Starting phenix.real_space_refine on Sun Apr 27 20:55:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xt9_38641/04_2025/8xt9_38641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xt9_38641/04_2025/8xt9_38641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xt9_38641/04_2025/8xt9_38641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xt9_38641/04_2025/8xt9_38641.map" model { file = "/net/cci-nas-00/data/ceres_data/8xt9_38641/04_2025/8xt9_38641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xt9_38641/04_2025/8xt9_38641.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 34 5.16 5 C 4186 2.51 5 N 1075 2.21 5 O 1184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 6479 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 5740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5740 Classifications: {'peptide': 737} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 37, 'TRANS': 699} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 739 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 101} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 3, 'PHE:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Time building chain proxies: 4.88, per 1000 atoms: 0.75 Number of scatterers: 6479 At special positions: 0 Unit cell: (69.615, 89.964, 171.36, 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 34 16.00 O 1184 8.00 N 1075 7.00 C 4186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 29 " - pdb=" SG CYS C 35 " distance=2.02 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 43 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 364 " distance=2.03 Simple disulfide: pdb=" SG CYS C 618 " - pdb=" SG CYS C 693 " distance=2.03 Simple disulfide: pdb=" SG CYS C 757 " - pdb=" SG CYS C 761 " distance=2.57 Simple disulfide: pdb=" SG CYS A 428 " - pdb=" SG CYS A 501 " distance=2.03 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: 1.62 Conformation dependent library (CDL) restraints added in 942.4 milliseconds 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1586 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 8 sheets defined 34.1% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'C' and resid 121 through 127 removed outlier: 3.588A pdb=" N ILE C 125 " --> pdb=" O PRO C 121 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG C 126 " --> pdb=" O SER C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 176 removed outlier: 4.272A pdb=" N LEU C 176 " --> pdb=" O PRO C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 289 through 292 removed outlier: 4.131A pdb=" N PHE C 292 " --> pdb=" O ASN C 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 292' Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 466 through 471 removed outlier: 3.928A pdb=" N CYS C 470 " --> pdb=" O TYR C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 566 Processing helix chain 'C' and resid 571 through 601 removed outlier: 3.849A pdb=" N PHE C 586 " --> pdb=" O VAL C 582 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET C 587 " --> pdb=" O SER C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 614 removed outlier: 3.656A pdb=" N PHE C 608 " --> pdb=" O ARG C 604 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TRP C 611 " --> pdb=" O GLU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 649 removed outlier: 3.942A pdb=" N LYS C 619 " --> pdb=" O GLY C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 679 removed outlier: 3.922A pdb=" N GLN C 661 " --> pdb=" O ASN C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 682 No H-bonds generated for 'chain 'C' and resid 680 through 682' Processing helix chain 'C' and resid 703 through 732 removed outlier: 4.055A pdb=" N THR C 707 " --> pdb=" O SER C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 769 Proline residue: C 762 - end of helix Processing helix chain 'C' and resid 770 through 772 No H-bonds generated for 'chain 'C' and resid 770 through 772' Processing helix chain 'C' and resid 778 through 790 Processing helix chain 'C' and resid 791 through 804 Proline residue: C 798 - end of helix Processing helix chain 'C' and resid 805 through 821 Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 467 through 470 removed outlier: 4.124A pdb=" N LYS A 470 " --> pdb=" O ASP A 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 467 through 470' Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.790A pdb=" N ILE A 517 " --> pdb=" O ASN A 514 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 35 through 36 removed outlier: 3.773A pdb=" N ARG C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU C 158 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP C 231 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'C' and resid 191 through 192 removed outlier: 4.115A pdb=" N ILE C 192 " --> pdb=" O SER C 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 262 through 263 Processing sheet with id=AA5, first strand: chain 'C' and resid 300 through 304 removed outlier: 6.527A pdb=" N LEU C 301 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N THR C 327 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE C 303 " --> pdb=" O THR C 327 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU C 348 " --> pdb=" O SER C 371 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU C 418 " --> pdb=" O LYS C 440 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 429 Processing sheet with id=AA7, first strand: chain 'A' and resid 463 through 465 removed outlier: 5.318A pdb=" N GLY A 453 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ARG A 444 " --> pdb=" O GLY A 453 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 455 " --> pdb=" O TRP A 442 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 463 through 465 removed outlier: 5.318A pdb=" N GLY A 453 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ARG A 444 " --> pdb=" O GLY A 453 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 455 " --> pdb=" O TRP A 442 " (cutoff:3.500A) 255 hydrogen bonds defined for protein. 735 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: 2.10 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1039 1.26 - 1.40: 1636 1.40 - 1.55: 3898 1.55 - 1.69: 12 1.69 - 1.83: 45 Bond restraints: 6630 Sorted by residual: bond pdb=" N PRO C 193 " pdb=" CD PRO C 193 " ideal model delta sigma weight residual 1.473 1.293 0.180 1.40e-02 5.10e+03 1.65e+02 bond pdb=" C GLN C 180 " pdb=" O GLN C 180 " ideal model delta sigma weight residual 1.235 1.120 0.115 1.24e-02 6.50e+03 8.64e+01 bond pdb=" CA ASP C 147 " pdb=" C ASP C 147 " ideal model delta sigma weight residual 1.525 1.647 -0.122 1.38e-02 5.25e+03 7.82e+01 bond pdb=" C CYS C 757 " pdb=" O CYS C 757 " ideal model delta sigma weight residual 1.237 1.137 0.100 1.16e-02 7.43e+03 7.42e+01 bond pdb=" C MET C 782 " pdb=" O MET C 782 " ideal model delta sigma weight residual 1.236 1.141 0.095 1.15e-02 7.56e+03 6.88e+01 ... (remaining 6625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 8799 3.91 - 7.82: 188 7.82 - 11.74: 25 11.74 - 15.65: 6 15.65 - 19.56: 3 Bond angle restraints: 9021 Sorted by residual: angle pdb=" N SER C 148 " pdb=" CA SER C 148 " pdb=" C SER C 148 " ideal model delta sigma weight residual 110.55 90.99 19.56 1.35e+00 5.49e-01 2.10e+02 angle pdb=" N GLU C 146 " pdb=" CA GLU C 146 " pdb=" C GLU C 146 " ideal model delta sigma weight residual 111.11 125.81 -14.70 1.20e+00 6.94e-01 1.50e+02 angle pdb=" N ASN A 489 " pdb=" CA ASN A 489 " pdb=" C ASN A 489 " ideal model delta sigma weight residual 109.50 127.94 -18.44 1.58e+00 4.01e-01 1.36e+02 angle pdb=" C ASP C 147 " pdb=" CA ASP C 147 " pdb=" CB ASP C 147 " ideal model delta sigma weight residual 111.06 94.50 16.56 1.55e+00 4.16e-01 1.14e+02 angle pdb=" N VAL C 204 " pdb=" CA VAL C 204 " pdb=" C VAL C 204 " ideal model delta sigma weight residual 111.81 119.89 -8.08 8.60e-01 1.35e+00 8.83e+01 ... (remaining 9016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 3355 17.17 - 34.33: 421 34.33 - 51.50: 127 51.50 - 68.66: 34 68.66 - 85.83: 4 Dihedral angle restraints: 3941 sinusoidal: 1501 harmonic: 2440 Sorted by residual: dihedral pdb=" CD ARG C 275 " pdb=" NE ARG C 275 " pdb=" CZ ARG C 275 " pdb=" NH1 ARG C 275 " ideal model delta sinusoidal sigma weight residual 0.00 67.65 -67.65 1 1.00e+01 1.00e-02 5.95e+01 dihedral pdb=" C ASP C 147 " pdb=" N ASP C 147 " pdb=" CA ASP C 147 " pdb=" CB ASP C 147 " ideal model delta harmonic sigma weight residual -122.60 -104.56 -18.04 0 2.50e+00 1.60e-01 5.21e+01 dihedral pdb=" C ASP C 162 " pdb=" N ASP C 162 " pdb=" CA ASP C 162 " pdb=" CB ASP C 162 " ideal model delta harmonic sigma weight residual -122.60 -140.53 17.93 0 2.50e+00 1.60e-01 5.14e+01 ... (remaining 3938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 974 0.135 - 0.269: 71 0.269 - 0.404: 7 0.404 - 0.538: 3 0.538 - 0.672: 2 Chirality restraints: 1057 Sorted by residual: chirality pdb=" CA ASP C 162 " pdb=" N ASP C 162 " pdb=" C ASP C 162 " pdb=" CB ASP C 162 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CA GLU C 146 " pdb=" N GLU C 146 " pdb=" C GLU C 146 " pdb=" CB GLU C 146 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CA ASP C 147 " pdb=" N ASP C 147 " pdb=" C ASP C 147 " pdb=" CB ASP C 147 " both_signs ideal model delta sigma weight residual False 2.51 3.03 -0.52 2.00e-01 2.50e+01 6.72e+00 ... (remaining 1054 not shown) Planarity restraints: 1142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 275 " 1.003 9.50e-02 1.11e+02 4.50e-01 1.22e+02 pdb=" NE ARG C 275 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG C 275 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG C 275 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 275 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 493 " -0.027 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C PRO A 493 " 0.086 2.00e-02 2.50e+03 pdb=" O PRO A 493 " -0.030 2.00e-02 2.50e+03 pdb=" N GLU A 494 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 782 " -0.024 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C MET C 782 " 0.085 2.00e-02 2.50e+03 pdb=" O MET C 782 " -0.032 2.00e-02 2.50e+03 pdb=" N LYS C 783 " -0.029 2.00e-02 2.50e+03 ... (remaining 1139 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1655 2.79 - 3.32: 6090 3.32 - 3.85: 10590 3.85 - 4.37: 12239 4.37 - 4.90: 21019 Nonbonded interactions: 51593 Sorted by model distance: nonbonded pdb=" N SER C 148 " pdb=" O SER C 148 " model vdw 2.268 2.496 nonbonded pdb=" O HIS C 365 " pdb=" OG SER C 390 " model vdw 2.327 3.040 nonbonded pdb=" OE1 GLU C 686 " pdb=" OG SER C 703 " model vdw 2.351 3.040 nonbonded pdb=" O THR C 526 " pdb=" OG1 THR C 526 " model vdw 2.382 3.040 nonbonded pdb=" O PRO A 447 " pdb=" NZ LYS A 449 " model vdw 2.386 3.120 ... (remaining 51588 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.430 Find NCS groups from input model: 0.070 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:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 : 0.010 0.541 6636 Z= 0.574 Angle : 1.319 19.559 9033 Z= 0.864 Chirality : 0.084 0.672 1057 Planarity : 0.015 0.450 1142 Dihedral : 17.170 85.831 2337 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.01 % Favored : 93.39 % Rotamer: Outliers : 6.04 % Allowed : 26.83 % Favored : 67.13 % Cbeta Deviations : 0.63 % 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 (0.29), residues: 832 helix: 1.19 (0.33), residues: 247 sheet: -0.72 (0.48), residues: 133 loop : -1.14 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 442 HIS 0.005 0.001 HIS C 256 PHE 0.022 0.001 PHE C 554 TYR 0.013 0.001 TYR C 725 ARG 0.003 0.000 ARG C 275 Details of bonding type rmsd hydrogen bonds : bond 0.16162 ( 244) hydrogen bonds : angle 6.15306 ( 735) SS BOND : bond 0.22106 ( 6) SS BOND : angle 5.68589 ( 12) covalent geometry : bond 0.00693 ( 6630) covalent geometry : angle 1.30344 ( 9021) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 80 time to evaluate : 0.683 Fit side-chains REVERT: C 440 LYS cc_start: 0.8571 (mtpp) cc_final: 0.8304 (mttp) REVERT: C 659 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6850 (pt) REVERT: A 445 GLN cc_start: 0.6414 (tp40) cc_final: 0.5246 (tp40) REVERT: A 485 TYR cc_start: 0.8931 (m-80) cc_final: 0.8504 (m-80) outliers start: 43 outliers final: 18 residues processed: 113 average time/residue: 0.1787 time to fit residues: 27.5273 Evaluate side-chains 78 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 792 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 39 optimal weight: 0.0980 chunk 48 optimal weight: 0.7980 chunk 75 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 ASN C 187 ASN C 402 HIS C 444 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.115843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.087049 restraints weight = 13056.365| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.20 r_work: 0.3240 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6636 Z= 0.127 Angle : 0.617 7.630 9033 Z= 0.305 Chirality : 0.044 0.184 1057 Planarity : 0.004 0.037 1142 Dihedral : 6.469 54.359 910 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.49 % Allowed : 28.09 % Favored : 67.42 % 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: -0.02 (0.29), residues: 832 helix: 1.73 (0.32), residues: 257 sheet: -0.55 (0.48), residues: 135 loop : -0.89 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 159 HIS 0.005 0.001 HIS C 256 PHE 0.013 0.001 PHE C 808 TYR 0.009 0.001 TYR C 725 ARG 0.003 0.000 ARG C 817 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 244) hydrogen bonds : angle 4.53014 ( 735) SS BOND : bond 0.00863 ( 6) SS BOND : angle 1.45997 ( 12) covalent geometry : bond 0.00295 ( 6630) covalent geometry : angle 0.61517 ( 9021) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 66 time to evaluate : 1.008 Fit side-chains REVERT: C 71 GLN cc_start: 0.8681 (pp30) cc_final: 0.8242 (pp30) REVERT: C 519 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7204 (tp) REVERT: C 659 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6559 (pp) REVERT: C 667 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8784 (tm) REVERT: A 440 MET cc_start: 0.6869 (tmm) cc_final: 0.6566 (tmm) REVERT: A 445 GLN cc_start: 0.7301 (tp40) cc_final: 0.6555 (tp40) REVERT: A 459 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7875 (mm) REVERT: A 485 TYR cc_start: 0.8715 (m-80) cc_final: 0.8503 (m-80) outliers start: 32 outliers final: 15 residues processed: 91 average time/residue: 0.1619 time to fit residues: 21.8246 Evaluate side-chains 78 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.0060 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.116067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.086559 restraints weight = 13370.285| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.28 r_work: 0.3223 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6636 Z= 0.122 Angle : 0.594 7.346 9033 Z= 0.292 Chirality : 0.043 0.166 1057 Planarity : 0.004 0.037 1142 Dihedral : 5.166 54.993 887 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.07 % Allowed : 29.78 % Favored : 66.15 % 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: 0.09 (0.29), residues: 832 helix: 1.95 (0.32), residues: 255 sheet: -0.57 (0.47), residues: 135 loop : -0.88 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 442 HIS 0.005 0.001 HIS C 256 PHE 0.011 0.001 PHE C 808 TYR 0.008 0.001 TYR C 725 ARG 0.001 0.000 ARG C 817 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 244) hydrogen bonds : angle 4.32971 ( 735) SS BOND : bond 0.00694 ( 6) SS BOND : angle 1.30923 ( 12) covalent geometry : bond 0.00293 ( 6630) covalent geometry : angle 0.59269 ( 9021) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 0.800 Fit side-chains REVERT: C 71 GLN cc_start: 0.8688 (pp30) cc_final: 0.8257 (pp30) REVERT: C 165 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7942 (pp) REVERT: C 260 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8562 (tp) REVERT: C 519 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7167 (tp) REVERT: C 659 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6565 (pp) REVERT: C 667 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8516 (tm) REVERT: C 671 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8445 (mm) REVERT: C 721 MET cc_start: 0.8764 (ptp) cc_final: 0.8509 (ptp) REVERT: C 725 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7298 (m-80) REVERT: A 445 GLN cc_start: 0.7312 (tp40) cc_final: 0.6800 (tp40) REVERT: A 485 TYR cc_start: 0.8704 (m-80) cc_final: 0.8491 (m-80) outliers start: 29 outliers final: 14 residues processed: 81 average time/residue: 0.1306 time to fit residues: 16.0982 Evaluate side-chains 76 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 74 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.113273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.083889 restraints weight = 13230.650| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.24 r_work: 0.3172 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6636 Z= 0.181 Angle : 0.619 7.192 9033 Z= 0.306 Chirality : 0.045 0.168 1057 Planarity : 0.004 0.042 1142 Dihedral : 5.057 54.490 885 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.20 % Allowed : 28.09 % Favored : 66.71 % 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 (0.29), residues: 832 helix: 2.01 (0.32), residues: 255 sheet: -0.55 (0.47), residues: 135 loop : -0.84 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 159 HIS 0.005 0.001 HIS C 256 PHE 0.011 0.001 PHE C 473 TYR 0.011 0.001 TYR C 725 ARG 0.002 0.000 ARG C 542 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 244) hydrogen bonds : angle 4.32673 ( 735) SS BOND : bond 0.00762 ( 6) SS BOND : angle 1.42685 ( 12) covalent geometry : bond 0.00442 ( 6630) covalent geometry : angle 0.61731 ( 9021) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 58 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: C 71 GLN cc_start: 0.8693 (pp30) cc_final: 0.8284 (pp30) REVERT: C 165 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7984 (pp) REVERT: C 367 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8769 (tp) REVERT: C 519 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7188 (tp) REVERT: C 659 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6867 (pp) REVERT: C 667 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8618 (tm) REVERT: C 671 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8447 (mm) REVERT: C 725 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.7346 (m-80) REVERT: A 445 GLN cc_start: 0.7493 (tp40) cc_final: 0.7103 (tp40) REVERT: A 485 TYR cc_start: 0.8748 (m-80) cc_final: 0.8518 (m-80) outliers start: 37 outliers final: 20 residues processed: 86 average time/residue: 0.1869 time to fit residues: 23.8485 Evaluate side-chains 84 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 618 CYS Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 64 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 10.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 658 HIS C 714 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.112651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.083152 restraints weight = 13225.468| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.25 r_work: 0.3195 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6636 Z= 0.181 Angle : 0.616 8.205 9033 Z= 0.303 Chirality : 0.044 0.153 1057 Planarity : 0.004 0.046 1142 Dihedral : 5.056 54.578 885 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 5.90 % Allowed : 27.11 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.29), residues: 832 helix: 2.21 (0.32), residues: 250 sheet: -0.55 (0.49), residues: 126 loop : -0.86 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 159 HIS 0.005 0.001 HIS C 256 PHE 0.011 0.001 PHE C 760 TYR 0.010 0.001 TYR C 725 ARG 0.002 0.000 ARG C 542 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 244) hydrogen bonds : angle 4.25272 ( 735) SS BOND : bond 0.00760 ( 6) SS BOND : angle 1.36957 ( 12) covalent geometry : bond 0.00442 ( 6630) covalent geometry : angle 0.61477 ( 9021) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 56 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: C 62 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7240 (tt) REVERT: C 66 MET cc_start: 0.8817 (mpp) cc_final: 0.8564 (mpp) REVERT: C 71 GLN cc_start: 0.8677 (pp30) cc_final: 0.8230 (pp30) REVERT: C 83 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8542 (tt) REVERT: C 165 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7945 (pp) REVERT: C 344 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8544 (mtm) REVERT: C 367 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8793 (tp) REVERT: C 381 LYS cc_start: 0.9327 (mttt) cc_final: 0.9012 (mtpp) REVERT: C 519 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7137 (tp) REVERT: C 659 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7053 (pp) REVERT: C 667 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8608 (tm) REVERT: C 725 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.7328 (m-80) REVERT: A 445 GLN cc_start: 0.7460 (tp40) cc_final: 0.7083 (tp40) REVERT: A 463 THR cc_start: 0.8787 (p) cc_final: 0.8359 (m) REVERT: A 485 TYR cc_start: 0.8909 (m-80) cc_final: 0.8672 (m-80) outliers start: 42 outliers final: 20 residues processed: 89 average time/residue: 0.1502 time to fit residues: 19.9256 Evaluate side-chains 86 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 618 CYS Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 64 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.113640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.083953 restraints weight = 13204.373| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.28 r_work: 0.3201 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6636 Z= 0.155 Angle : 0.612 7.990 9033 Z= 0.297 Chirality : 0.044 0.188 1057 Planarity : 0.004 0.048 1142 Dihedral : 4.953 52.739 885 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.48 % Allowed : 27.53 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.29), residues: 832 helix: 2.06 (0.32), residues: 256 sheet: -0.51 (0.48), residues: 128 loop : -0.82 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 442 HIS 0.005 0.001 HIS C 256 PHE 0.011 0.001 PHE C 760 TYR 0.010 0.001 TYR C 725 ARG 0.002 0.000 ARG C 542 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 244) hydrogen bonds : angle 4.21827 ( 735) SS BOND : bond 0.00728 ( 6) SS BOND : angle 1.40677 ( 12) covalent geometry : bond 0.00378 ( 6630) covalent geometry : angle 0.61024 ( 9021) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 61 time to evaluate : 0.937 Fit side-chains REVERT: C 62 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7296 (tt) REVERT: C 66 MET cc_start: 0.8835 (mpp) cc_final: 0.8573 (mpp) REVERT: C 71 GLN cc_start: 0.8691 (pp30) cc_final: 0.8233 (pp30) REVERT: C 165 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7952 (pp) REVERT: C 367 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8773 (tp) REVERT: C 381 LYS cc_start: 0.9326 (mttt) cc_final: 0.9021 (mtpp) REVERT: C 519 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7150 (tp) REVERT: C 659 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7113 (pp) REVERT: C 667 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8749 (tm) REVERT: C 671 LEU cc_start: 0.8918 (mm) cc_final: 0.8705 (pp) REVERT: C 725 TYR cc_start: 0.8800 (OUTLIER) cc_final: 0.7289 (m-80) REVERT: C 775 ILE cc_start: 0.6197 (OUTLIER) cc_final: 0.5963 (mp) REVERT: A 445 GLN cc_start: 0.7349 (tp40) cc_final: 0.6953 (tp40) REVERT: A 463 THR cc_start: 0.8805 (p) cc_final: 0.8399 (m) REVERT: A 485 TYR cc_start: 0.8908 (m-80) cc_final: 0.8693 (m-80) outliers start: 39 outliers final: 26 residues processed: 93 average time/residue: 0.1613 time to fit residues: 22.3804 Evaluate side-chains 92 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 58 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 618 CYS Chi-restraints excluded: chain C residue 637 MET Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 775 ILE Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 45 optimal weight: 0.0070 chunk 25 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.113205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.083908 restraints weight = 13074.128| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.23 r_work: 0.3207 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6636 Z= 0.151 Angle : 0.612 8.079 9033 Z= 0.298 Chirality : 0.044 0.147 1057 Planarity : 0.004 0.048 1142 Dihedral : 4.911 51.872 885 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 6.32 % Allowed : 26.54 % Favored : 67.13 % 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: 0.29 (0.29), residues: 832 helix: 2.24 (0.32), residues: 250 sheet: -0.50 (0.50), residues: 126 loop : -0.78 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 442 HIS 0.005 0.001 HIS C 256 PHE 0.010 0.001 PHE C 760 TYR 0.011 0.001 TYR C 725 ARG 0.002 0.000 ARG C 542 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 244) hydrogen bonds : angle 4.20506 ( 735) SS BOND : bond 0.00724 ( 6) SS BOND : angle 1.35639 ( 12) covalent geometry : bond 0.00369 ( 6630) covalent geometry : angle 0.61045 ( 9021) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 57 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: C 62 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7254 (tt) REVERT: C 66 MET cc_start: 0.8857 (mpp) cc_final: 0.8578 (mpp) REVERT: C 71 GLN cc_start: 0.8682 (pp30) cc_final: 0.8208 (pp30) REVERT: C 83 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8539 (tt) REVERT: C 165 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7931 (pp) REVERT: C 344 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8494 (mtm) REVERT: C 367 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8754 (tp) REVERT: C 381 LYS cc_start: 0.9322 (mttt) cc_final: 0.9010 (mtpp) REVERT: C 519 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7144 (tp) REVERT: C 659 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7098 (pp) REVERT: C 667 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8730 (tm) REVERT: C 725 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.7229 (m-80) REVERT: C 775 ILE cc_start: 0.6165 (OUTLIER) cc_final: 0.5927 (mp) REVERT: A 445 GLN cc_start: 0.7344 (tp40) cc_final: 0.6932 (tp40) REVERT: A 463 THR cc_start: 0.8800 (p) cc_final: 0.8417 (m) REVERT: A 485 TYR cc_start: 0.8913 (m-80) cc_final: 0.8706 (m-80) outliers start: 45 outliers final: 27 residues processed: 94 average time/residue: 0.1765 time to fit residues: 24.5207 Evaluate side-chains 95 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 58 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 618 CYS Chi-restraints excluded: chain C residue 637 MET Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 775 ILE Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 60 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.114554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.084891 restraints weight = 13274.288| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.30 r_work: 0.3224 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6636 Z= 0.126 Angle : 0.620 8.393 9033 Z= 0.298 Chirality : 0.044 0.165 1057 Planarity : 0.004 0.049 1142 Dihedral : 4.823 50.800 885 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.48 % Allowed : 26.40 % Favored : 68.12 % 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: 0.32 (0.29), residues: 832 helix: 2.25 (0.32), residues: 250 sheet: -0.50 (0.48), residues: 131 loop : -0.75 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 442 HIS 0.005 0.001 HIS C 256 PHE 0.011 0.001 PHE A 518 TYR 0.012 0.001 TYR C 725 ARG 0.008 0.000 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 244) hydrogen bonds : angle 4.16720 ( 735) SS BOND : bond 0.00651 ( 6) SS BOND : angle 1.31126 ( 12) covalent geometry : bond 0.00301 ( 6630) covalent geometry : angle 0.61885 ( 9021) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 61 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: C 62 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7289 (tt) REVERT: C 66 MET cc_start: 0.8877 (mpp) cc_final: 0.8562 (mpp) REVERT: C 71 GLN cc_start: 0.8621 (pp30) cc_final: 0.8186 (pp30) REVERT: C 83 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8530 (tt) REVERT: C 165 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7932 (pp) REVERT: C 354 ASN cc_start: 0.8222 (p0) cc_final: 0.7749 (p0) REVERT: C 367 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8700 (tp) REVERT: C 381 LYS cc_start: 0.9287 (mttt) cc_final: 0.8981 (mtpp) REVERT: C 519 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7137 (tp) REVERT: C 667 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8843 (tm) REVERT: C 725 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.7334 (m-80) REVERT: C 775 ILE cc_start: 0.6212 (OUTLIER) cc_final: 0.5957 (mp) REVERT: A 445 GLN cc_start: 0.7301 (tp40) cc_final: 0.6850 (tp40) REVERT: A 463 THR cc_start: 0.8822 (p) cc_final: 0.8461 (m) REVERT: A 485 TYR cc_start: 0.8906 (m-80) cc_final: 0.8702 (m-80) outliers start: 39 outliers final: 26 residues processed: 95 average time/residue: 0.2688 time to fit residues: 39.3219 Evaluate side-chains 91 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 57 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 637 MET Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 775 ILE Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 62 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.114937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.085292 restraints weight = 13563.940| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.35 r_work: 0.3231 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6636 Z= 0.119 Angle : 0.620 8.829 9033 Z= 0.298 Chirality : 0.043 0.173 1057 Planarity : 0.004 0.050 1142 Dihedral : 4.665 50.296 883 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.34 % Allowed : 26.26 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.29), residues: 832 helix: 2.26 (0.32), residues: 249 sheet: -0.53 (0.48), residues: 131 loop : -0.74 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 442 HIS 0.005 0.001 HIS C 256 PHE 0.011 0.001 PHE C 754 TYR 0.011 0.001 TYR C 725 ARG 0.007 0.000 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 244) hydrogen bonds : angle 4.15425 ( 735) SS BOND : bond 0.00618 ( 6) SS BOND : angle 1.28646 ( 12) covalent geometry : bond 0.00286 ( 6630) covalent geometry : angle 0.61873 ( 9021) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 60 time to evaluate : 0.715 Fit side-chains REVERT: C 62 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7264 (tt) REVERT: C 66 MET cc_start: 0.8846 (mpp) cc_final: 0.8537 (mpp) REVERT: C 71 GLN cc_start: 0.8595 (pp30) cc_final: 0.8154 (pp30) REVERT: C 83 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8484 (tt) REVERT: C 165 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7906 (pp) REVERT: C 354 ASN cc_start: 0.8212 (p0) cc_final: 0.7742 (p0) REVERT: C 367 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8660 (tp) REVERT: C 381 LYS cc_start: 0.9275 (mttt) cc_final: 0.8966 (mtpp) REVERT: C 519 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7164 (tp) REVERT: C 667 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8802 (tm) REVERT: C 721 MET cc_start: 0.8858 (ptp) cc_final: 0.8368 (ptp) REVERT: C 725 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: C 775 ILE cc_start: 0.6216 (OUTLIER) cc_final: 0.5963 (mp) REVERT: A 445 GLN cc_start: 0.7300 (tp40) cc_final: 0.6894 (tp40) REVERT: A 484 LEU cc_start: 0.7347 (tp) cc_final: 0.7055 (tp) REVERT: A 485 TYR cc_start: 0.8912 (m-80) cc_final: 0.8686 (m-80) outliers start: 38 outliers final: 26 residues processed: 92 average time/residue: 0.1478 time to fit residues: 20.2206 Evaluate side-chains 92 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 58 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 637 MET Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 775 ILE Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 0.0670 chunk 55 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 0.0870 chunk 48 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 0.0970 chunk 36 optimal weight: 0.8980 overall best weight: 0.3094 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.116256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.087402 restraints weight = 13261.023| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.26 r_work: 0.3269 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6636 Z= 0.104 Angle : 0.608 9.157 9033 Z= 0.290 Chirality : 0.043 0.185 1057 Planarity : 0.004 0.051 1142 Dihedral : 4.506 49.335 883 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.49 % Allowed : 27.25 % Favored : 68.26 % 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: 0.35 (0.29), residues: 832 helix: 2.30 (0.32), residues: 249 sheet: -0.55 (0.48), residues: 131 loop : -0.72 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 442 HIS 0.005 0.001 HIS C 256 PHE 0.009 0.001 PHE C 808 TYR 0.012 0.001 TYR C 725 ARG 0.007 0.000 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 244) hydrogen bonds : angle 4.07517 ( 735) SS BOND : bond 0.00533 ( 6) SS BOND : angle 1.26769 ( 12) covalent geometry : bond 0.00243 ( 6630) covalent geometry : angle 0.60710 ( 9021) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 0.730 Fit side-chains REVERT: C 62 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7158 (tt) REVERT: C 66 MET cc_start: 0.8810 (mpp) cc_final: 0.8509 (mpp) REVERT: C 71 GLN cc_start: 0.8563 (pp30) cc_final: 0.8109 (pp30) REVERT: C 83 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8547 (tt) REVERT: C 165 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7874 (pp) REVERT: C 354 ASN cc_start: 0.8161 (p0) cc_final: 0.7681 (p0) REVERT: C 381 LYS cc_start: 0.9223 (mttt) cc_final: 0.8799 (mtpp) REVERT: C 519 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6861 (tp) REVERT: C 554 PHE cc_start: 0.8636 (m-80) cc_final: 0.7850 (t80) REVERT: C 667 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8750 (tm) REVERT: C 721 MET cc_start: 0.8825 (ptp) cc_final: 0.8316 (ptp) REVERT: C 725 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: A 445 GLN cc_start: 0.7367 (tp40) cc_final: 0.7010 (tp40) REVERT: A 484 LEU cc_start: 0.7351 (tp) cc_final: 0.7051 (tp) REVERT: A 485 TYR cc_start: 0.8862 (m-80) cc_final: 0.8652 (m-80) outliers start: 32 outliers final: 23 residues processed: 87 average time/residue: 0.1335 time to fit residues: 17.2255 Evaluate side-chains 85 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 56 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 60 optimal weight: 0.0870 chunk 6 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.114745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.084993 restraints weight = 13717.158| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.37 r_work: 0.3227 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6636 Z= 0.137 Angle : 0.622 8.931 9033 Z= 0.298 Chirality : 0.043 0.178 1057 Planarity : 0.004 0.051 1142 Dihedral : 4.591 49.445 883 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.21 % Allowed : 27.67 % Favored : 68.12 % 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: 0.32 (0.29), residues: 832 helix: 2.27 (0.32), residues: 249 sheet: -0.55 (0.48), residues: 131 loop : -0.74 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 159 HIS 0.005 0.001 HIS C 256 PHE 0.010 0.001 PHE C 754 TYR 0.011 0.001 TYR C 725 ARG 0.007 0.000 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 244) hydrogen bonds : angle 4.13044 ( 735) SS BOND : bond 0.00659 ( 6) SS BOND : angle 1.29264 ( 12) covalent geometry : bond 0.00335 ( 6630) covalent geometry : angle 0.62108 ( 9021) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3834.40 seconds wall clock time: 69 minutes 16.69 seconds (4156.69 seconds total)