond pdb=" C18 FY5 A 701 " pdb=" O20 FY5 A 701 " ideal model delta sigma weight residual 1.372 1.421 -0.049 2.00e-02 2.50e+03 6.04e+00 bond pdb=" N VAL L 34 " pdb=" CA VAL L 34 " ideal model delta sigma weight residual 1.459 1.441 0.018 1.25e-02 6.40e+03 2.09e+00 bond pdb=" C SER H 36 " pdb=" N ILE H 37 " ideal model delta sigma weight residual 1.334 1.316 0.017 1.24e-02 6.50e+03 1.98e+00 ... (remaining 5486 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 7000 1.36 - 2.72: 372 2.72 - 4.07: 56 4.07 - 5.43: 18 5.43 - 6.79: 6 Bond angle restraints: 7452 Sorted by residual: angle pdb=" N ILE A 428 " pdb=" CA ILE A 428 " pdb=" C ILE A 428 " ideal model delta sigma weight residual 112.83 108.67 4.16 9.90e-01 1.02e+00 1.77e+01 angle pdb=" N TYR H 63 " pdb=" CA TYR H 63 " pdb=" C TYR H 63 " ideal model delta sigma weight residual 108.34 112.26 -3.92 1.31e+00 5.83e-01 8.93e+00 angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 127.23 -5.69 1.91e+00 2.74e-01 8.89e+00 angle pdb=" CA TYR A 590 " pdb=" CB TYR A 590 " pdb=" CG TYR A 590 " ideal model delta sigma weight residual 113.90 119.01 -5.11 1.80e+00 3.09e-01 8.05e+00 angle pdb=" C ASN A 403 " pdb=" CA ASN A 403 " pdb=" CB ASN A 403 " ideal model delta sigma weight residual 110.42 115.50 -5.08 1.99e+00 2.53e-01 6.51e+00 ... (remaining 7447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.98: 2818 11.98 - 23.96: 279 23.96 - 35.94: 111 35.94 - 47.92: 36 47.92 - 59.90: 11 Dihedral angle restraints: 3255 sinusoidal: 1292 harmonic: 1963 Sorted by residual: dihedral pdb=" CA CYS A 607 " pdb=" C CYS A 607 " pdb=" N GLY A 608 " pdb=" CA GLY A 608 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA GLY A 608 " pdb=" C GLY A 608 " pdb=" N THR A 609 " pdb=" CA THR A 609 " ideal model delta harmonic sigma weight residual -180.00 -154.57 -25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASN A 617 " pdb=" C ASN A 617 " pdb=" N SER A 618 " pdb=" CA SER A 618 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 3252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 496 0.029 - 0.058: 229 0.058 - 0.087: 76 0.087 - 0.115: 37 0.115 - 0.144: 9 Chirality restraints: 847 Sorted by residual: chirality pdb=" CA VAL A 473 " pdb=" N VAL A 473 " pdb=" C VAL A 473 " pdb=" CB VAL A 473 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA THR A 186 " pdb=" N THR A 186 " pdb=" C THR A 186 " pdb=" CB THR A 186 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA PRO A 220 " pdb=" N PRO A 220 " pdb=" C PRO A 220 " pdb=" CB PRO A 220 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 844 not shown) Planarity restraints: 905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 219 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO A 220 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 106 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO H 107 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 107 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 107 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 590 " -0.013 2.00e-02 2.50e+03 1.01e-02 2.05e+00 pdb=" CG TYR A 590 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 590 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 590 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 590 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 590 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 590 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 590 " -0.001 2.00e-02 2.50e+03 ... (remaining 902 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 793 2.75 - 3.29: 5508 3.29 - 3.82: 8421 3.82 - 4.36: 9687 4.36 - 4.90: 16556 Nonbonded interactions: 40965 Sorted by model distance: nonbonded pdb=" O CYS A 101 " pdb=" OG SER A 269 " model vdw 2.209 3.040 nonbonded pdb=" O ALA A 415 " pdb=" OG SER A 418 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.235 3.040 nonbonded pdb=" NH2 ARG H 70 " pdb=" O SER H 88 " model vdw 2.248 3.120 nonbonded pdb=" O CYS A 474 " pdb=" N ALA A 519 " model vdw 2.252 3.120 ... (remaining 40960 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.890 Find NCS groups from input model: 0.050 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 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 : 0.005 0.070 5497 Z= 0.233 Angle : 0.723 6.790 7464 Z= 0.423 Chirality : 0.041 0.144 847 Planarity : 0.005 0.058 905 Dihedral : 12.284 59.901 1991 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 6.20 % Allowed : 7.75 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.26), residues: 669 helix: -1.77 (0.25), residues: 283 sheet: -1.50 (0.57), residues: 81 loop : -3.36 (0.26), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 254 HIS 0.003 0.001 HIS A 115 PHE 0.010 0.001 PHE A 537 TYR 0.025 0.002 TYR A 590 ARG 0.003 0.000 ARG H 70 Details of bonding type rmsd hydrogen bonds : bond 0.13904 ( 256) hydrogen bonds : angle 5.86732 ( 750) SS BOND : bond 0.00428 ( 6) SS BOND : angle 1.12052 ( 12) covalent geometry : bond 0.00461 ( 5491) covalent geometry : angle 0.72217 ( 7452) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6160 (ttp80) REVERT: A 170 MET cc_start: 0.7729 (ttm) cc_final: 0.7378 (ttm) REVERT: A 218 ILE cc_start: 0.7663 (mm) cc_final: 0.7459 (tt) REVERT: A 253 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6436 (mtm110) REVERT: A 386 PHE cc_start: 0.8258 (t80) cc_final: 0.7730 (t80) REVERT: A 390 MET cc_start: 0.7207 (mtm) cc_final: 0.6897 (mtm) REVERT: A 417 MET cc_start: 0.6765 (mmm) cc_final: 0.6395 (mmm) REVERT: A 601 LYS cc_start: 0.7751 (tttp) cc_final: 0.7317 (tttp) REVERT: A 631 MET cc_start: 0.6745 (tpp) cc_final: 0.6223 (tpp) REVERT: H 32 PHE cc_start: 0.8359 (t80) cc_final: 0.8126 (t80) REVERT: L 18 ASP cc_start: 0.5539 (m-30) cc_final: 0.5334 (m-30) REVERT: L 43 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7601 (mmtm) outliers start: 36 outliers final: 16 residues processed: 167 average time/residue: 0.1453 time to fit residues: 32.1552 Evaluate side-chains 147 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.0040 chunk 27 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.144536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.124417 restraints weight = 9027.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.128354 restraints weight = 4462.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.130865 restraints weight = 2753.563| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5497 Z= 0.132 Angle : 0.603 7.545 7464 Z= 0.310 Chirality : 0.042 0.297 847 Planarity : 0.005 0.057 905 Dihedral : 8.106 59.016 886 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.02 % Allowed : 14.46 % Favored : 79.52 % 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: -1.71 (0.30), residues: 669 helix: 0.23 (0.30), residues: 291 sheet: -1.02 (0.60), residues: 78 loop : -2.62 (0.29), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.002 0.001 HIS H 38 PHE 0.023 0.001 PHE A 73 TYR 0.014 0.001 TYR A 625 ARG 0.003 0.000 ARG A 614 Details of bonding type rmsd hydrogen bonds : bond 0.04835 ( 256) hydrogen bonds : angle 4.51696 ( 750) SS BOND : bond 0.00426 ( 6) SS BOND : angle 1.12812 ( 12) covalent geometry : bond 0.00280 ( 5491) covalent geometry : angle 0.60204 ( 7452) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 170 MET cc_start: 0.7666 (ttm) cc_final: 0.7442 (ttm) REVERT: A 173 TYR cc_start: 0.7487 (m-80) cc_final: 0.7259 (m-80) REVERT: A 217 MET cc_start: 0.7926 (mmp) cc_final: 0.7563 (mmp) REVERT: A 253 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6713 (mtm110) REVERT: A 386 PHE cc_start: 0.8097 (t80) cc_final: 0.7417 (t80) REVERT: A 390 MET cc_start: 0.7201 (mtm) cc_final: 0.6844 (mtm) REVERT: A 417 MET cc_start: 0.6692 (mmm) cc_final: 0.6360 (mmm) REVERT: A 533 LYS cc_start: 0.7966 (mttm) cc_final: 0.7712 (mttm) REVERT: A 545 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7850 (mm) REVERT: A 601 LYS cc_start: 0.7571 (tttp) cc_final: 0.7200 (tttp) REVERT: A 631 MET cc_start: 0.6747 (tpp) cc_final: 0.6238 (tpp) REVERT: H 32 PHE cc_start: 0.8268 (t80) cc_final: 0.8034 (t80) REVERT: L 18 ASP cc_start: 0.6001 (m-30) cc_final: 0.5690 (m-30) REVERT: L 43 LYS cc_start: 0.7712 (mmtm) cc_final: 0.7506 (mmtm) outliers start: 35 outliers final: 18 residues processed: 153 average time/residue: 0.1401 time to fit residues: 28.7474 Evaluate side-chains 144 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 19 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 0.0050 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 2 optimal weight: 0.0770 overall best weight: 0.1150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.149775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.130655 restraints weight = 9068.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134358 restraints weight = 4530.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.136796 restraints weight = 2822.549| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5497 Z= 0.100 Angle : 0.555 6.868 7464 Z= 0.280 Chirality : 0.040 0.166 847 Planarity : 0.004 0.038 905 Dihedral : 6.890 58.775 877 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.34 % Allowed : 17.73 % Favored : 76.94 % 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: -0.76 (0.32), residues: 669 helix: 1.22 (0.31), residues: 296 sheet: -0.50 (0.63), residues: 78 loop : -2.41 (0.31), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.002 0.001 HIS H 38 PHE 0.012 0.001 PHE A 73 TYR 0.012 0.001 TYR A 239 ARG 0.004 0.000 ARG A 614 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 256) hydrogen bonds : angle 4.07677 ( 750) SS BOND : bond 0.00467 ( 6) SS BOND : angle 0.91974 ( 12) covalent geometry : bond 0.00201 ( 5491) covalent geometry : angle 0.55374 ( 7452) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.6281 (ttp-170) REVERT: A 386 PHE cc_start: 0.7913 (t80) cc_final: 0.7232 (t80) REVERT: A 390 MET cc_start: 0.7032 (mtm) cc_final: 0.6747 (mtm) REVERT: A 545 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7817 (mm) REVERT: A 601 LYS cc_start: 0.7156 (tttp) cc_final: 0.6893 (tttp) REVERT: A 631 MET cc_start: 0.6649 (tpp) cc_final: 0.6206 (tpp) outliers start: 31 outliers final: 19 residues processed: 156 average time/residue: 0.2113 time to fit residues: 43.9246 Evaluate side-chains 150 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.0470 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.0050 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 overall best weight: 0.4692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN ** L 7 GLN ** 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 = 0.3907 r_free = 0.3907 target = 0.146721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.127536 restraints weight = 9319.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.131286 restraints weight = 4629.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133773 restraints weight = 2864.345| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5497 Z= 0.124 Angle : 0.570 7.652 7464 Z= 0.287 Chirality : 0.041 0.154 847 Planarity : 0.004 0.038 905 Dihedral : 6.438 59.603 870 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 5.34 % Allowed : 18.93 % Favored : 75.73 % 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: -0.58 (0.33), residues: 669 helix: 1.42 (0.31), residues: 296 sheet: -0.63 (0.60), residues: 83 loop : -2.34 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 254 HIS 0.002 0.001 HIS H 38 PHE 0.011 0.001 PHE A 73 TYR 0.014 0.001 TYR L 50 ARG 0.006 0.000 ARG A 253 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 256) hydrogen bonds : angle 4.10071 ( 750) SS BOND : bond 0.00508 ( 6) SS BOND : angle 1.08898 ( 12) covalent geometry : bond 0.00268 ( 5491) covalent geometry : angle 0.56903 ( 7452) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.6282 (ttp80) REVERT: A 176 MET cc_start: 0.6617 (mmt) cc_final: 0.6408 (mmt) REVERT: A 386 PHE cc_start: 0.7934 (t80) cc_final: 0.7231 (t80) REVERT: A 390 MET cc_start: 0.7071 (mtm) cc_final: 0.6792 (mtm) REVERT: A 545 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7841 (mm) REVERT: A 601 LYS cc_start: 0.7319 (tttp) cc_final: 0.7002 (tttp) REVERT: A 631 MET cc_start: 0.6766 (tpp) cc_final: 0.6285 (tpp) REVERT: L 97 ILE cc_start: 0.6673 (OUTLIER) cc_final: 0.6178 (mm) outliers start: 31 outliers final: 22 residues processed: 146 average time/residue: 0.1532 time to fit residues: 29.5594 Evaluate side-chains 149 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 99 CYS Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 55 optimal weight: 0.0970 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.145650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.126033 restraints weight = 9065.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.129916 restraints weight = 4389.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.132426 restraints weight = 2673.987| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5497 Z= 0.145 Angle : 0.593 7.923 7464 Z= 0.297 Chirality : 0.041 0.162 847 Planarity : 0.004 0.040 905 Dihedral : 6.555 60.771 869 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 6.20 % Allowed : 19.28 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.33), residues: 669 helix: 1.42 (0.31), residues: 296 sheet: -0.60 (0.60), residues: 83 loop : -2.30 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 PHE 0.012 0.001 PHE A 73 TYR 0.017 0.001 TYR L 50 ARG 0.006 0.000 ARG A 614 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 256) hydrogen bonds : angle 4.14683 ( 750) SS BOND : bond 0.00651 ( 6) SS BOND : angle 1.24780 ( 12) covalent geometry : bond 0.00314 ( 5491) covalent geometry : angle 0.59168 ( 7452) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.571 Fit side-chains REVERT: A 58 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.6270 (ttp80) REVERT: A 176 MET cc_start: 0.6744 (mmt) cc_final: 0.6481 (mmt) REVERT: A 386 PHE cc_start: 0.7956 (t80) cc_final: 0.7263 (t80) REVERT: A 390 MET cc_start: 0.7174 (mtm) cc_final: 0.6855 (mtm) REVERT: A 545 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7818 (mm) REVERT: A 601 LYS cc_start: 0.7386 (tttp) cc_final: 0.7025 (tttp) REVERT: A 631 MET cc_start: 0.6854 (tpp) cc_final: 0.6323 (tpp) REVERT: L 97 ILE cc_start: 0.6804 (OUTLIER) cc_final: 0.6318 (mm) outliers start: 36 outliers final: 23 residues processed: 155 average time/residue: 0.1496 time to fit residues: 31.0228 Evaluate side-chains 156 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN ** L 7 GLN ** 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 = 0.3873 r_free = 0.3873 target = 0.144982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.125289 restraints weight = 9046.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.129153 restraints weight = 4474.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.131657 restraints weight = 2757.303| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5497 Z= 0.156 Angle : 0.610 7.956 7464 Z= 0.304 Chirality : 0.042 0.164 847 Planarity : 0.004 0.040 905 Dihedral : 6.481 61.645 867 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.68 % Allowed : 19.79 % Favored : 74.53 % 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: -0.57 (0.32), residues: 669 helix: 1.36 (0.31), residues: 297 sheet: -0.34 (0.62), residues: 78 loop : -2.34 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 PHE 0.013 0.001 PHE A 73 TYR 0.018 0.001 TYR L 50 ARG 0.004 0.000 ARG A 253 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 256) hydrogen bonds : angle 4.17616 ( 750) SS BOND : bond 0.00644 ( 6) SS BOND : angle 1.29855 ( 12) covalent geometry : bond 0.00340 ( 5491) covalent geometry : angle 0.60811 ( 7452) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.575 Fit side-chains REVERT: A 58 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.6310 (ttp80) REVERT: A 173 TYR cc_start: 0.7374 (m-80) cc_final: 0.7156 (m-80) REVERT: A 176 MET cc_start: 0.6778 (mmt) cc_final: 0.6475 (mmt) REVERT: A 386 PHE cc_start: 0.7964 (t80) cc_final: 0.7261 (t80) REVERT: A 390 MET cc_start: 0.7168 (mtm) cc_final: 0.6861 (mtm) REVERT: A 545 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7810 (mm) REVERT: A 601 LYS cc_start: 0.7401 (tttp) cc_final: 0.7036 (tttp) REVERT: A 631 MET cc_start: 0.6823 (tpp) cc_final: 0.6317 (tpp) REVERT: L 97 ILE cc_start: 0.6812 (OUTLIER) cc_final: 0.6380 (mm) outliers start: 33 outliers final: 28 residues processed: 151 average time/residue: 0.1495 time to fit residues: 30.1771 Evaluate side-chains 161 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 50 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 0.0970 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.145087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.125508 restraints weight = 8946.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.129337 restraints weight = 4463.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.131850 restraints weight = 2764.284| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5497 Z= 0.144 Angle : 0.607 7.927 7464 Z= 0.302 Chirality : 0.041 0.153 847 Planarity : 0.004 0.041 905 Dihedral : 6.457 62.294 867 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 6.88 % Allowed : 20.14 % Favored : 72.98 % 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: -0.55 (0.32), residues: 669 helix: 1.45 (0.31), residues: 293 sheet: -0.31 (0.61), residues: 78 loop : -2.37 (0.31), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 PHE 0.011 0.001 PHE A 276 TYR 0.016 0.001 TYR L 50 ARG 0.008 0.000 ARG A 614 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 256) hydrogen bonds : angle 4.14025 ( 750) SS BOND : bond 0.00580 ( 6) SS BOND : angle 1.26181 ( 12) covalent geometry : bond 0.00314 ( 5491) covalent geometry : angle 0.60526 ( 7452) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.595 Fit side-chains REVERT: A 58 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.6311 (ttp80) REVERT: A 173 TYR cc_start: 0.7351 (m-80) cc_final: 0.7131 (m-80) REVERT: A 176 MET cc_start: 0.6773 (mmt) cc_final: 0.6480 (mmt) REVERT: A 386 PHE cc_start: 0.7955 (t80) cc_final: 0.7254 (t80) REVERT: A 390 MET cc_start: 0.7169 (mtm) cc_final: 0.6861 (mtm) REVERT: A 463 CYS cc_start: 0.6390 (t) cc_final: 0.5747 (t) REVERT: A 545 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7814 (mm) REVERT: A 601 LYS cc_start: 0.7362 (tttp) cc_final: 0.7006 (tttp) REVERT: A 631 MET cc_start: 0.6822 (tpp) cc_final: 0.6306 (tpp) REVERT: H 121 TYR cc_start: 0.7157 (m-80) cc_final: 0.6888 (m-80) REVERT: L 97 ILE cc_start: 0.6800 (OUTLIER) cc_final: 0.6377 (mm) outliers start: 40 outliers final: 32 residues processed: 157 average time/residue: 0.1477 time to fit residues: 31.0165 Evaluate side-chains 169 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 27 optimal weight: 0.8980 chunk 58 optimal weight: 0.0010 chunk 25 optimal weight: 0.0370 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 0.0870 chunk 51 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN ** L 7 GLN ** 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 = 0.3932 r_free = 0.3932 target = 0.148983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.129954 restraints weight = 9090.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.133755 restraints weight = 4493.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.136267 restraints weight = 2770.262| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5497 Z= 0.103 Angle : 0.581 8.156 7464 Z= 0.286 Chirality : 0.040 0.142 847 Planarity : 0.004 0.039 905 Dihedral : 6.186 63.595 867 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.30 % Allowed : 22.38 % Favored : 73.32 % 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 (0.33), residues: 669 helix: 1.60 (0.31), residues: 296 sheet: -0.29 (0.61), residues: 78 loop : -2.27 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.003 0.001 HIS A 115 PHE 0.024 0.001 PHE H 32 TYR 0.009 0.001 TYR A 625 ARG 0.006 0.000 ARG A 614 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 256) hydrogen bonds : angle 3.94091 ( 750) SS BOND : bond 0.00394 ( 6) SS BOND : angle 1.07484 ( 12) covalent geometry : bond 0.00213 ( 5491) covalent geometry : angle 0.57980 ( 7452) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.522 Fit side-chains REVERT: A 58 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.6278 (ttp80) REVERT: A 169 TYR cc_start: 0.7099 (t80) cc_final: 0.6849 (t80) REVERT: A 176 MET cc_start: 0.6695 (mmt) cc_final: 0.6398 (mmt) REVERT: A 386 PHE cc_start: 0.7869 (t80) cc_final: 0.7211 (t80) REVERT: A 390 MET cc_start: 0.7096 (mtm) cc_final: 0.6811 (mtm) REVERT: A 545 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7733 (mm) REVERT: A 601 LYS cc_start: 0.7058 (tttp) cc_final: 0.6792 (tttp) REVERT: A 625 TYR cc_start: 0.7280 (t80) cc_final: 0.7065 (t80) REVERT: A 631 MET cc_start: 0.6807 (tpp) cc_final: 0.6322 (tpp) REVERT: L 97 ILE cc_start: 0.6718 (OUTLIER) cc_final: 0.6241 (mm) outliers start: 25 outliers final: 18 residues processed: 148 average time/residue: 0.1381 time to fit residues: 27.6068 Evaluate side-chains 151 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 0.0070 chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN ** L 7 GLN ** 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 = 0.3881 r_free = 0.3881 target = 0.145524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.126061 restraints weight = 8999.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.129878 restraints weight = 4463.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.132423 restraints weight = 2771.253| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5497 Z= 0.152 Angle : 0.624 7.599 7464 Z= 0.310 Chirality : 0.042 0.254 847 Planarity : 0.004 0.040 905 Dihedral : 6.288 62.652 865 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.79 % Allowed : 23.24 % Favored : 72.98 % 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: -0.44 (0.32), residues: 669 helix: 1.47 (0.31), residues: 296 sheet: -0.47 (0.60), residues: 83 loop : -2.22 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 254 HIS 0.002 0.001 HIS H 38 PHE 0.024 0.001 PHE H 32 TYR 0.017 0.001 TYR L 50 ARG 0.008 0.000 ARG A 614 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 256) hydrogen bonds : angle 4.09397 ( 750) SS BOND : bond 0.00625 ( 6) SS BOND : angle 1.35924 ( 12) covalent geometry : bond 0.00334 ( 5491) covalent geometry : angle 0.62173 ( 7452) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.515 Fit side-chains REVERT: A 58 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6230 (ttp80) REVERT: A 169 TYR cc_start: 0.7150 (t80) cc_final: 0.6884 (t80) REVERT: A 176 MET cc_start: 0.6775 (mmt) cc_final: 0.6477 (mmt) REVERT: A 386 PHE cc_start: 0.7922 (t80) cc_final: 0.7254 (t80) REVERT: A 390 MET cc_start: 0.7143 (mtm) cc_final: 0.6848 (mtm) REVERT: A 463 CYS cc_start: 0.6261 (t) cc_final: 0.5610 (t) REVERT: A 545 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7790 (mm) REVERT: A 601 LYS cc_start: 0.7326 (tttp) cc_final: 0.7009 (tttp) REVERT: A 631 MET cc_start: 0.6831 (tpp) cc_final: 0.6322 (tpp) REVERT: L 97 ILE cc_start: 0.6812 (OUTLIER) cc_final: 0.6391 (mm) outliers start: 22 outliers final: 18 residues processed: 145 average time/residue: 0.1407 time to fit residues: 27.5581 Evaluate side-chains 150 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN H 42 GLN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.144099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124327 restraints weight = 9021.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.128134 restraints weight = 4483.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130617 restraints weight = 2790.658| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5497 Z= 0.198 Angle : 0.671 9.187 7464 Z= 0.336 Chirality : 0.044 0.247 847 Planarity : 0.004 0.042 905 Dihedral : 6.511 62.261 865 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.13 % Allowed : 23.06 % Favored : 72.81 % 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: -0.62 (0.32), residues: 669 helix: 1.31 (0.31), residues: 289 sheet: -0.84 (0.59), residues: 88 loop : -2.12 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 254 HIS 0.003 0.001 HIS A 555 PHE 0.025 0.001 PHE H 32 TYR 0.021 0.002 TYR L 50 ARG 0.009 0.000 ARG A 614 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 256) hydrogen bonds : angle 4.32217 ( 750) SS BOND : bond 0.00731 ( 6) SS BOND : angle 1.62986 ( 12) covalent geometry : bond 0.00436 ( 5491) covalent geometry : angle 0.66883 ( 7452) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.614 Fit side-chains REVERT: A 58 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6303 (ttp80) REVERT: A 169 TYR cc_start: 0.7161 (t80) cc_final: 0.6897 (t80) REVERT: A 170 MET cc_start: 0.7701 (ttm) cc_final: 0.7492 (ttm) REVERT: A 176 MET cc_start: 0.6821 (mmt) cc_final: 0.6530 (mmt) REVERT: A 386 PHE cc_start: 0.7986 (t80) cc_final: 0.7255 (t80) REVERT: A 390 MET cc_start: 0.7175 (mtm) cc_final: 0.6832 (mtm) REVERT: A 463 CYS cc_start: 0.6523 (t) cc_final: 0.5932 (t) REVERT: A 545 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7832 (mm) REVERT: A 601 LYS cc_start: 0.7446 (tttp) cc_final: 0.7057 (tttp) REVERT: A 631 MET cc_start: 0.6840 (tpp) cc_final: 0.6310 (tpp) REVERT: H 121 TYR cc_start: 0.7171 (m-80) cc_final: 0.6863 (m-80) REVERT: L 97 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6505 (mm) outliers start: 24 outliers final: 21 residues processed: 150 average time/residue: 0.1471 time to fit residues: 30.2076 Evaluate side-chains 156 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 39 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 chunk 12 optimal weight: 0.0170 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 overall best weight: 0.3018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN H 42 GLN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.148174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.128960 restraints weight = 9099.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.132803 restraints weight = 4486.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.135357 restraints weight = 2758.929| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5497 Z= 0.113 Angle : 0.607 8.768 7464 Z= 0.300 Chirality : 0.041 0.229 847 Planarity : 0.004 0.042 905 Dihedral : 6.225 63.969 865 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.61 % Allowed : 23.92 % Favored : 72.46 % 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: -0.40 (0.32), residues: 669 helix: 1.53 (0.31), residues: 288 sheet: -0.20 (0.61), residues: 78 loop : -2.17 (0.31), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.003 0.001 HIS A 115 PHE 0.025 0.001 PHE H 32 TYR 0.011 0.001 TYR A 239 ARG 0.007 0.000 ARG A 614 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 256) hydrogen bonds : angle 4.02521 ( 750) SS BOND : bond 0.00455 ( 6) SS BOND : angle 1.11532 ( 12) covalent geometry : bond 0.00241 ( 5491) covalent geometry : angle 0.60601 ( 7452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2667.02 seconds wall clock time: 47 minutes 11.95 seconds (2831.95 seconds total)