Starting phenix.real_space_refine on Thu Sep 10 21:47:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cko_30389/09_2026/7cko_30389.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cko_30389/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7cko_30389/09_2026/7cko_30389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cko_30389/09_2026/7cko_30389.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7cko_30389/09_2026/7cko_30389.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cko_30389/09_2026/7cko_30389.cif" model { file = "/net/cci-nas-00/data/ceres_data/7cko_30389/09_2026/7cko_30389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cko_30389/09_2026/7cko_30389.cif" } 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-2.2.1-6174/lib/python3.11/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: 1.00, per 1000 atoms: 0.25 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: 0.36 Conformation dependent library (CDL) restraints added in 128.3 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: 0.08 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: 0.58 Time building geometry restraints manager: 0.39 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: 2046 15.71 - 31.42: 187 31.42 - 47.13: 74 47.13 - 62.84: 28 62.84 - 78.55: 4 Dihedral angle restraints: 2339 sinusoidal: 677 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 2336 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: 1.380 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: 0.000 Set scattering table: 0.010 Process input model: 5.280 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:8.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 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 : 16.636 78.549 1283 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/Z covalent geometry : bond 0.01167 / 0.69 ( 4118) covalent geometry : angle 1.32165 / 0.84 ( 5624) hydrogen bonds : bond 0.16673 / 10.90 ( 305) hydrogen bonds : angle 7.33227 / 5.41 ( 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 : 0.107 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: 0.4048 time to fit residues: 35.8916 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 : 0.136 ------------------------------------------------------------------------------- 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... A 165 ASN A 413 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.243352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.212944 restraints weight = 4751.157| |-----------------------------------------------------------------------------| r_work (start): 0.4446 rms_B_bonded: 2.11 r_work: 0.4368 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4260 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4118 Z= 0.162 Angle : 0.690 7.337 5624 Z= 0.358 Chirality : 0.043 0.150 661 Planarity : 0.006 0.065 721 Dihedral : 8.208 56.488 664 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % 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: -0.99 (0.34), residues: 585 helix: -0.08 (0.28), residues: 349 sheet: 0.57 (0.49), residues: 111 loop : -3.27 (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/Z covalent geometry : bond 0.00343 / 0.16 ( 4118) covalent geometry : angle 0.68999 / 0.36 ( 5624) hydrogen bonds : bond 0.05197 / 3.46 ( 305) hydrogen bonds : angle 5.25712 / 3.93 ( 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 96 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 60 TRP cc_start: 0.7225 (OUTLIER) cc_final: 0.6979 (m100) REVERT: A 91 VAL cc_start: 0.7616 (t) cc_final: 0.7314 (m) REVERT: A 105 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.6544 (m-10) REVERT: A 137 LYS cc_start: 0.6416 (tttt) cc_final: 0.5587 (tptt) REVERT: A 139 PHE cc_start: 0.6066 (OUTLIER) cc_final: 0.4974 (m-10) REVERT: A 147 ASN cc_start: 0.7466 (m-40) cc_final: 0.7045 (m-40) REVERT: A 273 MET cc_start: 0.7733 (ppp) cc_final: 0.7333 (ppp) REVERT: A 282 VAL cc_start: 0.8796 (t) cc_final: 0.8546 (p) REVERT: A 391 VAL cc_start: 0.8188 (p) cc_final: 0.7965 (t) REVERT: A 398 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: A 411 ARG cc_start: 0.7361 (ttt90) cc_final: 0.7037 (tpt90) REVERT: B 206 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6014 (mp) REVERT: B 209 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6045 (pt) outliers start: 25 outliers final: 6 residues processed: 87 average time/residue: 0.2827 time to fit residues: 26.0266 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 : 0.129 ------------------------------------------------------------------------------- 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: 0.8980 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 46 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.239397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.209597 restraints weight = 4738.845| |-----------------------------------------------------------------------------| r_work (start): 0.4419 rms_B_bonded: 1.98 r_work: 0.4334 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4227 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3335 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= 0.159 Angle : 0.659 7.260 5624 Z= 0.340 Chirality : 0.043 0.210 661 Planarity : 0.005 0.065 721 Dihedral : 7.311 59.154 643 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 7.98 % Allowed : 20.55 % 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: -0.32 (0.36), residues: 585 helix: 0.37 (0.29), residues: 357 sheet: 0.81 (0.51), residues: 111 loop : -2.88 (0.49), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 261 TYR 0.016 0.001 TYR A 445 PHE 0.015 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/Z covalent geometry : bond 0.00335 / 0.16 ( 4118) covalent geometry : angle 0.65903 / 0.34 ( 5624) hydrogen bonds : bond 0.04976 / 3.35 ( 305) hydrogen bonds : angle 4.91940 / 3.69 ( 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 101 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.115 Fit side-chains REVERT: A 27 PHE cc_start: 0.7944 (t80) cc_final: 0.7724 (t80) REVERT: A 60 TRP cc_start: 0.7350 (OUTLIER) cc_final: 0.7054 (m100) REVERT: A 70 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.7254 (t80) REVERT: A 91 VAL cc_start: 0.7597 (t) cc_final: 0.7163 (m) REVERT: A 94 CYS cc_start: 0.7762 (OUTLIER) cc_final: 0.6785 (m) REVERT: A 105 PHE cc_start: 0.6917 (OUTLIER) cc_final: 0.6562 (m-10) REVERT: A 137 LYS cc_start: 0.6460 (tttt) cc_final: 0.5613 (tptt) REVERT: A 139 PHE cc_start: 0.6384 (OUTLIER) cc_final: 0.5235 (m-80) REVERT: A 141 LYS cc_start: 0.5972 (OUTLIER) cc_final: 0.5499 (ptpt) REVERT: A 147 ASN cc_start: 0.7470 (m-40) cc_final: 0.7163 (m-40) REVERT: A 391 VAL cc_start: 0.8243 (p) cc_final: 0.7980 (t) REVERT: A 398 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: A 411 ARG cc_start: 0.7418 (ttt90) cc_final: 0.7059 (tpt90) REVERT: A 414 ASP cc_start: 0.6760 (OUTLIER) cc_final: 0.6328 (t0) REVERT: B 206 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6391 (mp) REVERT: B 209 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6341 (pp) outliers start: 26 outliers final: 7 residues processed: 90 average time/residue: 0.2855 time to fit residues: 27.2350 Evaluate side-chains 86 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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 188 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 352 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 40.0000 chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 30.0000 chunk 48 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.237948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.208020 restraints weight = 4725.501| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 1.97 r_work: 0.4342 rms_B_bonded: 2.28 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: 0.7050 moved from start: 0.3915 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= 0.153 Angle : 0.657 7.930 5624 Z= 0.336 Chirality : 0.043 0.174 661 Planarity : 0.005 0.065 721 Dihedral : 7.431 58.217 643 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 8.90 % Allowed : 21.47 % 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: -0.12 (0.36), residues: 585 helix: 0.47 (0.29), residues: 358 sheet: 0.92 (0.51), residues: 111 loop : -2.63 (0.52), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 261 TYR 0.015 0.001 TYR A 445 PHE 0.015 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/Z covalent geometry : bond 0.00332 / 0.15 ( 4118) covalent geometry : angle 0.65654 / 0.34 ( 5624) hydrogen bonds : bond 0.04779 / 3.22 ( 305) hydrogen bonds : angle 4.86576 / 3.63 ( 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 108 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.132 Fit side-chains REVERT: A 60 TRP cc_start: 0.7335 (OUTLIER) cc_final: 0.7072 (m100) REVERT: A 70 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.7272 (t80) REVERT: A 91 VAL cc_start: 0.7611 (t) cc_final: 0.7199 (m) REVERT: A 94 CYS cc_start: 0.7773 (OUTLIER) cc_final: 0.6833 (m) REVERT: A 105 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.6597 (m-10) REVERT: A 126 PHE cc_start: 0.7109 (m-10) cc_final: 0.6798 (m-10) REVERT: A 137 LYS cc_start: 0.6343 (tttt) cc_final: 0.5581 (tptt) REVERT: A 138 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.6915 (m-80) REVERT: A 139 PHE cc_start: 0.6427 (OUTLIER) cc_final: 0.5213 (m-80) REVERT: A 141 LYS cc_start: 0.5982 (pmtt) cc_final: 0.5459 (ptpt) REVERT: A 147 ASN cc_start: 0.7442 (m-40) cc_final: 0.7090 (m-40) REVERT: A 274 PHE cc_start: 0.7662 (m-80) cc_final: 0.7441 (m-80) REVERT: A 282 VAL cc_start: 0.8868 (t) cc_final: 0.8648 (p) REVERT: A 391 VAL cc_start: 0.8177 (p) cc_final: 0.7892 (t) REVERT: A 398 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: A 411 ARG cc_start: 0.7458 (ttt90) cc_final: 0.7096 (tpt90) REVERT: A 414 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6594 (t0) REVERT: A 415 MET cc_start: 0.6168 (OUTLIER) cc_final: 0.5790 (ptm) REVERT: B 209 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6294 (pt) outliers start: 29 outliers final: 10 residues processed: 97 average time/residue: 0.2648 time to fit residues: 27.2482 Evaluate side-chains 94 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 209 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 8.9990 chunk 27 optimal weight: 0.0070 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.240848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.210574 restraints weight = 4729.496| |-----------------------------------------------------------------------------| r_work (start): 0.4438 rms_B_bonded: 2.04 r_work: 0.4351 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4250 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.4239 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= 0.140 Angle : 0.665 8.692 5624 Z= 0.334 Chirality : 0.043 0.159 661 Planarity : 0.005 0.065 721 Dihedral : 7.274 54.982 643 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 8.28 % Allowed : 23.93 % Favored : 67.79 % 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: 0.11 (0.36), residues: 585 helix: 0.59 (0.29), residues: 358 sheet: 1.10 (0.52), residues: 109 loop : -2.38 (0.54), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 203 TYR 0.013 0.001 TYR A 445 PHE 0.022 0.001 PHE A 27 TRP 0.007 0.001 TRP A 174 HIS 0.001 0.000 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 4118) covalent geometry : angle 0.66537 / 0.33 ( 5624) hydrogen bonds : bond 0.04530 / 3.08 ( 305) hydrogen bonds : angle 4.67101 / 3.46 ( 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 106 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.121 Fit side-chains REVERT: A 60 TRP cc_start: 0.7304 (OUTLIER) cc_final: 0.7022 (m100) REVERT: A 70 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.7239 (t80) REVERT: A 94 CYS cc_start: 0.7765 (OUTLIER) cc_final: 0.6791 (m) REVERT: A 105 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.6542 (m-10) REVERT: A 126 PHE cc_start: 0.7049 (m-10) cc_final: 0.6791 (m-10) REVERT: A 137 LYS cc_start: 0.6363 (tttt) cc_final: 0.5546 (tptt) REVERT: A 138 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.6755 (m-80) REVERT: A 139 PHE cc_start: 0.6276 (OUTLIER) cc_final: 0.5499 (m-80) REVERT: A 147 ASN cc_start: 0.7453 (m-40) cc_final: 0.7049 (m-40) REVERT: A 282 VAL cc_start: 0.8851 (t) cc_final: 0.8631 (p) REVERT: A 302 LEU cc_start: 0.8246 (mt) cc_final: 0.7909 (mm) REVERT: A 313 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7572 (ttt-90) REVERT: A 391 VAL cc_start: 0.8195 (p) cc_final: 0.7922 (t) REVERT: A 398 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: A 411 ARG cc_start: 0.7528 (ttt90) cc_final: 0.7106 (tpt90) REVERT: A 414 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6511 (t0) REVERT: A 415 MET cc_start: 0.6121 (OUTLIER) cc_final: 0.5756 (ptm) REVERT: B 206 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6742 (pp) REVERT: B 209 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6414 (pp) outliers start: 27 outliers final: 7 residues processed: 97 average time/residue: 0.2532 time to fit residues: 26.1260 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 : 0.136 ------------------------------------------------------------------------------- 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 313 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 41 optimal weight: 40.0000 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 50.0000 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.232606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.203464 restraints weight = 4864.572| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 2.03 r_work: 0.4265 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4161 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.4666 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= 0.226 Angle : 0.782 10.572 5624 Z= 0.397 Chirality : 0.048 0.214 661 Planarity : 0.006 0.064 721 Dihedral : 7.730 59.715 643 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 8.90 % Allowed : 26.38 % Favored : 64.72 % 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: -0.42 (0.36), residues: 585 helix: 0.08 (0.28), residues: 361 sheet: 0.87 (0.52), residues: 109 loop : -2.29 (0.55), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 203 TYR 0.026 0.002 TYR A 445 PHE 0.017 0.002 PHE B 227 TRP 0.006 0.001 TRP A 424 HIS 0.005 0.002 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 ( 4118) covalent geometry : angle 0.78205 / 0.40 ( 5624) hydrogen bonds : bond 0.05840 / 3.91 ( 305) hydrogen bonds : angle 5.24755 / 3.89 ( 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 112 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.107 Fit side-chains REVERT: A 27 PHE cc_start: 0.7902 (t80) cc_final: 0.7598 (t80) REVERT: A 60 TRP cc_start: 0.7434 (OUTLIER) cc_final: 0.7087 (m100) REVERT: A 70 TYR cc_start: 0.7895 (t80) cc_final: 0.7468 (t80) REVERT: A 91 VAL cc_start: 0.7697 (t) cc_final: 0.7198 (m) REVERT: A 94 CYS cc_start: 0.7662 (OUTLIER) cc_final: 0.6551 (m) REVERT: A 105 PHE cc_start: 0.6974 (OUTLIER) cc_final: 0.6511 (m-10) REVERT: A 126 PHE cc_start: 0.7117 (m-10) cc_final: 0.6785 (m-10) REVERT: A 138 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7043 (m-80) REVERT: A 139 PHE cc_start: 0.6383 (OUTLIER) cc_final: 0.5592 (m-80) REVERT: A 147 ASN cc_start: 0.7497 (m-40) cc_final: 0.6996 (m-40) REVERT: A 275 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7752 (m-80) REVERT: A 302 LEU cc_start: 0.8378 (mt) cc_final: 0.8066 (mm) REVERT: A 356 PHE cc_start: 0.7472 (m-80) cc_final: 0.7215 (m-80) REVERT: A 391 VAL cc_start: 0.8230 (p) cc_final: 0.7944 (t) REVERT: A 398 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: A 411 ARG cc_start: 0.7674 (ttt90) cc_final: 0.7243 (tpt90) REVERT: A 414 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.6950 (t0) REVERT: B 206 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6868 (pp) outliers start: 29 outliers final: 12 residues processed: 100 average time/residue: 0.2239 time to fit residues: 23.9813 Evaluate side-chains 102 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 190 VAL Chi-restraints excluded: chain A residue 275 PHE 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 393 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 443 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 220 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.236321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.206908 restraints weight = 4863.172| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 2.04 r_work: 0.4297 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4195 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4784 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 : 0.730 13.465 5624 Z= 0.355 Chirality : 0.044 0.179 661 Planarity : 0.005 0.065 721 Dihedral : 7.150 58.666 643 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 8.28 % Allowed : 28.83 % 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: -0.05 (0.36), residues: 585 helix: 0.41 (0.28), residues: 362 sheet: 0.96 (0.52), residues: 109 loop : -2.22 (0.55), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 203 TYR 0.013 0.001 TYR A 445 PHE 0.010 0.001 PHE A 51 TRP 0.009 0.001 TRP A 174 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 4118) covalent geometry : angle 0.72973 / 0.35 ( 5624) hydrogen bonds : bond 0.04781 / 3.24 ( 305) hydrogen bonds : angle 4.93737 / 3.64 ( 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 : 0.107 Fit side-chains REVERT: A 27 PHE cc_start: 0.7812 (t80) cc_final: 0.7602 (t80) REVERT: A 60 TRP cc_start: 0.7443 (OUTLIER) cc_final: 0.7087 (m100) REVERT: A 70 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.7313 (t80) REVERT: A 88 VAL cc_start: 0.8402 (t) cc_final: 0.8139 (m) REVERT: A 91 VAL cc_start: 0.7690 (t) cc_final: 0.7192 (m) REVERT: A 94 CYS cc_start: 0.7616 (OUTLIER) cc_final: 0.6826 (m) REVERT: A 105 PHE cc_start: 0.6886 (OUTLIER) cc_final: 0.6489 (m-10) REVERT: A 126 PHE cc_start: 0.6889 (m-10) cc_final: 0.6611 (m-10) REVERT: A 137 LYS cc_start: 0.6466 (tttt) cc_final: 0.5678 (tptt) REVERT: A 138 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.6614 (m-80) REVERT: A 139 PHE cc_start: 0.6219 (OUTLIER) cc_final: 0.5455 (m-80) REVERT: A 147 ASN cc_start: 0.7464 (m-40) cc_final: 0.7004 (m-40) REVERT: A 302 LEU cc_start: 0.8279 (mt) cc_final: 0.7947 (mm) REVERT: A 329 ILE cc_start: 0.8236 (tp) cc_final: 0.7757 (tt) REVERT: A 356 PHE cc_start: 0.7487 (m-80) cc_final: 0.7163 (m-80) REVERT: A 391 VAL cc_start: 0.8239 (p) cc_final: 0.7952 (t) REVERT: A 411 ARG cc_start: 0.7580 (ttt90) cc_final: 0.7159 (tpt90) REVERT: A 414 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6651 (t0) REVERT: A 415 MET cc_start: 0.6348 (OUTLIER) cc_final: 0.5889 (ptm) REVERT: B 206 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6667 (pp) outliers start: 27 outliers final: 9 residues processed: 94 average time/residue: 0.2615 time to fit residues: 26.1039 Evaluate side-chains 91 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.095 ------------------------------------------------------------------------------- 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 319 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 LEU 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 A residue 443 ILE Chi-restraints excluded: chain B residue 206 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 50.0000 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 40.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.236180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.207939 restraints weight = 4711.847| |-----------------------------------------------------------------------------| r_work (start): 0.4399 rms_B_bonded: 1.97 r_work: 0.4306 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4201 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.4990 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= 0.154 Angle : 0.736 11.917 5624 Z= 0.359 Chirality : 0.045 0.197 661 Planarity : 0.005 0.064 721 Dihedral : 6.040 49.112 638 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 7.36 % Allowed : 29.45 % 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: 0.11 (0.36), residues: 585 helix: 0.51 (0.29), residues: 363 sheet: 0.98 (0.52), residues: 109 loop : -2.05 (0.56), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 203 TYR 0.015 0.001 TYR A 445 PHE 0.009 0.001 PHE A 27 TRP 0.007 0.001 TRP A 174 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 4118) covalent geometry : angle 0.73646 / 0.36 ( 5624) hydrogen bonds : bond 0.04740 / 3.21 ( 305) hydrogen bonds : angle 4.88169 / 3.60 ( 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 99 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.141 Fit side-chains REVERT: A 60 TRP cc_start: 0.7428 (OUTLIER) cc_final: 0.7088 (m100) REVERT: A 70 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.7272 (t80) REVERT: A 91 VAL cc_start: 0.7700 (t) cc_final: 0.7229 (m) REVERT: A 94 CYS cc_start: 0.7575 (OUTLIER) cc_final: 0.6779 (m) REVERT: A 105 PHE cc_start: 0.6860 (OUTLIER) cc_final: 0.6462 (m-10) REVERT: A 126 PHE cc_start: 0.6872 (m-10) cc_final: 0.6625 (m-10) REVERT: A 137 LYS cc_start: 0.6470 (tttt) cc_final: 0.5626 (tptt) REVERT: A 138 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.6629 (m-80) REVERT: A 139 PHE cc_start: 0.6218 (OUTLIER) cc_final: 0.5571 (m-80) REVERT: A 147 ASN cc_start: 0.7438 (m-40) cc_final: 0.6980 (m-40) REVERT: A 302 LEU cc_start: 0.8295 (mt) cc_final: 0.7970 (mm) REVERT: A 356 PHE cc_start: 0.7474 (m-80) cc_final: 0.7165 (m-80) REVERT: A 378 LEU cc_start: 0.7674 (tm) cc_final: 0.7442 (tp) REVERT: A 391 VAL cc_start: 0.8263 (p) cc_final: 0.7961 (t) REVERT: A 411 ARG cc_start: 0.7580 (ttt90) cc_final: 0.7155 (tpt90) REVERT: A 414 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6533 (t0) REVERT: A 415 MET cc_start: 0.6311 (OUTLIER) cc_final: 0.5845 (ptm) outliers start: 24 outliers final: 9 residues processed: 89 average time/residue: 0.2459 time to fit residues: 23.3544 Evaluate side-chains 91 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 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 190 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 LEU 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 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: 0.9990 chunk 47 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 50.0000 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.230408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.200940 restraints weight = 4850.876| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 2.22 r_work: 0.4238 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4127 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4118 Z= 0.208 Angle : 0.788 11.590 5624 Z= 0.392 Chirality : 0.047 0.196 661 Planarity : 0.006 0.063 721 Dihedral : 6.139 53.139 636 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 6.13 % Allowed : 31.29 % 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: -0.26 (0.36), residues: 585 helix: 0.20 (0.28), residues: 362 sheet: 0.84 (0.52), residues: 109 loop : -2.09 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 203 TYR 0.022 0.002 TYR A 445 PHE 0.020 0.002 PHE A 27 TRP 0.006 0.001 TRP A 174 HIS 0.004 0.002 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 ( 4118) covalent geometry : angle 0.78767 / 0.39 ( 5624) hydrogen bonds : bond 0.05545 / 3.70 ( 305) hydrogen bonds : angle 5.24817 / 3.88 ( 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 101 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.131 Fit side-chains REVERT: A 27 PHE cc_start: 0.7833 (t80) cc_final: 0.7631 (t80) REVERT: A 60 TRP cc_start: 0.7463 (OUTLIER) cc_final: 0.7073 (m100) REVERT: A 70 TYR cc_start: 0.7831 (t80) cc_final: 0.7422 (t80) REVERT: A 91 VAL cc_start: 0.7738 (t) cc_final: 0.7172 (m) REVERT: A 94 CYS cc_start: 0.7603 (OUTLIER) cc_final: 0.6703 (m) REVERT: A 105 PHE cc_start: 0.6986 (OUTLIER) cc_final: 0.6520 (m-10) REVERT: A 126 PHE cc_start: 0.6982 (m-10) cc_final: 0.6667 (m-10) REVERT: A 138 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.6786 (m-80) REVERT: A 139 PHE cc_start: 0.6424 (OUTLIER) cc_final: 0.5801 (m-80) REVERT: A 147 ASN cc_start: 0.7411 (m-40) cc_final: 0.6901 (m-40) REVERT: A 302 LEU cc_start: 0.8371 (mt) cc_final: 0.8083 (mm) REVERT: A 356 PHE cc_start: 0.7527 (m-80) cc_final: 0.7169 (m-80) REVERT: A 378 LEU cc_start: 0.7666 (tm) cc_final: 0.7450 (tp) REVERT: A 391 VAL cc_start: 0.8199 (p) cc_final: 0.7906 (t) REVERT: A 411 ARG cc_start: 0.7635 (ttt90) cc_final: 0.7144 (tpt90) REVERT: A 414 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.6901 (t0) REVERT: A 415 MET cc_start: 0.6339 (OUTLIER) cc_final: 0.5906 (ptm) outliers start: 20 outliers final: 9 residues processed: 92 average time/residue: 0.2180 time to fit residues: 21.5880 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 : 0.130 ------------------------------------------------------------------------------- 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 190 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 LEU 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 A residue 443 ILE Chi-restraints excluded: chain B residue 209 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: 0.4980 chunk 28 optimal weight: 0.5980 chunk 41 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.226734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.197619 restraints weight = 4822.925| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 2.15 r_work: 0.4210 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4105 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 4118 Z= 0.243 Angle : 0.838 12.250 5624 Z= 0.415 Chirality : 0.049 0.199 661 Planarity : 0.006 0.063 721 Dihedral : 6.473 54.477 636 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.83 % Allowed : 31.90 % Favored : 62.27 % Cbeta Deviations : 0.00 % 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: -0.72 (0.35), residues: 585 helix: -0.05 (0.28), residues: 356 sheet: 0.56 (0.52), residues: 109 loop : -2.45 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 203 TYR 0.019 0.002 TYR A 445 PHE 0.022 0.002 PHE A 27 TRP 0.008 0.001 TRP A 174 HIS 0.004 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.24 ( 4118) covalent geometry : angle 0.83768 / 0.42 ( 5624) hydrogen bonds : bond 0.05921 / 3.90 ( 305) hydrogen bonds : angle 5.41641 / 4.00 ( 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 100 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: A 60 TRP cc_start: 0.7527 (OUTLIER) cc_final: 0.7102 (m100) REVERT: A 91 VAL cc_start: 0.7748 (t) cc_final: 0.7160 (m) REVERT: A 94 CYS cc_start: 0.7635 (OUTLIER) cc_final: 0.6661 (m) REVERT: A 105 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6586 (m-10) REVERT: A 126 PHE cc_start: 0.7089 (m-10) cc_final: 0.6706 (m-10) REVERT: A 138 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.6714 (m-80) REVERT: A 139 PHE cc_start: 0.6506 (OUTLIER) cc_final: 0.5918 (m-80) REVERT: A 147 ASN cc_start: 0.7463 (m-40) cc_final: 0.6948 (m-40) REVERT: A 302 LEU cc_start: 0.8353 (mt) cc_final: 0.8054 (mm) REVERT: A 356 PHE cc_start: 0.7565 (m-80) cc_final: 0.7175 (m-80) REVERT: A 391 VAL cc_start: 0.8189 (p) cc_final: 0.7911 (t) REVERT: A 411 ARG cc_start: 0.7602 (ttt90) cc_final: 0.7138 (tpt90) REVERT: A 414 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.6841 (t0) outliers start: 19 outliers final: 9 residues processed: 91 average time/residue: 0.2099 time to fit residues: 20.5349 Evaluate side-chains 94 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.077 ------------------------------------------------------------------------------- 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 190 VAL Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 VAL 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 443 ILE Chi-restraints excluded: chain B residue 209 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 55 optimal weight: 0.0040 chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.233304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.205267 restraints weight = 4867.794| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 2.14 r_work: 0.4281 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4174 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.5469 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= 0.144 Angle : 0.772 13.913 5624 Z= 0.365 Chirality : 0.044 0.181 661 Planarity : 0.005 0.066 721 Dihedral : 5.738 47.743 636 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.21 % Allowed : 32.82 % Favored : 61.96 % 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: -0.09 (0.36), residues: 585 helix: 0.40 (0.29), residues: 362 sheet: 0.90 (0.53), residues: 107 loop : -2.23 (0.53), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 201 TYR 0.013 0.001 TYR A 266 PHE 0.009 0.001 PHE A 51 TRP 0.009 0.001 TRP A 174 HIS 0.002 0.000 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 4118) covalent geometry : angle 0.77219 / 0.37 ( 5624) hydrogen bonds : bond 0.04628 / 3.12 ( 305) hydrogen bonds : angle 4.90533 / 3.59 ( 885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1621.99 seconds wall clock time: 28 minutes 24.45 seconds (1704.45 seconds total)