Starting phenix.real_space_refine on Tue Mar 3 12:21:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cko_30389/03_2026/7cko_30389.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cko_30389/03_2026/7cko_30389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cko_30389/03_2026/7cko_30389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cko_30389/03_2026/7cko_30389.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cko_30389/03_2026/7cko_30389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cko_30389/03_2026/7cko_30389.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 sd= 0.070 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 25 5.16 5 C 2624 2.51 5 N 681 2.21 5 O 699 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4029 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2846 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 17, 'TRANS': 357} Chain breaks: 1 Chain: "B" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1160 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 543 Unresolved non-hydrogen angles: 696 Unresolved non-hydrogen dihedrals: 455 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'PHE:plan': 5, 'GLU:plan': 16, 'ASP:plan': 12, 'ASN:plan1': 7, 'HIS:plan': 4, 'ARG:plan': 6, 'TRP:plan': 4, 'GLN:plan1': 6, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 289 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'G5L': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.05, per 1000 atoms: 0.26 Number of scatterers: 4029 At special positions: 0 Unit cell: (103.726, 58.1877, 116.375, 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 25 16.00 O 699 8.00 N 681 7.00 C 2624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 154.1 milliseconds 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1056 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 4 sheets defined 62.9% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 17 through 40 removed outlier: 4.008A pdb=" N ALA A 21 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Proline residue: A 37 - end of helix Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 54 through 84 removed outlier: 4.143A pdb=" N ILE A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 85 through 104 Processing helix chain 'A' and resid 108 through 139 Proline residue: A 130 - end of helix removed outlier: 3.764A pdb=" N PHE A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 4.018A pdb=" N SER A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Proline residue: A 155 - end of helix Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 173 through 192 removed outlier: 4.000A pdb=" N GLY A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 removed outlier: 3.878A pdb=" N PHE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 291 removed outlier: 5.729A pdb=" N SER A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N SER A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 321 removed outlier: 4.013A pdb=" N VAL A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Proline residue: A 314 - end of helix removed outlier: 3.797A pdb=" N ASN A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 330 through 347 removed outlier: 3.745A pdb=" N ALA A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 383 removed outlier: 3.912A pdb=" N TYR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 399 removed outlier: 3.590A pdb=" N THR A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 415 Proline residue: A 406 - end of helix removed outlier: 4.011A pdb=" N ARG A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 449 removed outlier: 3.970A pdb=" N VAL A 428 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 153 through 156 Processing helix chain 'B' and resid 209 through 238 removed outlier: 3.652A pdb=" N THR B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Proline residue: B 235 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 33 Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.067A pdb=" N GLY B 95 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.501A pdb=" N ARG B 166 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 117 removed outlier: 6.449A pdb=" N GLU B 114 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ARG B 203 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE B 116 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 192 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP B 139 " --> pdb=" O LEU B 150 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 885 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: 0.53 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 635 1.29 - 1.42: 1108 1.42 - 1.55: 2307 1.55 - 1.68: 30 1.68 - 1.81: 38 Bond restraints: 4118 Sorted by residual: bond pdb=" C18 G5L A 601 " pdb=" O20 G5L A 601 " ideal model delta sigma weight residual 1.204 1.396 -0.192 2.00e-02 2.50e+03 9.23e+01 bond pdb=" C1 G5L A 601 " pdb=" C2 G5L A 601 " ideal model delta sigma weight residual 1.388 1.526 -0.138 2.00e-02 2.50e+03 4.73e+01 bond pdb=" C3 G5L A 601 " pdb=" C4 G5L A 601 " ideal model delta sigma weight residual 1.388 1.523 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" C5 G5L A 601 " pdb=" C6 G5L A 601 " ideal model delta sigma weight residual 1.391 1.524 -0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" C TYR A 113 " pdb=" O TYR A 113 " ideal model delta sigma weight residual 1.237 1.161 0.076 1.19e-02 7.06e+03 4.05e+01 ... (remaining 4113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 5340 2.70 - 5.41: 245 5.41 - 8.11: 26 8.11 - 10.81: 10 10.81 - 13.52: 3 Bond angle restraints: 5624 Sorted by residual: angle pdb=" CA PRO B 91 " pdb=" N PRO B 91 " pdb=" CD PRO B 91 " ideal model delta sigma weight residual 111.50 97.98 13.52 1.40e+00 5.10e-01 9.32e+01 angle pdb=" CA PRO B 93 " pdb=" N PRO B 93 " pdb=" CD PRO B 93 " ideal model delta sigma weight residual 111.50 99.06 12.44 1.40e+00 5.10e-01 7.90e+01 angle pdb=" CA TYR A 113 " pdb=" C TYR A 113 " pdb=" O TYR A 113 " ideal model delta sigma weight residual 120.42 113.85 6.57 1.06e+00 8.90e-01 3.84e+01 angle pdb=" C TYR A 113 " pdb=" CA TYR A 113 " pdb=" CB TYR A 113 " ideal model delta sigma weight residual 110.85 101.67 9.18 1.70e+00 3.46e-01 2.91e+01 angle pdb=" N ILE B 142 " pdb=" CA ILE B 142 " pdb=" C ILE B 142 " ideal model delta sigma weight residual 108.12 114.95 -6.83 1.34e+00 5.57e-01 2.60e+01 ... (remaining 5619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.71: 2048 15.71 - 31.42: 187 31.42 - 47.13: 74 47.13 - 62.84: 28 62.84 - 78.55: 4 Dihedral angle restraints: 2341 sinusoidal: 679 harmonic: 1662 Sorted by residual: dihedral pdb=" C VAL B 50 " pdb=" N VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual -122.00 -139.05 17.05 0 2.50e+00 1.60e-01 4.65e+01 dihedral pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual 123.40 139.10 -15.70 0 2.50e+00 1.60e-01 3.94e+01 dihedral pdb=" CA ALA A 347 " pdb=" C ALA A 347 " pdb=" N PRO A 348 " pdb=" CA PRO A 348 " ideal model delta harmonic sigma weight residual 180.00 149.79 30.21 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 2338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.365: 652 0.365 - 0.730: 7 0.730 - 1.095: 0 1.095 - 1.461: 0 1.461 - 1.826: 2 Chirality restraints: 661 Sorted by residual: chirality pdb=" CG LEU A 374 " pdb=" CB LEU A 374 " pdb=" CD1 LEU A 374 " pdb=" CD2 LEU A 374 " both_signs ideal model delta sigma weight residual False -2.59 -0.76 -1.83 2.00e-01 2.50e+01 8.33e+01 chirality pdb=" CG LEU A 66 " pdb=" CB LEU A 66 " pdb=" CD1 LEU A 66 " pdb=" CD2 LEU A 66 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.60e+01 chirality pdb=" CA GLU B 172 " pdb=" N GLU B 172 " pdb=" C GLU B 172 " pdb=" CB GLU B 172 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.91e+00 ... (remaining 658 not shown) Planarity restraints: 721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 90 " -0.081 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO B 91 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO B 91 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 91 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 113 " 0.032 2.00e-02 2.50e+03 2.84e-02 1.61e+01 pdb=" CG TYR A 113 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR A 113 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 113 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 113 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 113 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 113 " -0.040 2.00e-02 2.50e+03 pdb=" OH TYR A 113 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 406 " 0.037 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO A 407 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 407 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 407 " 0.030 5.00e-02 4.00e+02 ... (remaining 718 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 31 2.55 - 3.14: 3367 3.14 - 3.73: 6077 3.73 - 4.31: 8329 4.31 - 4.90: 13848 Nonbonded interactions: 31652 Sorted by model distance: nonbonded pdb=" NH1 ARG A 196 " pdb=" O PRO A 197 " model vdw 1.964 3.120 nonbonded pdb=" O TYR A 293 " pdb=" OG SER A 294 " model vdw 2.083 3.040 nonbonded pdb=" O ASN A 107 " pdb=" OG1 THR A 108 " model vdw 2.150 3.040 nonbonded pdb=" O TYR A 140 " pdb=" NH2 ARG A 143 " model vdw 2.215 3.120 nonbonded pdb=" O LEU B 209 " pdb=" N PHE B 212 " model vdw 2.225 3.120 ... (remaining 31647 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.460 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 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 : 0.012 0.192 4118 Z= 0.691 Angle : 1.322 13.517 5624 Z= 0.844 Chirality : 0.133 1.826 661 Planarity : 0.007 0.112 721 Dihedral : 16.623 78.549 1285 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.06 % Favored : 90.77 % Rotamer: Outliers : 12.88 % Allowed : 19.02 % Favored : 68.10 % Cbeta Deviations : 1.89 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.32), residues: 585 helix: -1.47 (0.26), residues: 348 sheet: 0.29 (0.53), residues: 94 loop : -3.68 (0.39), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 142 TYR 0.056 0.003 TYR A 113 PHE 0.017 0.002 PHE A 332 TRP 0.008 0.002 TRP A 18 HIS 0.005 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.01167 ( 4118) covalent geometry : angle 1.32165 ( 5624) hydrogen bonds : bond 0.16673 ( 305) hydrogen bonds : angle 7.33227 ( 885) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 55 time to evaluate : 0.133 Fit side-chains REVERT: A 80 VAL cc_start: 0.8184 (p) cc_final: 0.7946 (m) REVERT: A 87 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7145 (mt) REVERT: A 94 CYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6182 (m) REVERT: A 105 PHE cc_start: 0.6491 (OUTLIER) cc_final: 0.6191 (m-10) REVERT: A 107 ASN cc_start: 0.5961 (p0) cc_final: 0.5755 (p0) REVERT: A 137 LYS cc_start: 0.5748 (OUTLIER) cc_final: 0.5019 (tptt) REVERT: A 139 PHE cc_start: 0.6571 (OUTLIER) cc_final: 0.5804 (m-10) REVERT: A 273 MET cc_start: 0.6638 (ppp) cc_final: 0.6314 (ppp) REVERT: A 398 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: A 446 ARG cc_start: 0.3800 (OUTLIER) cc_final: 0.3467 (mmp80) outliers start: 42 outliers final: 10 residues processed: 85 average time/residue: 0.3861 time to fit residues: 34.3125 Evaluate side-chains 66 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 223 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 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 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.243080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.212729 restraints weight = 4749.288| |-----------------------------------------------------------------------------| r_work (start): 0.4447 rms_B_bonded: 2.09 r_work: 0.4369 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4262 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4118 Z= 0.164 Angle : 0.692 7.291 5624 Z= 0.359 Chirality : 0.043 0.145 661 Planarity : 0.006 0.065 721 Dihedral : 8.176 56.587 666 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 7.67 % Allowed : 20.86 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.34), residues: 585 helix: -0.08 (0.28), residues: 349 sheet: 0.54 (0.48), residues: 111 loop : -3.26 (0.46), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 411 TYR 0.016 0.001 TYR A 445 PHE 0.014 0.001 PHE A 27 TRP 0.007 0.001 TRP A 424 HIS 0.003 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 4118) covalent geometry : angle 0.69175 ( 5624) hydrogen bonds : bond 0.05171 ( 305) hydrogen bonds : angle 5.25065 ( 885) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 60 TRP cc_start: 0.7214 (OUTLIER) cc_final: 0.6989 (m100) REVERT: A 91 VAL cc_start: 0.7617 (t) cc_final: 0.7246 (m) REVERT: A 105 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6534 (m-10) REVERT: A 137 LYS cc_start: 0.6406 (tttt) cc_final: 0.5580 (tptt) REVERT: A 139 PHE cc_start: 0.6113 (OUTLIER) cc_final: 0.4958 (m-10) REVERT: A 147 ASN cc_start: 0.7469 (m-40) cc_final: 0.7046 (m-40) REVERT: A 273 MET cc_start: 0.7755 (ppp) cc_final: 0.7358 (ppp) REVERT: A 391 VAL cc_start: 0.8192 (p) cc_final: 0.7980 (t) REVERT: A 398 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: A 411 ARG cc_start: 0.7367 (ttt90) cc_final: 0.7035 (tpt90) REVERT: B 206 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6020 (mp) REVERT: B 209 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6064 (pt) outliers start: 25 outliers final: 6 residues processed: 87 average time/residue: 0.3019 time to fit residues: 27.7927 Evaluate side-chains 81 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 46 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 35 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 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.237775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.207950 restraints weight = 4740.521| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 2.00 r_work: 0.4343 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4246 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4118 Z= 0.162 Angle : 0.663 7.272 5624 Z= 0.342 Chirality : 0.044 0.169 661 Planarity : 0.005 0.064 721 Dihedral : 7.381 59.556 645 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 8.90 % Allowed : 19.94 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.35), residues: 585 helix: 0.35 (0.28), residues: 357 sheet: 0.75 (0.51), residues: 111 loop : -2.92 (0.48), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 261 TYR 0.019 0.002 TYR A 445 PHE 0.016 0.001 PHE A 27 TRP 0.007 0.001 TRP A 174 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4118) covalent geometry : angle 0.66333 ( 5624) hydrogen bonds : bond 0.04998 ( 305) hydrogen bonds : angle 4.92060 ( 885) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.140 Fit side-chains REVERT: A 27 PHE cc_start: 0.7905 (t80) cc_final: 0.7700 (t80) REVERT: A 60 TRP cc_start: 0.7428 (OUTLIER) cc_final: 0.7138 (m100) REVERT: A 70 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.7357 (t80) REVERT: A 91 VAL cc_start: 0.7571 (t) cc_final: 0.7131 (m) REVERT: A 94 CYS cc_start: 0.7741 (OUTLIER) cc_final: 0.6788 (m) REVERT: A 105 PHE cc_start: 0.6927 (OUTLIER) cc_final: 0.6520 (m-10) REVERT: A 132 LEU cc_start: 0.8384 (mt) cc_final: 0.8166 (pp) REVERT: A 137 LYS cc_start: 0.6469 (tttt) cc_final: 0.5677 (tptt) REVERT: A 139 PHE cc_start: 0.6500 (OUTLIER) cc_final: 0.5268 (m-80) REVERT: A 141 LYS cc_start: 0.6182 (OUTLIER) cc_final: 0.5680 (ptpt) REVERT: A 147 ASN cc_start: 0.7380 (m-40) cc_final: 0.7006 (m-40) REVERT: A 274 PHE cc_start: 0.7708 (m-80) cc_final: 0.7452 (m-80) REVERT: A 302 LEU cc_start: 0.8252 (mt) cc_final: 0.7957 (mm) REVERT: A 379 MET cc_start: 0.7848 (tpt) cc_final: 0.7232 (tpt) REVERT: A 391 VAL cc_start: 0.8229 (p) cc_final: 0.7949 (t) REVERT: A 398 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6579 (mp0) REVERT: A 411 ARG cc_start: 0.7353 (ttt90) cc_final: 0.7011 (tpt90) REVERT: A 414 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6563 (t0) REVERT: B 206 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6149 (mp) REVERT: B 209 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6379 (pt) outliers start: 29 outliers final: 6 residues processed: 93 average time/residue: 0.2966 time to fit residues: 29.3044 Evaluate side-chains 89 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 0.0770 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 40.0000 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.237521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.207720 restraints weight = 4734.757| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 1.95 r_work: 0.4346 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4241 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4118 Z= 0.152 Angle : 0.661 8.254 5624 Z= 0.337 Chirality : 0.043 0.187 661 Planarity : 0.005 0.065 721 Dihedral : 7.371 57.346 645 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 7.67 % Allowed : 22.70 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.36), residues: 585 helix: 0.50 (0.29), residues: 358 sheet: 0.89 (0.51), residues: 111 loop : -2.64 (0.52), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 203 TYR 0.016 0.001 TYR A 445 PHE 0.014 0.001 PHE A 27 TRP 0.007 0.001 TRP A 174 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4118) covalent geometry : angle 0.66112 ( 5624) hydrogen bonds : bond 0.04682 ( 305) hydrogen bonds : angle 4.81881 ( 885) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.126 Fit side-chains REVERT: A 27 PHE cc_start: 0.7864 (t80) cc_final: 0.7647 (t80) REVERT: A 60 TRP cc_start: 0.7356 (OUTLIER) cc_final: 0.7067 (m100) REVERT: A 70 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.7324 (t80) REVERT: A 94 CYS cc_start: 0.7788 (OUTLIER) cc_final: 0.6820 (m) REVERT: A 105 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.6630 (m-10) REVERT: A 110 GLN cc_start: 0.7878 (mp10) cc_final: 0.7677 (pm20) REVERT: A 126 PHE cc_start: 0.7024 (m-10) cc_final: 0.6785 (m-10) REVERT: A 132 LEU cc_start: 0.8295 (mt) cc_final: 0.8067 (pp) REVERT: A 137 LYS cc_start: 0.6337 (tttt) cc_final: 0.5573 (tptt) REVERT: A 138 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.6804 (m-80) REVERT: A 139 PHE cc_start: 0.6334 (OUTLIER) cc_final: 0.5459 (m-10) REVERT: A 141 LYS cc_start: 0.5989 (pmtt) cc_final: 0.5675 (pmtt) REVERT: A 147 ASN cc_start: 0.7418 (m-40) cc_final: 0.7017 (m-40) REVERT: A 195 MET cc_start: 0.7314 (mmm) cc_final: 0.6993 (mmt) REVERT: A 282 VAL cc_start: 0.8862 (t) cc_final: 0.8638 (p) REVERT: A 329 ILE cc_start: 0.8154 (tp) cc_final: 0.7780 (tt) REVERT: A 379 MET cc_start: 0.7915 (tpt) cc_final: 0.7567 (tpt) REVERT: A 391 VAL cc_start: 0.8198 (p) cc_final: 0.7902 (t) REVERT: A 398 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: A 411 ARG cc_start: 0.7450 (ttt90) cc_final: 0.7101 (tpt90) REVERT: A 414 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6548 (t0) REVERT: A 415 MET cc_start: 0.6187 (OUTLIER) cc_final: 0.5678 (ptm) outliers start: 25 outliers final: 10 residues processed: 97 average time/residue: 0.2941 time to fit residues: 30.0503 Evaluate side-chains 94 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 206 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 50.0000 chunk 11 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 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 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.237665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.207121 restraints weight = 4688.477| |-----------------------------------------------------------------------------| r_work (start): 0.4407 rms_B_bonded: 2.13 r_work: 0.4324 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4216 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4118 Z= 0.147 Angle : 0.652 8.740 5624 Z= 0.332 Chirality : 0.043 0.155 661 Planarity : 0.005 0.065 721 Dihedral : 7.317 54.668 645 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 8.90 % Allowed : 23.93 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.36), residues: 585 helix: 0.55 (0.29), residues: 358 sheet: 0.99 (0.52), residues: 109 loop : -2.34 (0.54), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 203 TYR 0.018 0.001 TYR A 445 PHE 0.016 0.001 PHE A 27 TRP 0.006 0.001 TRP A 174 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4118) covalent geometry : angle 0.65160 ( 5624) hydrogen bonds : bond 0.04608 ( 305) hydrogen bonds : angle 4.72454 ( 885) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.115 Fit side-chains REVERT: A 27 PHE cc_start: 0.7896 (t80) cc_final: 0.7694 (t80) REVERT: A 60 TRP cc_start: 0.7271 (OUTLIER) cc_final: 0.6950 (m100) REVERT: A 70 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.7305 (t80) REVERT: A 88 VAL cc_start: 0.8361 (t) cc_final: 0.8084 (m) REVERT: A 94 CYS cc_start: 0.7666 (OUTLIER) cc_final: 0.6673 (m) REVERT: A 105 PHE cc_start: 0.6913 (OUTLIER) cc_final: 0.6491 (m-10) REVERT: A 126 PHE cc_start: 0.6936 (m-10) cc_final: 0.6687 (m-10) REVERT: A 132 LEU cc_start: 0.8358 (mt) cc_final: 0.8063 (pp) REVERT: A 137 LYS cc_start: 0.6319 (tttt) cc_final: 0.5455 (tptt) REVERT: A 138 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.6746 (m-80) REVERT: A 139 PHE cc_start: 0.6230 (OUTLIER) cc_final: 0.5406 (m-80) REVERT: A 147 ASN cc_start: 0.7421 (m-40) cc_final: 0.6967 (m-40) REVERT: A 195 MET cc_start: 0.7393 (mmm) cc_final: 0.7178 (mmt) REVERT: A 282 VAL cc_start: 0.8904 (t) cc_final: 0.8637 (p) REVERT: A 302 LEU cc_start: 0.8250 (mt) cc_final: 0.7894 (mm) REVERT: A 329 ILE cc_start: 0.8179 (tp) cc_final: 0.7789 (tt) REVERT: A 379 MET cc_start: 0.7799 (tpt) cc_final: 0.7303 (tpt) REVERT: A 391 VAL cc_start: 0.8133 (p) cc_final: 0.7856 (t) REVERT: A 398 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: A 411 ARG cc_start: 0.7613 (ttt90) cc_final: 0.7148 (tpt90) REVERT: A 414 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6509 (t0) REVERT: A 415 MET cc_start: 0.6170 (OUTLIER) cc_final: 0.5677 (ptm) REVERT: B 206 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6568 (pp) outliers start: 29 outliers final: 7 residues processed: 100 average time/residue: 0.2943 time to fit residues: 31.1533 Evaluate side-chains 94 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 206 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 14 optimal weight: 0.0070 chunk 41 optimal weight: 40.0000 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 50.0000 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 overall best weight: 1.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.233069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.204202 restraints weight = 4881.517| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 2.06 r_work: 0.4267 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4163 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4118 Z= 0.196 Angle : 0.722 7.948 5624 Z= 0.370 Chirality : 0.046 0.206 661 Planarity : 0.005 0.063 721 Dihedral : 7.641 57.727 645 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 8.90 % Allowed : 25.46 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.36), residues: 585 helix: 0.29 (0.28), residues: 361 sheet: 0.89 (0.52), residues: 109 loop : -2.17 (0.55), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 203 TYR 0.025 0.002 TYR A 445 PHE 0.015 0.001 PHE A 27 TRP 0.006 0.001 TRP A 174 HIS 0.004 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 4118) covalent geometry : angle 0.72249 ( 5624) hydrogen bonds : bond 0.05447 ( 305) hydrogen bonds : angle 5.13305 ( 885) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.164 Fit side-chains REVERT: A 27 PHE cc_start: 0.7935 (t80) cc_final: 0.7713 (t80) REVERT: A 60 TRP cc_start: 0.7459 (OUTLIER) cc_final: 0.7111 (m100) REVERT: A 70 TYR cc_start: 0.7799 (t80) cc_final: 0.7432 (t80) REVERT: A 91 VAL cc_start: 0.7663 (t) cc_final: 0.7158 (m) REVERT: A 94 CYS cc_start: 0.7597 (OUTLIER) cc_final: 0.6448 (m) REVERT: A 105 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.6484 (m-10) REVERT: A 126 PHE cc_start: 0.7024 (m-10) cc_final: 0.6750 (m-10) REVERT: A 132 LEU cc_start: 0.8423 (mt) cc_final: 0.8121 (pp) REVERT: A 134 MET cc_start: 0.8434 (tpp) cc_final: 0.7600 (mmt) REVERT: A 138 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.6826 (m-80) REVERT: A 139 PHE cc_start: 0.6422 (OUTLIER) cc_final: 0.5691 (m-80) REVERT: A 147 ASN cc_start: 0.7411 (m-40) cc_final: 0.6914 (m-40) REVERT: A 195 MET cc_start: 0.7691 (mmm) cc_final: 0.7463 (mmt) REVERT: A 302 LEU cc_start: 0.8356 (mt) cc_final: 0.8058 (mm) REVERT: A 329 ILE cc_start: 0.8401 (tp) cc_final: 0.7967 (tt) REVERT: A 356 PHE cc_start: 0.7524 (m-80) cc_final: 0.7197 (m-80) REVERT: A 379 MET cc_start: 0.7811 (tpt) cc_final: 0.7284 (tpt) REVERT: A 386 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6860 (mtt-85) REVERT: A 391 VAL cc_start: 0.8224 (p) cc_final: 0.7911 (t) REVERT: A 398 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: A 411 ARG cc_start: 0.7620 (ttt90) cc_final: 0.7232 (tpt90) REVERT: A 414 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.6888 (t0) REVERT: A 415 MET cc_start: 0.6358 (OUTLIER) cc_final: 0.5912 (ptm) REVERT: B 206 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6619 (pp) outliers start: 29 outliers final: 11 residues processed: 98 average time/residue: 0.2758 time to fit residues: 28.7782 Evaluate side-chains 104 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 25 optimal weight: 0.0170 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.238656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.210798 restraints weight = 4859.005| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 2.08 r_work: 0.4322 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4216 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4118 Z= 0.138 Angle : 0.683 10.497 5624 Z= 0.335 Chirality : 0.042 0.169 661 Planarity : 0.005 0.065 721 Dihedral : 6.990 59.031 645 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 8.28 % Allowed : 28.22 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.36), residues: 585 helix: 0.65 (0.29), residues: 362 sheet: 1.01 (0.52), residues: 109 loop : -2.04 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 203 TYR 0.010 0.001 TYR A 445 PHE 0.017 0.001 PHE A 27 TRP 0.008 0.001 TRP A 174 HIS 0.002 0.000 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4118) covalent geometry : angle 0.68330 ( 5624) hydrogen bonds : bond 0.04420 ( 305) hydrogen bonds : angle 4.79218 ( 885) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.115 Fit side-chains REVERT: A 60 TRP cc_start: 0.7397 (OUTLIER) cc_final: 0.7037 (m100) REVERT: A 70 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.7228 (t80) REVERT: A 88 VAL cc_start: 0.8373 (t) cc_final: 0.8125 (m) REVERT: A 94 CYS cc_start: 0.7616 (OUTLIER) cc_final: 0.6792 (m) REVERT: A 105 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.6410 (m-10) REVERT: A 126 PHE cc_start: 0.6938 (m-10) cc_final: 0.6733 (m-10) REVERT: A 132 LEU cc_start: 0.8310 (mt) cc_final: 0.8004 (pp) REVERT: A 134 MET cc_start: 0.8358 (tpp) cc_final: 0.7630 (mmt) REVERT: A 137 LYS cc_start: 0.6218 (tttt) cc_final: 0.5472 (tptt) REVERT: A 138 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.6509 (m-80) REVERT: A 139 PHE cc_start: 0.6164 (OUTLIER) cc_final: 0.5425 (m-80) REVERT: A 147 ASN cc_start: 0.7400 (m-40) cc_final: 0.6983 (m-40) REVERT: A 188 CYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7480 (t) REVERT: A 195 MET cc_start: 0.7546 (mmm) cc_final: 0.7304 (mmt) REVERT: A 302 LEU cc_start: 0.8229 (mt) cc_final: 0.7890 (mm) REVERT: A 329 ILE cc_start: 0.8107 (tp) cc_final: 0.7685 (tt) REVERT: A 356 PHE cc_start: 0.7420 (m-80) cc_final: 0.7058 (m-80) REVERT: A 379 MET cc_start: 0.7797 (tpt) cc_final: 0.7483 (tpt) REVERT: A 391 VAL cc_start: 0.8230 (p) cc_final: 0.7907 (t) REVERT: A 411 ARG cc_start: 0.7476 (ttt90) cc_final: 0.7090 (tpt90) REVERT: A 414 ASP cc_start: 0.7150 (OUTLIER) cc_final: 0.6450 (t0) REVERT: A 415 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.5806 (ptm) REVERT: B 206 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6460 (pp) outliers start: 27 outliers final: 11 residues processed: 94 average time/residue: 0.2916 time to fit residues: 29.0672 Evaluate side-chains 96 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 50.0000 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 40.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.236228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.207848 restraints weight = 4748.398| |-----------------------------------------------------------------------------| r_work (start): 0.4399 rms_B_bonded: 2.09 r_work: 0.4303 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4196 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4118 Z= 0.157 Angle : 0.696 10.031 5624 Z= 0.345 Chirality : 0.044 0.194 661 Planarity : 0.005 0.064 721 Dihedral : 6.307 47.132 642 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 7.98 % Allowed : 28.22 % Favored : 63.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.37), residues: 585 helix: 0.61 (0.29), residues: 362 sheet: 1.05 (0.52), residues: 109 loop : -1.96 (0.57), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 203 TYR 0.016 0.001 TYR A 445 PHE 0.021 0.001 PHE A 27 TRP 0.007 0.001 TRP A 174 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 4118) covalent geometry : angle 0.69598 ( 5624) hydrogen bonds : bond 0.04693 ( 305) hydrogen bonds : angle 4.85055 ( 885) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.119 Fit side-chains REVERT: A 60 TRP cc_start: 0.7392 (OUTLIER) cc_final: 0.7034 (m100) REVERT: A 70 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.7236 (t80) REVERT: A 91 VAL cc_start: 0.7663 (t) cc_final: 0.7154 (m) REVERT: A 94 CYS cc_start: 0.7595 (OUTLIER) cc_final: 0.6748 (m) REVERT: A 105 PHE cc_start: 0.6837 (OUTLIER) cc_final: 0.6436 (m-10) REVERT: A 126 PHE cc_start: 0.6947 (m-10) cc_final: 0.6680 (m-10) REVERT: A 132 LEU cc_start: 0.8364 (mt) cc_final: 0.8035 (pp) REVERT: A 138 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.6702 (m-80) REVERT: A 139 PHE cc_start: 0.6237 (OUTLIER) cc_final: 0.5535 (m-80) REVERT: A 147 ASN cc_start: 0.7382 (m-40) cc_final: 0.6877 (m-40) REVERT: A 195 MET cc_start: 0.7592 (mmm) cc_final: 0.7295 (mmt) REVERT: A 302 LEU cc_start: 0.8285 (mt) cc_final: 0.7948 (mm) REVERT: A 356 PHE cc_start: 0.7470 (m-80) cc_final: 0.7114 (m-80) REVERT: A 378 LEU cc_start: 0.7654 (tm) cc_final: 0.7434 (tp) REVERT: A 379 MET cc_start: 0.7831 (tpt) cc_final: 0.7524 (tpt) REVERT: A 391 VAL cc_start: 0.8237 (p) cc_final: 0.7917 (t) REVERT: A 411 ARG cc_start: 0.7563 (ttt90) cc_final: 0.7140 (tpt90) REVERT: A 414 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6562 (t0) REVERT: A 415 MET cc_start: 0.6265 (OUTLIER) cc_final: 0.5792 (ptm) outliers start: 26 outliers final: 13 residues processed: 89 average time/residue: 0.2887 time to fit residues: 27.3088 Evaluate side-chains 95 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 220 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 37 optimal weight: 50.0000 chunk 26 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 34 optimal weight: 0.0470 chunk 46 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 39 optimal weight: 40.0000 chunk 12 optimal weight: 0.0170 chunk 3 optimal weight: 3.9990 overall best weight: 1.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.227698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.199151 restraints weight = 4922.660| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.13 r_work: 0.4232 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4123 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4118 Z= 0.220 Angle : 0.772 10.831 5624 Z= 0.391 Chirality : 0.047 0.196 661 Planarity : 0.006 0.063 721 Dihedral : 6.258 52.541 638 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 7.06 % Allowed : 29.75 % Favored : 63.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.36), residues: 585 helix: 0.11 (0.28), residues: 358 sheet: 0.89 (0.54), residues: 104 loop : -2.12 (0.52), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 203 TYR 0.025 0.002 TYR A 445 PHE 0.015 0.002 PHE B 227 TRP 0.006 0.001 TRP A 174 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 4118) covalent geometry : angle 0.77189 ( 5624) hydrogen bonds : bond 0.05708 ( 305) hydrogen bonds : angle 5.31018 ( 885) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.144 Fit side-chains REVERT: A 27 PHE cc_start: 0.7833 (t80) cc_final: 0.7586 (t80) REVERT: A 60 TRP cc_start: 0.7295 (OUTLIER) cc_final: 0.6841 (m100) REVERT: A 70 TYR cc_start: 0.7816 (t80) cc_final: 0.7288 (t80) REVERT: A 91 VAL cc_start: 0.7479 (t) cc_final: 0.6849 (m) REVERT: A 94 CYS cc_start: 0.7427 (OUTLIER) cc_final: 0.6364 (m) REVERT: A 105 PHE cc_start: 0.6832 (OUTLIER) cc_final: 0.6313 (m-10) REVERT: A 126 PHE cc_start: 0.7010 (m-10) cc_final: 0.6683 (m-10) REVERT: A 132 LEU cc_start: 0.8351 (mt) cc_final: 0.7916 (pp) REVERT: A 138 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.6581 (m-80) REVERT: A 139 PHE cc_start: 0.6159 (OUTLIER) cc_final: 0.5621 (m-80) REVERT: A 147 ASN cc_start: 0.7456 (m-40) cc_final: 0.6860 (m-40) REVERT: A 195 MET cc_start: 0.7575 (mmm) cc_final: 0.7251 (mmt) REVERT: A 302 LEU cc_start: 0.8241 (mt) cc_final: 0.7909 (mm) REVERT: A 345 MET cc_start: 0.7227 (tpt) cc_final: 0.7004 (mmm) REVERT: A 356 PHE cc_start: 0.7512 (m-80) cc_final: 0.7110 (m-80) REVERT: A 379 MET cc_start: 0.7694 (tpt) cc_final: 0.7141 (tpt) REVERT: A 386 ARG cc_start: 0.7327 (mtp85) cc_final: 0.7112 (mtp180) REVERT: A 391 VAL cc_start: 0.8137 (p) cc_final: 0.7850 (t) REVERT: A 411 ARG cc_start: 0.7481 (ttt90) cc_final: 0.6953 (tpt90) REVERT: A 414 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.6818 (t0) outliers start: 23 outliers final: 10 residues processed: 95 average time/residue: 0.2326 time to fit residues: 23.7205 Evaluate side-chains 97 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 220 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 41 optimal weight: 50.0000 chunk 39 optimal weight: 20.0000 chunk 37 optimal weight: 50.0000 chunk 43 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 49 optimal weight: 0.0370 overall best weight: 0.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.232322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.204748 restraints weight = 4873.618| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 2.13 r_work: 0.4282 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4175 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4118 Z= 0.152 Angle : 0.729 12.193 5624 Z= 0.356 Chirality : 0.044 0.181 661 Planarity : 0.005 0.065 721 Dihedral : 5.733 48.082 638 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.21 % Allowed : 32.21 % Favored : 62.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.36), residues: 585 helix: 0.47 (0.28), residues: 361 sheet: 0.90 (0.53), residues: 107 loop : -1.99 (0.53), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 201 TYR 0.013 0.001 TYR A 445 PHE 0.013 0.001 PHE A 51 TRP 0.008 0.001 TRP A 174 HIS 0.005 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 4118) covalent geometry : angle 0.72933 ( 5624) hydrogen bonds : bond 0.04718 ( 305) hydrogen bonds : angle 4.95705 ( 885) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.140 Fit side-chains REVERT: A 60 TRP cc_start: 0.7397 (OUTLIER) cc_final: 0.6968 (m100) REVERT: A 91 VAL cc_start: 0.7604 (t) cc_final: 0.7035 (m) REVERT: A 94 CYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6594 (m) REVERT: A 105 PHE cc_start: 0.6829 (OUTLIER) cc_final: 0.6418 (m-10) REVERT: A 126 PHE cc_start: 0.6909 (m-10) cc_final: 0.6581 (m-10) REVERT: A 132 LEU cc_start: 0.8360 (mt) cc_final: 0.8000 (pp) REVERT: A 134 MET cc_start: 0.8456 (tpp) cc_final: 0.7525 (mmt) REVERT: A 138 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.6437 (m-80) REVERT: A 139 PHE cc_start: 0.6151 (OUTLIER) cc_final: 0.5590 (m-80) REVERT: A 147 ASN cc_start: 0.7375 (m-40) cc_final: 0.6838 (m-40) REVERT: A 195 MET cc_start: 0.7525 (mmm) cc_final: 0.7182 (mmt) REVERT: A 302 LEU cc_start: 0.8230 (mt) cc_final: 0.7911 (mm) REVERT: A 329 ILE cc_start: 0.8081 (tp) cc_final: 0.7553 (tt) REVERT: A 356 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.7041 (m-80) REVERT: A 379 MET cc_start: 0.7762 (tpt) cc_final: 0.7352 (tpt) REVERT: A 391 VAL cc_start: 0.8198 (p) cc_final: 0.7894 (t) REVERT: A 411 ARG cc_start: 0.7449 (ttt90) cc_final: 0.6970 (tpt90) REVERT: A 414 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6475 (t0) outliers start: 17 outliers final: 9 residues processed: 84 average time/residue: 0.2592 time to fit residues: 23.3672 Evaluate side-chains 88 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 220 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.232134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.204340 restraints weight = 4906.565| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.16 r_work: 0.4271 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4164 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4118 Z= 0.155 Angle : 0.727 11.886 5624 Z= 0.356 Chirality : 0.044 0.178 661 Planarity : 0.005 0.064 721 Dihedral : 5.669 48.555 638 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.83 % Allowed : 31.29 % Favored : 62.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.36), residues: 585 helix: 0.57 (0.29), residues: 361 sheet: 0.97 (0.53), residues: 107 loop : -1.98 (0.53), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 201 TYR 0.016 0.001 TYR A 445 PHE 0.024 0.001 PHE A 27 TRP 0.006 0.001 TRP A 174 HIS 0.004 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 4118) covalent geometry : angle 0.72743 ( 5624) hydrogen bonds : bond 0.04726 ( 305) hydrogen bonds : angle 4.89156 ( 885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1772.34 seconds wall clock time: 30 minutes 46.38 seconds (1846.38 seconds total)