Starting phenix.real_space_refine on Thu Mar 6 07:54:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bd8_44446/03_2025/9bd8_44446.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bd8_44446/03_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_44446/03_2025/9bd8_44446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bd8_44446/03_2025/9bd8_44446.map" model { file = "/net/cci-nas-00/data/ceres_data/9bd8_44446/03_2025/9bd8_44446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bd8_44446/03_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-5624/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: 3.98, per 1000 atoms: 0.74 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: 1.25 Conformation dependent library (CDL) restraints added in 735.6 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: 0.60 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: 1.62 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 2.240 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: 0.050 Process input model: 17.160 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.470 ------------------------------------------------------------------------------- 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 : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1422 time to fit residues: 6.2842 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 : 0.617 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.026069 restraints weight = 67619.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.026933 restraints weight = 50022.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.027591 restraints weight = 39638.729| |-----------------------------------------------------------------------------| 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 : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1412 time to fit residues: 6.1777 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 : 0.670 ------------------------------------------------------------------------------- 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: 0.6980 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 281 GLN ** 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 = 0.2873 r_free = 0.2873 target = 0.032780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.025541 restraints weight = 69990.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.026353 restraints weight = 52012.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.026971 restraints weight = 41346.082| |-----------------------------------------------------------------------------| r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5475 Z= 0.267 Angle : 0.639 6.215 7486 Z= 0.339 Chirality : 0.044 0.177 902 Planarity : 0.004 0.041 964 Dihedral : 5.503 20.049 775 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 23.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % 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: -2.59 (0.31), residues: 706 helix: 0.99 (0.64), residues: 79 sheet: -1.58 (0.31), residues: 252 loop : -2.47 (0.30), residues: 375 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 0.014 0.002 PHE B 402 TYR 0.027 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 27 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9479 (mp) cc_final: 0.9025 (tp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1102 time to fit residues: 5.1575 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 : 0.622 ------------------------------------------------------------------------------- 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: 0.8980 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 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 96 GLN A 349 ASN ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.033528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.025870 restraints weight = 69912.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.026751 restraints weight = 51199.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.027428 restraints weight = 40345.120| |-----------------------------------------------------------------------------| r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1382 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= 0.202 Angle : 0.613 6.785 7486 Z= 0.320 Chirality : 0.044 0.147 902 Planarity : 0.004 0.041 964 Dihedral : 5.358 19.092 775 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: -2.50 (0.31), residues: 706 helix: 1.23 (0.66), residues: 75 sheet: -1.51 (0.32), residues: 257 loop : -2.43 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 562 HIS 0.003 0.001 HIS A 828 PHE 0.015 0.002 PHE B 655 TYR 0.021 0.002 TYR B 442 ARG 0.006 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 : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9486 (mp) cc_final: 0.9047 (tp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1410 time to fit residues: 6.3521 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 : 0.682 ------------------------------------------------------------------------------- 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: 0.8980 chunk 63 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.2882 r_free = 0.2882 target = 0.033117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.025595 restraints weight = 68359.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.026417 restraints weight = 50933.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.027032 restraints weight = 40615.405| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5475 Z= 0.234 Angle : 0.615 6.754 7486 Z= 0.323 Chirality : 0.044 0.192 902 Planarity : 0.004 0.045 964 Dihedral : 5.407 19.998 775 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.31), residues: 706 helix: 1.00 (0.64), residues: 79 sheet: -1.55 (0.32), residues: 257 loop : -2.50 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 562 HIS 0.003 0.001 HIS A 828 PHE 0.017 0.002 PHE A 831 TYR 0.032 0.002 TYR B 442 ARG 0.005 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 28 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9468 (mp) cc_final: 0.9022 (tp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1486 time to fit residues: 6.5315 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 : 0.676 ------------------------------------------------------------------------------- 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: 1.9990 chunk 27 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.0970 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 = 0.2901 r_free = 0.2901 target = 0.033539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.025846 restraints weight = 68247.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.026699 restraints weight = 50483.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.027360 restraints weight = 39933.194| |-----------------------------------------------------------------------------| r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5475 Z= 0.207 Angle : 0.622 7.558 7486 Z= 0.319 Chirality : 0.044 0.174 902 Planarity : 0.004 0.041 964 Dihedral : 5.314 19.334 775 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: -2.54 (0.31), residues: 706 helix: 1.06 (0.63), residues: 81 sheet: -1.57 (0.32), residues: 257 loop : -2.45 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 562 HIS 0.003 0.001 HIS A 828 PHE 0.016 0.002 PHE A 831 TYR 0.027 0.002 TYR B 442 ARG 0.003 0.000 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 30 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9483 (mp) cc_final: 0.9028 (tp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1399 time to fit residues: 6.5530 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 : 0.666 ------------------------------------------------------------------------------- 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: 0.6980 chunk 60 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 52 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 ** 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 = 0.033474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.025880 restraints weight = 68585.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.026733 restraints weight = 50471.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.027380 restraints weight = 39909.492| |-----------------------------------------------------------------------------| r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1789 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= 0.210 Angle : 0.617 6.538 7486 Z= 0.319 Chirality : 0.044 0.234 902 Planarity : 0.004 0.042 964 Dihedral : 5.297 20.136 775 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.31), residues: 706 helix: 1.01 (0.62), residues: 81 sheet: -1.56 (0.31), residues: 258 loop : -2.49 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 562 HIS 0.003 0.001 HIS A 828 PHE 0.016 0.002 PHE A 831 TYR 0.029 0.002 TYR B 442 ARG 0.003 0.000 ARG A 158 *********************** 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 28 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 442 TYR cc_start: 0.8221 (m-10) cc_final: 0.8012 (m-80) REVERT: B 585 ILE cc_start: 0.9458 (mp) cc_final: 0.8985 (tp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1367 time to fit residues: 6.0287 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 : 0.585 ------------------------------------------------------------------------------- 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: 0.0980 chunk 43 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN B 548 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.033315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.025632 restraints weight = 68677.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.026461 restraints weight = 51023.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.027096 restraints weight = 40567.423| |-----------------------------------------------------------------------------| r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1862 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= 0.233 Angle : 0.627 6.537 7486 Z= 0.329 Chirality : 0.044 0.210 902 Planarity : 0.004 0.042 964 Dihedral : 5.415 19.999 775 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: -2.61 (0.31), residues: 706 helix: 1.02 (0.62), residues: 81 sheet: -1.62 (0.32), residues: 258 loop : -2.50 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 562 HIS 0.004 0.001 HIS A 265 PHE 0.016 0.002 PHE A 831 TYR 0.027 0.002 TYR B 442 ARG 0.002 0.000 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 : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9461 (mp) cc_final: 0.9003 (tp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1364 time to fit residues: 6.1487 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 : 0.591 ------------------------------------------------------------------------------- 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: 4.9990 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** 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 = 0.2890 r_free = 0.2890 target = 0.033364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.025697 restraints weight = 67923.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.026538 restraints weight = 50183.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.027188 restraints weight = 39826.193| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5475 Z= 0.225 Angle : 0.631 6.496 7486 Z= 0.328 Chirality : 0.044 0.194 902 Planarity : 0.004 0.042 964 Dihedral : 5.425 20.432 775 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % 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: -2.63 (0.31), residues: 706 helix: 0.92 (0.62), residues: 81 sheet: -1.73 (0.31), residues: 264 loop : -2.41 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 562 HIS 0.008 0.001 HIS A 265 PHE 0.015 0.002 PHE A 831 TYR 0.027 0.002 TYR B 442 ARG 0.003 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 : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9459 (mp) cc_final: 0.9011 (tp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1504 time to fit residues: 6.3412 Evaluate side-chains 21 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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: 0.7980 chunk 32 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 0.0670 chunk 41 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 ** 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 = 0.2907 r_free = 0.2907 target = 0.033738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.026061 restraints weight = 67515.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.026925 restraints weight = 49745.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.027579 restraints weight = 39334.747| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1975 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= 0.195 Angle : 0.613 6.388 7486 Z= 0.315 Chirality : 0.044 0.190 902 Planarity : 0.004 0.042 964 Dihedral : 5.308 20.296 775 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % 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: -2.55 (0.31), residues: 706 helix: 0.93 (0.62), residues: 81 sheet: -1.68 (0.31), residues: 264 loop : -2.33 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 562 HIS 0.007 0.001 HIS A 265 PHE 0.014 0.001 PHE A 831 TYR 0.025 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 28 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 525 ASP cc_start: 0.9121 (m-30) cc_final: 0.8876 (t70) REVERT: B 585 ILE cc_start: 0.9441 (mp) cc_final: 0.8986 (tp) REVERT: B 652 MET cc_start: 0.9655 (tpp) cc_final: 0.9441 (tpp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1554 time to fit residues: 6.8737 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 : 0.906 ------------------------------------------------------------------------------- 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: 6.9990 chunk 62 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.2904 r_free = 0.2904 target = 0.033604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.025990 restraints weight = 69219.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.026838 restraints weight = 51302.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.027479 restraints weight = 40630.246| |-----------------------------------------------------------------------------| r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5475 Z= 0.208 Angle : 0.620 6.430 7486 Z= 0.320 Chirality : 0.044 0.181 902 Planarity : 0.004 0.042 964 Dihedral : 5.345 20.291 775 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.55 (0.31), residues: 706 helix: 0.99 (0.62), residues: 81 sheet: -1.69 (0.32), residues: 264 loop : -2.34 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 562 HIS 0.007 0.001 HIS A 265 PHE 0.013 0.002 PHE A 831 TYR 0.025 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: 1833.48 seconds wall clock time: 32 minutes 41.44 seconds (1961.44 seconds total)