Starting phenix.real_space_refine on Wed Mar 5 23:50:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cko_30389/03_2025/7cko_30389.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cko_30389/03_2025/7cko_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_30389/03_2025/7cko_30389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cko_30389/03_2025/7cko_30389.map" model { file = "/net/cci-nas-00/data/ceres_data/7cko_30389/03_2025/7cko_30389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cko_30389/03_2025/7cko_30389.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 6, 'ASP:plan': 12, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 6} 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: 3.48, per 1000 atoms: 0.86 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: 1.11 Conformation dependent library (CDL) restraints added in 545.8 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: 0.49 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: 1.27 Time building geometry restraints manager: 1.29 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: 0.900 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 15.630 Find NCS groups from input model: 0.040 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:14.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.880 ------------------------------------------------------------------------------- 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= 0.794 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 : 11.96 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (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 TRP 0.008 0.002 TRP A 18 HIS 0.005 0.001 HIS A 260 PHE 0.017 0.002 PHE A 332 TYR 0.056 0.003 TYR A 113 ARG 0.006 0.001 ARG A 142 *********************** 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 : 0.448 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: 0.7146 (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: 0.6513 (mp0) REVERT: A 446 ARG cc_start: 0.3800 (OUTLIER) cc_final: 0.3466 (mmp80) outliers start: 42 outliers final: 10 residues processed: 85 average time/residue: 1.1596 time to fit residues: 102.6544 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 : 0.428 ------------------------------------------------------------------------------- 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 48 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.4664 r_free = 0.4664 target = 0.239496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.208043 restraints weight = 4717.361| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 2.15 r_work: 0.4310 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4202 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4118 Z= 0.271 Angle : 0.723 7.642 5624 Z= 0.377 Chirality : 0.044 0.168 661 Planarity : 0.006 0.064 721 Dihedral : 8.442 58.110 666 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 9.20 % Allowed : 20.55 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.34), residues: 585 helix: -0.28 (0.27), residues: 350 sheet: 0.44 (0.49), residues: 111 loop : -3.43 (0.45), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 424 HIS 0.003 0.001 HIS B 205 PHE 0.013 0.001 PHE A 332 TYR 0.022 0.002 TYR A 445 ARG 0.006 0.001 ARG A 411 *********************** 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 109 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 60 TRP cc_start: 0.7271 (OUTLIER) cc_final: 0.6958 (m100) REVERT: A 91 VAL cc_start: 0.7605 (t) cc_final: 0.7253 (m) REVERT: A 94 CYS cc_start: 0.7617 (OUTLIER) cc_final: 0.6476 (m) REVERT: A 105 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.6473 (m-10) REVERT: A 137 LYS cc_start: 0.6605 (tttt) cc_final: 0.5710 (tptt) REVERT: A 139 PHE cc_start: 0.6314 (OUTLIER) cc_final: 0.5241 (m-10) REVERT: A 141 LYS cc_start: 0.6389 (OUTLIER) cc_final: 0.6162 (pmtt) REVERT: A 147 ASN cc_start: 0.7569 (m-40) cc_final: 0.7117 (m-40) REVERT: A 273 MET cc_start: 0.7817 (ppp) cc_final: 0.7468 (ppp) REVERT: A 391 VAL cc_start: 0.8210 (p) cc_final: 0.8007 (t) REVERT: A 393 LEU cc_start: 0.7930 (mt) cc_final: 0.7714 (mt) REVERT: A 398 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: A 411 ARG cc_start: 0.7445 (ttt90) cc_final: 0.7027 (tpt90) REVERT: A 414 ASP cc_start: 0.6774 (OUTLIER) cc_final: 0.6432 (t0) REVERT: B 206 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6172 (mp) outliers start: 30 outliers final: 8 residues processed: 98 average time/residue: 0.5997 time to fit residues: 62.4964 Evaluate side-chains 94 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 69 MET 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 57 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 50.0000 chunk 28 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 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 = 0.4666 r_free = 0.4666 target = 0.237121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.207119 restraints weight = 4728.520| |-----------------------------------------------------------------------------| r_work (start): 0.4416 rms_B_bonded: 1.99 r_work: 0.4337 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4239 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4118 Z= 0.218 Angle : 0.657 7.308 5624 Z= 0.340 Chirality : 0.042 0.130 661 Planarity : 0.005 0.065 721 Dihedral : 7.615 59.219 647 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 7.06 % Allowed : 23.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.36), residues: 585 helix: 0.37 (0.29), residues: 356 sheet: 0.60 (0.51), residues: 111 loop : -2.99 (0.48), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 174 HIS 0.002 0.001 HIS A 292 PHE 0.019 0.001 PHE A 27 TYR 0.015 0.001 TYR A 445 ARG 0.004 0.001 ARG A 261 *********************** 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 102 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.479 Fit side-chains REVERT: A 60 TRP cc_start: 0.7355 (OUTLIER) cc_final: 0.7040 (m100) REVERT: A 70 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.7324 (t80) REVERT: A 91 VAL cc_start: 0.7658 (t) cc_final: 0.7201 (m) REVERT: A 105 PHE cc_start: 0.6986 (OUTLIER) cc_final: 0.6569 (m-10) REVERT: A 137 LYS cc_start: 0.6502 (tttt) cc_final: 0.5761 (tptt) REVERT: A 138 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.6965 (m-80) REVERT: A 139 PHE cc_start: 0.6496 (OUTLIER) cc_final: 0.5526 (m-10) REVERT: A 141 LYS cc_start: 0.6412 (pttt) cc_final: 0.6122 (pmtt) REVERT: A 147 ASN cc_start: 0.7472 (m-40) cc_final: 0.7089 (m-40) REVERT: A 379 MET cc_start: 0.7834 (tpt) cc_final: 0.7232 (tpt) REVERT: A 391 VAL cc_start: 0.8224 (p) cc_final: 0.7940 (t) REVERT: A 398 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6565 (mp0) REVERT: A 411 ARG cc_start: 0.7412 (ttt90) cc_final: 0.7087 (tpt90) REVERT: A 414 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6642 (t0) REVERT: B 206 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6586 (mp) REVERT: B 226 ILE cc_start: 0.6750 (OUTLIER) cc_final: 0.6435 (pt) outliers start: 23 outliers final: 8 residues processed: 93 average time/residue: 0.6183 time to fit residues: 61.1811 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 : 0.384 ------------------------------------------------------------------------------- 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 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 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 A residue 443 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 226 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.236868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.206664 restraints weight = 4649.829| |-----------------------------------------------------------------------------| r_work (start): 0.4411 rms_B_bonded: 2.07 r_work: 0.4327 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4220 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.4081 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= 0.214 Angle : 0.666 7.771 5624 Z= 0.339 Chirality : 0.043 0.131 661 Planarity : 0.005 0.065 721 Dihedral : 7.626 55.679 646 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 8.59 % Allowed : 21.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.36), residues: 585 helix: 0.46 (0.29), residues: 358 sheet: 0.82 (0.51), residues: 109 loop : -2.63 (0.50), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 174 HIS 0.002 0.001 HIS A 292 PHE 0.013 0.001 PHE A 332 TYR 0.016 0.001 TYR A 445 ARG 0.003 0.000 ARG B 203 *********************** 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 109 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.441 Fit side-chains REVERT: A 27 PHE cc_start: 0.7752 (t80) cc_final: 0.7512 (t80) REVERT: A 60 TRP cc_start: 0.7318 (OUTLIER) cc_final: 0.6994 (m100) REVERT: A 65 MET cc_start: 0.8077 (ttt) cc_final: 0.7875 (ttm) REVERT: A 70 TYR cc_start: 0.7673 (t80) cc_final: 0.7274 (t80) REVERT: A 91 VAL cc_start: 0.7567 (t) cc_final: 0.7071 (m) REVERT: A 94 CYS cc_start: 0.7716 (OUTLIER) cc_final: 0.6743 (m) REVERT: A 105 PHE cc_start: 0.6996 (OUTLIER) cc_final: 0.6644 (m-10) REVERT: A 126 PHE cc_start: 0.7124 (m-10) cc_final: 0.6788 (m-10) REVERT: A 137 LYS cc_start: 0.6503 (tttt) cc_final: 0.5708 (tptt) REVERT: A 138 TYR cc_start: 0.7793 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: A 139 PHE cc_start: 0.6388 (OUTLIER) cc_final: 0.5118 (m-10) REVERT: A 147 ASN cc_start: 0.7527 (m-40) cc_final: 0.7078 (m-40) REVERT: A 302 LEU cc_start: 0.8259 (mt) cc_final: 0.7926 (mm) REVERT: A 313 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7655 (ttt-90) REVERT: A 379 MET cc_start: 0.7868 (tpt) cc_final: 0.7545 (tpt) REVERT: A 391 VAL cc_start: 0.8263 (p) cc_final: 0.7988 (t) REVERT: A 398 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: A 411 ARG cc_start: 0.7588 (ttt90) cc_final: 0.7192 (tpt90) REVERT: A 414 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6641 (t0) REVERT: A 415 MET cc_start: 0.6309 (OUTLIER) cc_final: 0.5837 (ptm) outliers start: 28 outliers final: 9 residues processed: 100 average time/residue: 0.8140 time to fit residues: 86.5178 Evaluate side-chains 98 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 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 338 VAL 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 26 optimal weight: 0.8980 chunk 38 optimal weight: 50.0000 chunk 47 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4664 r_free = 0.4664 target = 0.237698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.208542 restraints weight = 4903.179| |-----------------------------------------------------------------------------| r_work (start): 0.4401 rms_B_bonded: 2.07 r_work: 0.4316 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4213 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4118 Z= 0.208 Angle : 0.674 10.120 5624 Z= 0.338 Chirality : 0.043 0.156 661 Planarity : 0.005 0.064 721 Dihedral : 7.528 56.298 646 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 8.90 % Allowed : 23.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.36), residues: 585 helix: 0.58 (0.29), residues: 357 sheet: 0.89 (0.51), residues: 109 loop : -2.45 (0.51), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 174 HIS 0.002 0.001 HIS A 292 PHE 0.010 0.001 PHE A 332 TYR 0.016 0.001 TYR A 445 ARG 0.004 0.001 ARG B 203 *********************** 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 111 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.437 Fit side-chains REVERT: A 27 PHE cc_start: 0.7762 (t80) cc_final: 0.7545 (t80) REVERT: A 60 TRP cc_start: 0.7379 (OUTLIER) cc_final: 0.7052 (m100) REVERT: A 70 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.7374 (t80) REVERT: A 88 VAL cc_start: 0.8415 (t) cc_final: 0.8172 (m) REVERT: A 105 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.6560 (m-10) REVERT: A 126 PHE cc_start: 0.6973 (m-10) cc_final: 0.6667 (m-10) REVERT: A 137 LYS cc_start: 0.6459 (tttt) cc_final: 0.5641 (tptt) REVERT: A 138 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.6872 (m-80) REVERT: A 139 PHE cc_start: 0.6340 (OUTLIER) cc_final: 0.5455 (m-10) REVERT: A 141 LYS cc_start: 0.6019 (pmtt) cc_final: 0.5711 (pmtt) REVERT: A 147 ASN cc_start: 0.7506 (m-40) cc_final: 0.7076 (m-40) REVERT: A 302 LEU cc_start: 0.8271 (mt) cc_final: 0.7938 (mm) REVERT: A 391 VAL cc_start: 0.8276 (p) cc_final: 0.7988 (t) REVERT: A 393 LEU cc_start: 0.8248 (mt) cc_final: 0.7760 (mp) REVERT: A 398 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: A 411 ARG cc_start: 0.7611 (ttt90) cc_final: 0.7192 (tpt90) REVERT: A 414 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6509 (t0) REVERT: A 415 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.5717 (ptm) REVERT: B 206 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.6477 (pp) REVERT: B 226 ILE cc_start: 0.6694 (OUTLIER) cc_final: 0.6386 (pt) outliers start: 29 outliers final: 8 residues processed: 100 average time/residue: 0.8493 time to fit residues: 91.1556 Evaluate side-chains 98 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 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 292 HIS 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 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 Chi-restraints excluded: chain B residue 226 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 45 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.233565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.205154 restraints weight = 4759.988| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 2.00 r_work: 0.4286 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4183 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4118 Z= 0.253 Angle : 0.722 11.861 5624 Z= 0.360 Chirality : 0.044 0.155 661 Planarity : 0.005 0.064 721 Dihedral : 7.698 58.736 646 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 8.28 % Allowed : 26.38 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.36), residues: 585 helix: 0.37 (0.29), residues: 363 sheet: 0.81 (0.51), residues: 109 loop : -2.33 (0.53), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 174 HIS 0.003 0.001 HIS A 292 PHE 0.012 0.001 PHE B 227 TYR 0.020 0.002 TYR A 445 ARG 0.004 0.001 ARG B 203 *********************** 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 117 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.388 Fit side-chains REVERT: A 27 PHE cc_start: 0.7840 (t80) cc_final: 0.7610 (t80) REVERT: A 60 TRP cc_start: 0.7354 (OUTLIER) cc_final: 0.7019 (m100) REVERT: A 70 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.7366 (t80) REVERT: A 91 VAL cc_start: 0.7591 (t) cc_final: 0.7065 (m) REVERT: A 94 CYS cc_start: 0.7799 (OUTLIER) cc_final: 0.6849 (m) REVERT: A 105 PHE cc_start: 0.6964 (OUTLIER) cc_final: 0.6507 (m-10) REVERT: A 126 PHE cc_start: 0.6983 (m-10) cc_final: 0.6710 (m-10) REVERT: A 138 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.6786 (m-80) REVERT: A 139 PHE cc_start: 0.6362 (OUTLIER) cc_final: 0.5503 (m-80) REVERT: A 147 ASN cc_start: 0.7414 (m-40) cc_final: 0.6956 (m-40) REVERT: A 302 LEU cc_start: 0.8332 (mt) cc_final: 0.8009 (mm) REVERT: A 356 PHE cc_start: 0.7496 (m-80) cc_final: 0.7214 (m-80) REVERT: A 391 VAL cc_start: 0.8223 (p) cc_final: 0.7914 (t) REVERT: A 393 LEU cc_start: 0.8237 (mt) cc_final: 0.7727 (mp) REVERT: A 398 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: A 411 ARG cc_start: 0.7650 (ttt90) cc_final: 0.7233 (tpt90) REVERT: A 414 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6769 (t0) REVERT: A 415 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.5829 (ptm) REVERT: B 206 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6568 (pp) outliers start: 27 outliers final: 9 residues processed: 105 average time/residue: 0.9172 time to fit residues: 102.7389 Evaluate side-chains 103 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 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 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 220 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.234646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.204162 restraints weight = 4748.506| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 2.09 r_work: 0.4290 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4188 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4118 Z= 0.218 Angle : 0.719 13.270 5624 Z= 0.352 Chirality : 0.043 0.187 661 Planarity : 0.005 0.064 721 Dihedral : 7.209 59.715 646 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.36), residues: 585 helix: 0.53 (0.29), residues: 363 sheet: 0.87 (0.51), residues: 109 loop : -2.14 (0.55), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 174 HIS 0.002 0.001 HIS A 292 PHE 0.010 0.001 PHE A 27 TYR 0.014 0.001 TYR A 445 ARG 0.005 0.001 ARG B 203 *********************** 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 104 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.410 Fit side-chains REVERT: A 60 TRP cc_start: 0.7444 (OUTLIER) cc_final: 0.7033 (m100) REVERT: A 70 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.7289 (t80) REVERT: A 88 VAL cc_start: 0.8411 (t) cc_final: 0.8128 (m) REVERT: A 91 VAL cc_start: 0.7649 (t) cc_final: 0.7119 (m) REVERT: A 94 CYS cc_start: 0.7655 (OUTLIER) cc_final: 0.6773 (m) REVERT: A 105 PHE cc_start: 0.6837 (OUTLIER) cc_final: 0.6460 (m-10) REVERT: A 126 PHE cc_start: 0.6913 (m-10) cc_final: 0.6691 (m-10) REVERT: A 137 LYS cc_start: 0.6455 (tttt) cc_final: 0.5639 (tptt) REVERT: A 138 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.6655 (m-80) REVERT: A 139 PHE cc_start: 0.6182 (OUTLIER) cc_final: 0.5415 (m-80) REVERT: A 147 ASN cc_start: 0.7431 (m-40) cc_final: 0.6924 (m-40) REVERT: A 302 LEU cc_start: 0.8276 (mt) cc_final: 0.7966 (mm) REVERT: A 356 PHE cc_start: 0.7528 (m-80) cc_final: 0.7157 (m-80) REVERT: A 378 LEU cc_start: 0.7669 (tm) cc_final: 0.7451 (tp) REVERT: A 391 VAL cc_start: 0.8192 (p) cc_final: 0.7878 (t) REVERT: A 393 LEU cc_start: 0.8251 (mt) cc_final: 0.7809 (mp) REVERT: A 398 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: A 411 ARG cc_start: 0.7571 (ttt90) cc_final: 0.7157 (tpt90) REVERT: A 414 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6623 (t0) REVERT: A 415 MET cc_start: 0.6253 (OUTLIER) cc_final: 0.5804 (ptm) REVERT: B 206 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6424 (pp) REVERT: B 226 ILE cc_start: 0.6722 (OUTLIER) cc_final: 0.6371 (pt) outliers start: 24 outliers final: 8 residues processed: 95 average time/residue: 0.7273 time to fit residues: 73.1240 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 : 0.435 ------------------------------------------------------------------------------- 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 190 VAL Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 328 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 Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 226 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 4.9990 chunk 44 optimal weight: 0.0570 chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 0.0040 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.239321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.212275 restraints weight = 4744.033| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 2.04 r_work: 0.4340 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4241 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.5039 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= 0.179 Angle : 0.703 12.116 5624 Z= 0.338 Chirality : 0.042 0.189 661 Planarity : 0.005 0.065 721 Dihedral : 6.682 59.167 646 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 7.36 % Allowed : 30.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.37), residues: 585 helix: 0.81 (0.29), residues: 361 sheet: 1.15 (0.52), residues: 108 loop : -2.05 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 174 HIS 0.001 0.000 HIS A 52 PHE 0.021 0.001 PHE A 27 TYR 0.009 0.001 TYR A 445 ARG 0.002 0.000 ARG B 203 *********************** 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: 24 poor density : 76 time to evaluate : 0.401 Fit side-chains REVERT: A 60 TRP cc_start: 0.7388 (OUTLIER) cc_final: 0.7040 (m100) REVERT: A 88 VAL cc_start: 0.8369 (t) cc_final: 0.8107 (m) REVERT: A 94 CYS cc_start: 0.7536 (OUTLIER) cc_final: 0.6768 (m) REVERT: A 105 PHE cc_start: 0.6769 (OUTLIER) cc_final: 0.6428 (m-10) REVERT: A 126 PHE cc_start: 0.6832 (m-10) cc_final: 0.6588 (m-10) REVERT: A 137 LYS cc_start: 0.6340 (tttt) cc_final: 0.5464 (tptt) REVERT: A 138 TYR cc_start: 0.7723 (OUTLIER) cc_final: 0.6611 (m-80) REVERT: A 139 PHE cc_start: 0.6107 (OUTLIER) cc_final: 0.5495 (m-80) REVERT: A 147 ASN cc_start: 0.7473 (m-40) cc_final: 0.7050 (m-40) REVERT: A 188 CYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7263 (t) REVERT: A 302 LEU cc_start: 0.8197 (mt) cc_final: 0.7866 (mm) REVERT: A 356 PHE cc_start: 0.7311 (m-80) cc_final: 0.7007 (m-80) REVERT: A 391 VAL cc_start: 0.8154 (p) cc_final: 0.7829 (t) REVERT: A 393 LEU cc_start: 0.8206 (mt) cc_final: 0.7778 (mp) REVERT: A 411 ARG cc_start: 0.7493 (ttt90) cc_final: 0.7074 (tpt90) REVERT: A 414 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6447 (t0) outliers start: 24 outliers final: 8 residues processed: 92 average time/residue: 0.6487 time to fit residues: 63.3167 Evaluate side-chains 89 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 328 ARG 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 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 19 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 50 optimal weight: 0.0770 chunk 57 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN A 330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.239359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.211703 restraints weight = 4743.537| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 2.07 r_work: 0.4336 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4231 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.5153 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= 0.189 Angle : 0.712 11.607 5624 Z= 0.345 Chirality : 0.044 0.265 661 Planarity : 0.005 0.064 721 Dihedral : 5.580 44.531 639 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.21 % Allowed : 33.44 % Favored : 61.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.37), residues: 585 helix: 0.87 (0.29), residues: 361 sheet: 1.18 (0.52), residues: 109 loop : -1.84 (0.56), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 174 HIS 0.002 0.000 HIS A 292 PHE 0.035 0.001 PHE A 307 TYR 0.016 0.001 TYR A 70 ARG 0.003 0.000 ARG B 203 *********************** 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 92 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.381 Fit side-chains REVERT: A 60 TRP cc_start: 0.7342 (OUTLIER) cc_final: 0.6968 (m100) REVERT: A 94 CYS cc_start: 0.7583 (OUTLIER) cc_final: 0.6804 (m) REVERT: A 105 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6473 (m-10) REVERT: A 126 PHE cc_start: 0.6856 (m-10) cc_final: 0.6591 (m-10) REVERT: A 137 LYS cc_start: 0.6252 (tttt) cc_final: 0.5465 (tptt) REVERT: A 138 TYR cc_start: 0.7712 (OUTLIER) cc_final: 0.6608 (m-80) REVERT: A 139 PHE cc_start: 0.6034 (OUTLIER) cc_final: 0.5449 (m-80) REVERT: A 147 ASN cc_start: 0.7470 (m-40) cc_final: 0.7020 (m-40) REVERT: A 302 LEU cc_start: 0.8213 (mt) cc_final: 0.7904 (mm) REVERT: A 356 PHE cc_start: 0.7321 (m-80) cc_final: 0.6984 (m-80) REVERT: A 391 VAL cc_start: 0.8131 (p) cc_final: 0.7818 (t) REVERT: A 393 LEU cc_start: 0.8197 (mt) cc_final: 0.7732 (mp) REVERT: A 411 ARG cc_start: 0.7493 (ttt90) cc_final: 0.7067 (tpt90) REVERT: A 414 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6478 (t0) outliers start: 17 outliers final: 10 residues processed: 86 average time/residue: 0.9665 time to fit residues: 86.7891 Evaluate side-chains 91 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 328 ARG Chi-restraints excluded: chain A residue 338 VAL 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 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 23 optimal weight: 2.9990 chunk 39 optimal weight: 50.0000 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4603 r_free = 0.4603 target = 0.231631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.203678 restraints weight = 4852.575| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 2.10 r_work: 0.4274 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4169 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4118 Z= 0.239 Angle : 0.752 11.495 5624 Z= 0.367 Chirality : 0.046 0.220 661 Planarity : 0.005 0.063 721 Dihedral : 5.872 49.088 639 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.21 % Allowed : 33.13 % Favored : 61.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.37), residues: 585 helix: 0.60 (0.29), residues: 363 sheet: 1.11 (0.53), residues: 107 loop : -1.77 (0.57), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 174 HIS 0.002 0.001 HIS B 205 PHE 0.032 0.002 PHE A 307 TYR 0.020 0.002 TYR A 445 ARG 0.005 0.001 ARG B 203 ********************** 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 94 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.426 Fit side-chains REVERT: A 60 TRP cc_start: 0.7305 (OUTLIER) cc_final: 0.6884 (m100) REVERT: A 91 VAL cc_start: 0.7517 (t) cc_final: 0.6956 (m) REVERT: A 94 CYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6528 (m) REVERT: A 105 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6456 (m-10) REVERT: A 126 PHE cc_start: 0.7006 (m-10) cc_final: 0.6729 (m-10) REVERT: A 138 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: A 139 PHE cc_start: 0.6055 (OUTLIER) cc_final: 0.5525 (m-80) REVERT: A 147 ASN cc_start: 0.7432 (m-40) cc_final: 0.6897 (m-40) REVERT: A 302 LEU cc_start: 0.8272 (mt) cc_final: 0.7954 (mm) REVERT: A 356 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7040 (m-80) REVERT: A 391 VAL cc_start: 0.8128 (p) cc_final: 0.7831 (t) REVERT: A 393 LEU cc_start: 0.8172 (mt) cc_final: 0.7685 (mp) REVERT: A 411 ARG cc_start: 0.7472 (ttt90) cc_final: 0.7030 (tpt90) REVERT: A 414 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6499 (t0) outliers start: 17 outliers final: 9 residues processed: 87 average time/residue: 0.5809 time to fit residues: 54.1168 Evaluate side-chains 92 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 328 ARG Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 356 PHE 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 B residue 209 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 0.0050 chunk 33 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.4625 r_free = 0.4625 target = 0.234735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.207211 restraints weight = 4832.209| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 2.12 r_work: 0.4302 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4196 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.5362 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= 0.194 Angle : 0.727 11.967 5624 Z= 0.350 Chirality : 0.044 0.239 661 Planarity : 0.005 0.064 721 Dihedral : 5.572 44.931 639 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.91 % Allowed : 34.97 % Favored : 60.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.37), residues: 585 helix: 0.82 (0.29), residues: 360 sheet: 1.08 (0.52), residues: 109 loop : -1.85 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 174 HIS 0.002 0.001 HIS A 292 PHE 0.032 0.001 PHE A 307 TYR 0.011 0.001 TYR A 70 ARG 0.002 0.000 ARG B 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4031.77 seconds wall clock time: 72 minutes 15.68 seconds (4335.68 seconds total)