Starting phenix.real_space_refine on Tue Feb 11 11:17:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bd8_44446/02_2025/9bd8_44446.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bd8_44446/02_2025/9bd8_44446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bd8_44446/02_2025/9bd8_44446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bd8_44446/02_2025/9bd8_44446.map" model { file = "/net/cci-nas-00/data/ceres_data/9bd8_44446/02_2025/9bd8_44446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bd8_44446/02_2025/9bd8_44446.cif" } resolution = 4.8 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= 0.003 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 20 5.16 5 C 3406 2.51 5 N 880 2.21 5 O 1063 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-5592/modules/chem_data/mon_lib" Total number of atoms: 5369 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3423 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 24, 'TRANS': 437} Chain breaks: 7 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 164 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "B" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1932 Classifications: {'peptide': 264} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 1 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 106 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.08, per 1000 atoms: 0.76 Number of scatterers: 5369 At special positions: 0 Unit cell: (61.42, 94.62, 129.48, 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 20 16.00 O 1063 8.00 N 880 7.00 C 3406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 39 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 390 " 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 Links applied NAG-ASN " NAG A4601 " - " ASN A 185 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 686.0 milliseconds 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1360 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 9 sheets defined 14.2% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 118 through 129 removed outlier: 4.327A pdb=" N TYR A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 139 Processing helix chain 'A' and resid 150 through 165 Processing helix chain 'A' and resid 232 through 238 Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.832A pdb=" N ASN A 274 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 321 through 330 removed outlier: 3.872A pdb=" N VAL A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 334 Processing helix chain 'A' and resid 343 through 357 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 375 through 384 removed outlier: 3.863A pdb=" N GLN A 380 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 393 removed outlier: 4.282A pdb=" N THR A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 58 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 51 through 58 current: chain 'A' and resid 72 through 83 removed outlier: 6.836A pdb=" N ALA A 73 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU A 101 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG A 75 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A 99 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN A 77 " --> pdb=" O CYS A 97 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS A 97 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 112 " --> pdb=" O TYR A 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 111 through 115 current: chain 'A' and resid 142 through 144 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 142 through 144 current: chain 'A' and resid 186 through 195 removed outlier: 5.912A pdb=" N SER A 187 " --> pdb=" O ASP A 208 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASP A 208 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 206 " --> pdb=" O HIS A 189 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLU A 202 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG A 195 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA A 200 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 829 through 839 removed outlier: 4.938A pdb=" N ILE A 830 " --> pdb=" O ILE A 854 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 854 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN A 845 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU A 942 " --> pdb=" O ILE A 953 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 961 through 962 Processing sheet with id=AA4, first strand: chain 'B' and resid 401 through 405 removed outlier: 6.085A pdb=" N LYS B 411 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N SER B 421 " --> pdb=" O LYS B 411 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 440 through 443 Processing sheet with id=AA6, first strand: chain 'B' and resid 476 through 482 removed outlier: 3.942A pdb=" N GLY B 478 " --> pdb=" O THR B 491 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 491 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 518 through 524 removed outlier: 5.921A pdb=" N THR B 534 " --> pdb=" O ARG B 520 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE B 522 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR B 532 " --> pdb=" O ILE B 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 563 through 568 removed outlier: 6.591A pdb=" N VAL B 578 " --> pdb=" O ASN B 564 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILE B 566 " --> pdb=" O TYR B 576 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR B 576 " --> pdb=" O ILE B 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 612 through 614 181 hydrogen bonds defined for protein. 474 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: 1.81 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1760 1.34 - 1.46: 1227 1.46 - 1.58: 2460 1.58 - 1.70: 0 1.70 - 1.82: 28 Bond restraints: 5475 Sorted by residual: bond pdb=" CA SER B 648 " pdb=" C SER B 648 " ideal model delta sigma weight residual 1.531 1.523 0.008 7.40e-03 1.83e+04 1.30e+00 bond pdb=" CA SER B 648 " pdb=" CB SER B 648 " ideal model delta sigma weight residual 1.522 1.529 -0.007 7.00e-03 2.04e+04 1.01e+00 bond pdb=" N ALA B 437 " pdb=" CA ALA B 437 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 8.85e-01 bond pdb=" N ASN B 425 " pdb=" CA ASN B 425 " ideal model delta sigma weight residual 1.457 1.468 -0.010 1.29e-02 6.01e+03 6.35e-01 bond pdb=" CB PRO B 519 " pdb=" CG PRO B 519 " ideal model delta sigma weight residual 1.492 1.530 -0.038 5.00e-02 4.00e+02 5.88e-01 ... (remaining 5470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 7141 1.32 - 2.63: 282 2.63 - 3.95: 47 3.95 - 5.26: 10 5.26 - 6.58: 6 Bond angle restraints: 7486 Sorted by residual: angle pdb=" C ALA B 437 " pdb=" CA ALA B 437 " pdb=" CB ALA B 437 " ideal model delta sigma weight residual 110.42 115.72 -5.30 1.99e+00 2.53e-01 7.08e+00 angle pdb=" N LEU A 268 " pdb=" CA LEU A 268 " pdb=" C LEU A 268 " ideal model delta sigma weight residual 109.81 115.67 -5.86 2.21e+00 2.05e-01 7.02e+00 angle pdb=" C GLN B 561 " pdb=" N TRP B 562 " pdb=" CA TRP B 562 " ideal model delta sigma weight residual 121.80 126.80 -5.00 2.44e+00 1.68e-01 4.20e+00 angle pdb=" N ILE B 624 " pdb=" CA ILE B 624 " pdb=" C ILE B 624 " ideal model delta sigma weight residual 112.35 109.50 2.85 1.41e+00 5.03e-01 4.09e+00 angle pdb=" C ILE B 451 " pdb=" N CYS B 452 " pdb=" CA CYS B 452 " ideal model delta sigma weight residual 122.08 118.62 3.46 1.84e+00 2.95e-01 3.53e+00 ... (remaining 7481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 2943 17.13 - 34.27: 253 34.27 - 51.40: 44 51.40 - 68.53: 6 68.53 - 85.66: 3 Dihedral angle restraints: 3249 sinusoidal: 1151 harmonic: 2098 Sorted by residual: dihedral pdb=" CB CYS A 385 " pdb=" SG CYS A 385 " pdb=" SG CYS A 390 " pdb=" CB CYS A 390 " ideal model delta sinusoidal sigma weight residual 93.00 42.65 50.35 1 1.00e+01 1.00e-02 3.47e+01 dihedral pdb=" CB CYS A 245 " pdb=" SG CYS A 245 " pdb=" SG CYS A 261 " pdb=" CB CYS A 261 " ideal model delta sinusoidal sigma weight residual 93.00 47.91 45.09 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CA LEU A 288 " pdb=" C LEU A 288 " pdb=" N GLU A 289 " pdb=" CA GLU A 289 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 3246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 580 0.034 - 0.068: 204 0.068 - 0.102: 82 0.102 - 0.135: 33 0.135 - 0.169: 3 Chirality restraints: 902 Sorted by residual: chirality pdb=" CA ILE A 830 " pdb=" N ILE A 830 " pdb=" C ILE A 830 " pdb=" CB ILE A 830 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CA ILE A 891 " pdb=" N ILE A 891 " pdb=" C ILE A 891 " pdb=" CB ILE A 891 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA ILE A 91 " pdb=" N ILE A 91 " pdb=" C ILE A 91 " pdb=" CB ILE A 91 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 899 not shown) Planarity restraints: 965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 562 " 0.017 2.00e-02 2.50e+03 1.32e-02 4.36e+00 pdb=" CG TRP B 562 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP B 562 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 562 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 562 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 562 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 562 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 562 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 562 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 562 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 855 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.16e+00 pdb=" N PRO A 856 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 856 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 856 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 619 " -0.011 2.00e-02 2.50e+03 8.73e-03 1.33e+00 pdb=" CG PHE B 619 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE B 619 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 619 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 619 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 619 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 619 " -0.001 2.00e-02 2.50e+03 ... (remaining 962 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 237 2.69 - 3.24: 6075 3.24 - 3.80: 9493 3.80 - 4.35: 11963 4.35 - 4.90: 18465 Nonbonded interactions: 46233 Sorted by model distance: nonbonded pdb=" OG SER A 937 " pdb=" O LEU A1001 " model vdw 2.141 3.040 nonbonded pdb=" O ALA A 163 " pdb=" OH TYR A 247 " model vdw 2.146 3.040 nonbonded pdb=" OG SER A 60 " pdb=" OG1 THR A 74 " model vdw 2.181 3.040 nonbonded pdb=" O SER B 470 " pdb=" NH1 ARG B 508 " model vdw 2.210 3.120 nonbonded pdb=" O LEU A 268 " pdb=" OG SER A 271 " model vdw 2.216 3.040 ... (remaining 46228 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: 1.600 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.180 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 0.003 0.038 5475 Z= 0.181 Angle : 0.626 6.575 7486 Z= 0.328 Chirality : 0.044 0.169 902 Planarity : 0.003 0.037 964 Dihedral : 13.216 85.664 1874 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 25.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: -2.18 (0.32), residues: 706 helix: 1.25 (0.69), residues: 76 sheet: -1.26 (0.32), residues: 253 loop : -2.19 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 562 HIS 0.008 0.002 HIS A 265 PHE 0.020 0.002 PHE B 619 TYR 0.012 0.001 TYR B 442 ARG 0.002 0.000 ARG B 574 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1479 time to fit residues: 6.6359 Evaluate side-chains 25 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 65 optimal weight: 5.9990 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 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.033799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.026070 restraints weight = 67619.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.026935 restraints weight = 49993.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.027592 restraints weight = 39630.233| |-----------------------------------------------------------------------------| r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5475 Z= 0.204 Angle : 0.603 6.280 7486 Z= 0.319 Chirality : 0.043 0.149 902 Planarity : 0.004 0.040 964 Dihedral : 5.284 18.806 775 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.31), residues: 706 helix: 1.24 (0.66), residues: 79 sheet: -1.42 (0.32), residues: 251 loop : -2.33 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 562 HIS 0.003 0.001 HIS A 907 PHE 0.013 0.002 PHE A 831 TYR 0.037 0.002 TYR B 442 ARG 0.004 0.001 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1314 time to fit residues: 5.8459 Evaluate side-chains 24 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 71 optimal weight: 0.0270 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.033234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.025774 restraints weight = 67625.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.026640 restraints weight = 49565.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.027306 restraints weight = 38925.173| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5475 Z= 0.232 Angle : 0.615 6.137 7486 Z= 0.324 Chirality : 0.044 0.190 902 Planarity : 0.004 0.040 964 Dihedral : 5.361 19.221 775 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % 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: -2.47 (0.31), residues: 706 helix: 1.27 (0.66), residues: 75 sheet: -1.52 (0.32), residues: 252 loop : -2.37 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 562 HIS 0.003 0.001 HIS B 607 PHE 0.013 0.002 PHE A 831 TYR 0.026 0.002 TYR B 442 ARG 0.007 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9455 (mp) cc_final: 0.8985 (tp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1412 time to fit residues: 6.2162 Evaluate side-chains 25 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 70 optimal weight: 0.0050 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.033478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.025781 restraints weight = 69562.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.026660 restraints weight = 51011.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.027330 restraints weight = 40152.435| |-----------------------------------------------------------------------------| r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5475 Z= 0.205 Angle : 0.601 6.776 7486 Z= 0.314 Chirality : 0.044 0.148 902 Planarity : 0.004 0.041 964 Dihedral : 5.270 19.218 775 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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: -2.46 (0.31), residues: 706 helix: 1.25 (0.66), residues: 75 sheet: -1.46 (0.32), residues: 258 loop : -2.41 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 562 HIS 0.003 0.001 HIS A 828 PHE 0.015 0.002 PHE B 655 TYR 0.020 0.002 TYR B 442 ARG 0.005 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9474 (mp) cc_final: 0.9025 (tp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1088 time to fit residues: 5.4228 Evaluate side-chains 22 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 0.0980 chunk 63 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN A 902 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.033501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.026062 restraints weight = 69898.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.026902 restraints weight = 51769.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.027544 restraints weight = 41122.980| |-----------------------------------------------------------------------------| r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5475 Z= 0.210 Angle : 0.607 6.671 7486 Z= 0.318 Chirality : 0.044 0.190 902 Planarity : 0.004 0.043 964 Dihedral : 5.272 19.513 775 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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: -2.53 (0.31), residues: 706 helix: 1.02 (0.65), residues: 79 sheet: -1.46 (0.32), residues: 258 loop : -2.50 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 562 HIS 0.006 0.001 HIS B 607 PHE 0.018 0.002 PHE A 831 TYR 0.034 0.002 TYR B 442 ARG 0.004 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9477 (mp) cc_final: 0.9035 (tp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1635 time to fit residues: 6.8959 Evaluate side-chains 24 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.033191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.025551 restraints weight = 68755.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.026382 restraints weight = 51016.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.027022 restraints weight = 40653.449| |-----------------------------------------------------------------------------| r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5475 Z= 0.230 Angle : 0.629 7.391 7486 Z= 0.327 Chirality : 0.044 0.168 902 Planarity : 0.004 0.042 964 Dihedral : 5.346 19.967 775 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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: -2.52 (0.31), residues: 706 helix: 1.09 (0.64), residues: 81 sheet: -1.56 (0.31), residues: 266 loop : -2.45 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 562 HIS 0.002 0.001 HIS A 828 PHE 0.016 0.002 PHE A 831 TYR 0.028 0.002 TYR B 442 ARG 0.004 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9444 (mp) cc_final: 0.8984 (tp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1414 time to fit residues: 6.4440 Evaluate side-chains 22 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 33 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.0970 chunk 38 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 0.1980 chunk 1 optimal weight: 0.0870 chunk 52 optimal weight: 0.0570 chunk 46 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.034531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.026413 restraints weight = 64060.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.027355 restraints weight = 46340.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.028069 restraints weight = 36309.230| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5475 Z= 0.166 Angle : 0.612 6.295 7486 Z= 0.309 Chirality : 0.045 0.239 902 Planarity : 0.004 0.040 964 Dihedral : 5.054 19.464 775 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.18 % Allowed : 2.15 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.31), residues: 706 helix: 0.93 (0.63), residues: 81 sheet: -1.45 (0.31), residues: 261 loop : -2.35 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 562 HIS 0.004 0.001 HIS A 828 PHE 0.016 0.001 PHE A 267 TYR 0.027 0.002 TYR B 442 ARG 0.002 0.000 ARG B 633 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9471 (mp) cc_final: 0.9019 (tp) outliers start: 1 outliers final: 0 residues processed: 31 average time/residue: 0.1455 time to fit residues: 6.9401 Evaluate side-chains 25 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 0.0000 chunk 71 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.033634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.025755 restraints weight = 65885.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.026622 restraints weight = 48276.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.027304 restraints weight = 38116.501| |-----------------------------------------------------------------------------| r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5475 Z= 0.230 Angle : 0.617 6.712 7486 Z= 0.321 Chirality : 0.043 0.210 902 Planarity : 0.004 0.041 964 Dihedral : 5.195 19.826 775 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.31), residues: 706 helix: 0.93 (0.62), residues: 81 sheet: -1.44 (0.31), residues: 259 loop : -2.41 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 562 HIS 0.002 0.001 HIS B 607 PHE 0.016 0.002 PHE A 831 TYR 0.026 0.002 TYR B 442 ARG 0.004 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9444 (mp) cc_final: 0.8992 (tp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1692 time to fit residues: 7.3514 Evaluate side-chains 23 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.033631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.025881 restraints weight = 67290.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.026752 restraints weight = 49669.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.027412 restraints weight = 39222.631| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5475 Z= 0.202 Angle : 0.603 6.634 7486 Z= 0.311 Chirality : 0.043 0.194 902 Planarity : 0.004 0.042 964 Dihedral : 5.187 20.284 775 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: -2.47 (0.31), residues: 706 helix: 0.95 (0.63), residues: 81 sheet: -1.49 (0.31), residues: 258 loop : -2.39 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 562 HIS 0.002 0.001 HIS A 828 PHE 0.015 0.002 PHE A 831 TYR 0.025 0.002 TYR B 442 ARG 0.002 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9460 (mp) cc_final: 0.9016 (tp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1430 time to fit residues: 6.0832 Evaluate side-chains 23 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.0010 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.033584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.025906 restraints weight = 67874.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.026755 restraints weight = 50294.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.027403 restraints weight = 39989.390| |-----------------------------------------------------------------------------| r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5475 Z= 0.209 Angle : 0.612 6.669 7486 Z= 0.315 Chirality : 0.044 0.195 902 Planarity : 0.004 0.042 964 Dihedral : 5.253 20.541 775 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: -2.45 (0.31), residues: 706 helix: 0.97 (0.62), residues: 81 sheet: -1.51 (0.31), residues: 259 loop : -2.35 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 562 HIS 0.002 0.001 HIS A 828 PHE 0.015 0.002 PHE A 831 TYR 0.026 0.002 TYR B 442 ARG 0.002 0.000 ARG A 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9478 (mp) cc_final: 0.9048 (tp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1499 time to fit residues: 6.3327 Evaluate side-chains 23 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 0.0040 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.033518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.025758 restraints weight = 68291.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.026629 restraints weight = 50336.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.027288 restraints weight = 39718.533| |-----------------------------------------------------------------------------| r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5475 Z= 0.217 Angle : 0.613 6.690 7486 Z= 0.317 Chirality : 0.044 0.185 902 Planarity : 0.004 0.043 964 Dihedral : 5.279 20.429 775 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: -2.47 (0.31), residues: 706 helix: 0.98 (0.62), residues: 81 sheet: -1.53 (0.32), residues: 258 loop : -2.35 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 562 HIS 0.006 0.001 HIS A 265 PHE 0.015 0.002 PHE A 831 TYR 0.026 0.002 TYR B 442 ARG 0.002 0.000 ARG B 574 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1802.13 seconds wall clock time: 33 minutes 10.89 seconds (1990.89 seconds total)