Starting phenix.real_space_refine on Thu Mar 6 05:07:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wo7_32641/03_2025/7wo7_32641.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wo7_32641/03_2025/7wo7_32641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wo7_32641/03_2025/7wo7_32641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wo7_32641/03_2025/7wo7_32641.map" model { file = "/net/cci-nas-00/data/ceres_data/7wo7_32641/03_2025/7wo7_32641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wo7_32641/03_2025/7wo7_32641.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3069 2.51 5 N 816 2.21 5 O 965 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: 4870 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "B" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.01, per 1000 atoms: 1.23 Number of scatterers: 4870 At special positions: 0 Unit cell: (74.9, 95.23, 107, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 965 8.00 N 816 7.00 C 3069 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 91 " distance=2.03 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 560.1 milliseconds 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1168 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 13 sheets defined 5.4% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.625A pdb=" N LYS A 65 " --> pdb=" O ASP A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.520A pdb=" N THR A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.516A pdb=" N ASP B 85 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 86 " --> pdb=" O THR B 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 82 through 86' Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.876A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.709A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.222A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.797A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 5 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 7 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 20 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.986A pdb=" N GLY A 10 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET A 34 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 36 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 59 " --> pdb=" O ASN A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.986A pdb=" N GLY A 10 " --> pdb=" O THR A 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.654A pdb=" N SER A 186 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER A 185 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A 172 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 187 " --> pdb=" O HIS A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.127A pdb=" N VAL B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 107 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.127A pdb=" N VAL B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 107 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 102 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.743A pdb=" N ILE B 20 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 197 through 199 removed outlier: 3.586A pdb=" N CYS B 199 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS B 210 " --> pdb=" O CYS B 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.873A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.602A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.582A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) 73 hydrogen bonds defined for protein. 153 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: 1.40 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1472 1.33 - 1.45: 883 1.45 - 1.57: 2618 1.57 - 1.70: 0 1.70 - 1.82: 23 Bond restraints: 4996 Sorted by residual: bond pdb=" C GLN B 114 " pdb=" N PRO B 115 " ideal model delta sigma weight residual 1.326 1.387 -0.061 1.44e-02 4.82e+03 1.79e+01 bond pdb=" CA GLN B 114 " pdb=" C GLN B 114 " ideal model delta sigma weight residual 1.523 1.558 -0.035 1.25e-02 6.40e+03 7.77e+00 bond pdb=" C GLU A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.333 1.351 -0.018 7.80e-03 1.64e+04 5.42e+00 bond pdb=" N ALA A 120 " pdb=" CA ALA A 120 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.27e+00 bond pdb=" C TYR B 146 " pdb=" N PRO B 147 " ideal model delta sigma weight residual 1.332 1.356 -0.025 1.30e-02 5.92e+03 3.56e+00 ... (remaining 4991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 6475 1.49 - 2.97: 297 2.97 - 4.46: 28 4.46 - 5.94: 7 5.94 - 7.43: 4 Bond angle restraints: 6811 Sorted by residual: angle pdb=" C GLN B 114 " pdb=" N PRO B 115 " pdb=" CA PRO B 115 " ideal model delta sigma weight residual 120.98 115.18 5.80 1.07e+00 8.73e-01 2.94e+01 angle pdb=" C PRO A 153 " pdb=" N GLU A 154 " pdb=" CA GLU A 154 " ideal model delta sigma weight residual 122.28 118.32 3.96 1.02e+00 9.61e-01 1.51e+01 angle pdb=" N THR A 197 " pdb=" CA THR A 197 " pdb=" C THR A 197 " ideal model delta sigma weight residual 112.68 107.71 4.97 1.33e+00 5.65e-01 1.40e+01 angle pdb=" N ALA A 120 " pdb=" CA ALA A 120 " pdb=" C ALA A 120 " ideal model delta sigma weight residual 110.80 118.23 -7.43 2.13e+00 2.20e-01 1.22e+01 angle pdb=" N LYS C 378 " pdb=" CA LYS C 378 " pdb=" C LYS C 378 " ideal model delta sigma weight residual 108.17 114.22 -6.05 1.85e+00 2.92e-01 1.07e+01 ... (remaining 6806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 2797 16.83 - 33.66: 130 33.66 - 50.49: 41 50.49 - 67.32: 10 67.32 - 84.15: 2 Dihedral angle restraints: 2980 sinusoidal: 1145 harmonic: 1835 Sorted by residual: dihedral pdb=" N ALA A 120 " pdb=" C ALA A 120 " pdb=" CA ALA A 120 " pdb=" CB ALA A 120 " ideal model delta harmonic sigma weight residual 122.90 132.46 -9.56 0 2.50e+00 1.60e-01 1.46e+01 dihedral pdb=" C ALA A 120 " pdb=" N ALA A 120 " pdb=" CA ALA A 120 " pdb=" CB ALA A 120 " ideal model delta harmonic sigma weight residual -122.60 -131.98 9.38 0 2.50e+00 1.60e-01 1.41e+01 dihedral pdb=" CB GLU B 189 " pdb=" CG GLU B 189 " pdb=" CD GLU B 189 " pdb=" OE1 GLU B 189 " ideal model delta sinusoidal sigma weight residual 0.00 -84.15 84.15 1 3.00e+01 1.11e-03 9.58e+00 ... (remaining 2977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 676 0.073 - 0.145: 71 0.145 - 0.218: 2 0.218 - 0.290: 0 0.290 - 0.363: 1 Chirality restraints: 750 Sorted by residual: chirality pdb=" CA ALA A 120 " pdb=" N ALA A 120 " pdb=" C ALA A 120 " pdb=" CB ALA A 120 " both_signs ideal model delta sigma weight residual False 2.48 2.12 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA LYS C 378 " pdb=" N LYS C 378 " pdb=" C LYS C 378 " pdb=" CB LYS C 378 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA TYR C 369 " pdb=" N TYR C 369 " pdb=" C TYR C 369 " pdb=" CB TYR C 369 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 747 not shown) Planarity restraints: 883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 190 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.80e+00 pdb=" N PRO A 191 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 191 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 191 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 27 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C GLY B 27 " 0.027 2.00e-02 2.50e+03 pdb=" O GLY B 27 " -0.010 2.00e-02 2.50e+03 pdb=" N SER B 28 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 125 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO B 126 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " -0.019 5.00e-02 4.00e+02 ... (remaining 880 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 207 2.71 - 3.26: 4598 3.26 - 3.81: 7752 3.81 - 4.35: 9274 4.35 - 4.90: 15771 Nonbonded interactions: 37602 Sorted by model distance: nonbonded pdb=" O LYS B 155 " pdb=" OG SER B 198 " model vdw 2.163 3.040 nonbonded pdb=" OG1 THR B 122 " pdb=" O LEU B 141 " model vdw 2.254 3.040 nonbonded pdb=" O ARG C 408 " pdb=" NE2 GLN C 414 " model vdw 2.266 3.120 nonbonded pdb=" O ALA B 163 " pdb=" OG SER B 185 " model vdw 2.277 3.040 nonbonded pdb=" O SER B 13 " pdb=" NZ LYS B 16 " model vdw 2.315 3.120 ... (remaining 37597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.040 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 4996 Z= 0.194 Angle : 0.706 7.428 6811 Z= 0.447 Chirality : 0.044 0.363 750 Planarity : 0.004 0.042 882 Dihedral : 11.244 84.155 1788 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 8.82 % Allowed : 7.17 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.28), residues: 628 helix: -4.77 (0.47), residues: 12 sheet: -2.88 (0.35), residues: 172 loop : -3.42 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 33 HIS 0.001 0.000 HIS A 206 PHE 0.009 0.001 PHE C 400 TYR 0.010 0.001 TYR C 369 ARG 0.001 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8329 (mt0) REVERT: A 184 LEU cc_start: 0.6631 (tp) cc_final: 0.6263 (tp) REVERT: A 212 LYS cc_start: 0.6387 (mmtt) cc_final: 0.5984 (mmtt) REVERT: B 29 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8955 (tt) REVERT: B 113 SER cc_start: 0.6507 (OUTLIER) cc_final: 0.6204 (p) REVERT: B 168 THR cc_start: 0.5662 (OUTLIER) cc_final: 0.5215 (p) REVERT: B 189 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.6904 (mm-30) REVERT: B 190 GLN cc_start: 0.6304 (OUTLIER) cc_final: 0.6037 (tt0) REVERT: B 192 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.5021 (mmmt) REVERT: B 194 HIS cc_start: 0.6438 (OUTLIER) cc_final: 0.6054 (m90) REVERT: B 195 ARG cc_start: 0.6583 (mmm160) cc_final: 0.5683 (mpp-170) REVERT: C 356 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7948 (tptp) REVERT: C 378 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8526 (mmmt) REVERT: C 394 ASN cc_start: 0.7748 (m-40) cc_final: 0.7288 (m-40) REVERT: C 452 LEU cc_start: 0.8394 (mt) cc_final: 0.8036 (mp) REVERT: C 516 GLU cc_start: 0.6658 (pt0) cc_final: 0.6439 (pt0) REVERT: C 517 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7591 (tm) outliers start: 48 outliers final: 15 residues processed: 177 average time/residue: 0.2002 time to fit residues: 43.2140 Evaluate side-chains 105 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 517 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 0.0270 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 203 ASN A 206 HIS B 92 GLN B 99 HIS B 100 ASN B 190 GLN ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 409 GLN C 439 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN C 493 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.149878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.124349 restraints weight = 11927.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.123009 restraints weight = 8276.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.124465 restraints weight = 6296.375| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4996 Z= 0.254 Angle : 0.617 7.188 6811 Z= 0.322 Chirality : 0.046 0.282 750 Planarity : 0.006 0.082 882 Dihedral : 9.665 82.920 767 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer: Outliers : 7.90 % Allowed : 11.95 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.29), residues: 628 helix: -4.45 (0.71), residues: 18 sheet: -2.30 (0.36), residues: 189 loop : -3.15 (0.26), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 36 HIS 0.002 0.001 HIS B 99 PHE 0.020 0.002 PHE C 400 TYR 0.015 0.002 TYR A 182 ARG 0.003 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 99 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7236 (t0) cc_final: 0.6557 (t70) REVERT: A 102 TYR cc_start: 0.9253 (t80) cc_final: 0.8992 (t80) REVERT: A 147 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.5775 (mp) REVERT: A 184 LEU cc_start: 0.6832 (tp) cc_final: 0.6621 (tp) REVERT: B 154 TRP cc_start: 0.6555 (m-90) cc_final: 0.6313 (m-90) REVERT: B 189 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7775 (mm-30) REVERT: B 194 HIS cc_start: 0.6593 (OUTLIER) cc_final: 0.6337 (m90) REVERT: B 195 ARG cc_start: 0.6464 (mmm160) cc_final: 0.5235 (mpp-170) REVERT: C 378 LYS cc_start: 0.9022 (mmtm) cc_final: 0.8327 (tptp) REVERT: C 406 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6496 (tt0) REVERT: C 461 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5860 (tp) REVERT: C 517 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7956 (tm) outliers start: 43 outliers final: 23 residues processed: 129 average time/residue: 0.1915 time to fit residues: 30.4887 Evaluate side-chains 99 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 LYS Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.147024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.122355 restraints weight = 12014.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.121166 restraints weight = 7938.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.122610 restraints weight = 6392.975| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4996 Z= 0.297 Angle : 0.648 6.892 6811 Z= 0.337 Chirality : 0.047 0.214 750 Planarity : 0.006 0.089 882 Dihedral : 8.734 83.028 747 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.97 % Favored : 85.03 % Rotamer: Outliers : 7.90 % Allowed : 14.71 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.30), residues: 628 helix: -4.48 (0.75), residues: 18 sheet: -2.23 (0.34), residues: 203 loop : -3.11 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.007 0.002 HIS B 203 PHE 0.021 0.002 PHE C 400 TYR 0.014 0.002 TYR A 151 ARG 0.003 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 77 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 PHE cc_start: 0.8722 (t80) cc_final: 0.8498 (t80) REVERT: A 73 ASP cc_start: 0.7331 (t0) cc_final: 0.7093 (t70) REVERT: A 76 LYS cc_start: 0.8360 (pttp) cc_final: 0.8041 (pttm) REVERT: B 176 ASN cc_start: 0.6107 (m-40) cc_final: 0.5784 (t0) REVERT: B 189 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7835 (mm-30) REVERT: B 195 ARG cc_start: 0.6441 (mmm160) cc_final: 0.5283 (mpp-170) REVERT: C 378 LYS cc_start: 0.8937 (mmtm) cc_final: 0.8590 (mmtm) REVERT: C 452 LEU cc_start: 0.8890 (mp) cc_final: 0.8637 (mt) REVERT: C 505 TYR cc_start: 0.7893 (m-10) cc_final: 0.7633 (m-10) REVERT: C 517 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7654 (tm) outliers start: 43 outliers final: 25 residues processed: 110 average time/residue: 0.1967 time to fit residues: 27.7232 Evaluate side-chains 98 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 517 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 3 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 0.0170 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 474 GLN ** 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 = 0.4134 r_free = 0.4134 target = 0.146998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.119688 restraints weight = 12059.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.121262 restraints weight = 7686.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.122166 restraints weight = 5727.733| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4996 Z= 0.323 Angle : 0.674 7.326 6811 Z= 0.348 Chirality : 0.047 0.231 750 Planarity : 0.006 0.086 882 Dihedral : 8.668 83.082 741 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.08 % Favored : 83.92 % Rotamer: Outliers : 7.54 % Allowed : 16.36 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.30), residues: 628 helix: -4.43 (0.78), residues: 18 sheet: -2.11 (0.35), residues: 200 loop : -3.06 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 47 HIS 0.006 0.002 HIS A 206 PHE 0.026 0.002 PHE C 400 TYR 0.012 0.002 TYR C 380 ARG 0.003 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 72 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 PHE cc_start: 0.8808 (t80) cc_final: 0.8571 (t80) REVERT: B 114 GLN cc_start: 0.7411 (mp10) cc_final: 0.7074 (mp10) REVERT: B 176 ASN cc_start: 0.6383 (m-40) cc_final: 0.5923 (t0) REVERT: B 195 ARG cc_start: 0.6326 (mmm160) cc_final: 0.5179 (mpp-170) REVERT: C 378 LYS cc_start: 0.8903 (mmtm) cc_final: 0.8548 (mmtm) REVERT: C 406 GLU cc_start: 0.6982 (tt0) cc_final: 0.6481 (tt0) REVERT: C 505 TYR cc_start: 0.7863 (m-10) cc_final: 0.7646 (m-10) REVERT: C 517 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7692 (tm) outliers start: 41 outliers final: 29 residues processed: 103 average time/residue: 0.2835 time to fit residues: 37.6274 Evaluate side-chains 95 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.2980 chunk 60 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 22 optimal weight: 0.0870 chunk 34 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.146915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.122124 restraints weight = 11927.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.122663 restraints weight = 9178.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.123984 restraints weight = 6953.537| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4996 Z= 0.201 Angle : 0.608 6.410 6811 Z= 0.311 Chirality : 0.046 0.209 750 Planarity : 0.005 0.090 882 Dihedral : 7.511 64.111 736 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.38 % Favored : 86.62 % Rotamer: Outliers : 4.96 % Allowed : 19.85 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.31), residues: 628 helix: -4.48 (0.73), residues: 18 sheet: -1.91 (0.36), residues: 201 loop : -3.00 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 154 HIS 0.004 0.001 HIS B 203 PHE 0.018 0.001 PHE C 400 TYR 0.011 0.001 TYR B 50 ARG 0.002 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 29 PHE cc_start: 0.8765 (t80) cc_final: 0.8556 (t80) REVERT: A 73 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.7024 (t70) REVERT: A 76 LYS cc_start: 0.8154 (pttp) cc_final: 0.7917 (pttm) REVERT: B 116 LYS cc_start: 0.6754 (tmtt) cc_final: 0.6471 (tptt) REVERT: B 135 LYS cc_start: 0.4475 (OUTLIER) cc_final: 0.4212 (tptt) REVERT: B 176 ASN cc_start: 0.6277 (m-40) cc_final: 0.5851 (t0) REVERT: B 195 ARG cc_start: 0.6293 (mmm160) cc_final: 0.5177 (mpp-170) REVERT: C 378 LYS cc_start: 0.8767 (mmtm) cc_final: 0.8234 (tptp) REVERT: C 406 GLU cc_start: 0.6380 (tt0) cc_final: 0.6105 (tt0) REVERT: C 452 LEU cc_start: 0.8708 (mp) cc_final: 0.8463 (tp) REVERT: C 505 TYR cc_start: 0.7709 (m-10) cc_final: 0.7477 (m-10) outliers start: 27 outliers final: 19 residues processed: 93 average time/residue: 0.2140 time to fit residues: 25.7614 Evaluate side-chains 82 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 0.0070 chunk 43 optimal weight: 0.0020 chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 0.0370 chunk 20 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 19 optimal weight: 0.0270 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.0050 chunk 25 optimal weight: 0.4980 overall best weight: 0.0156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** 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 = 0.4248 r_free = 0.4248 target = 0.156062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.128503 restraints weight = 12143.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.130403 restraints weight = 8424.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.131492 restraints weight = 5286.138| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 4996 Z= 0.159 Angle : 0.568 6.085 6811 Z= 0.290 Chirality : 0.045 0.190 750 Planarity : 0.005 0.093 882 Dihedral : 6.902 58.948 734 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.10 % Favored : 87.90 % Rotamer: Outliers : 2.94 % Allowed : 22.24 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.31), residues: 628 helix: -4.60 (0.59), residues: 18 sheet: -1.44 (0.38), residues: 195 loop : -2.91 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.004 0.001 HIS B 203 PHE 0.013 0.001 PHE C 400 TYR 0.010 0.001 TYR B 50 ARG 0.002 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 29 PHE cc_start: 0.8736 (t80) cc_final: 0.8535 (t80) REVERT: A 102 TYR cc_start: 0.9026 (t80) cc_final: 0.8807 (t80) REVERT: B 190 GLN cc_start: 0.6468 (mp10) cc_final: 0.6100 (tt0) REVERT: B 192 LYS cc_start: 0.6689 (OUTLIER) cc_final: 0.4980 (tptp) REVERT: C 378 LYS cc_start: 0.8874 (mmtm) cc_final: 0.8421 (tptp) REVERT: C 406 GLU cc_start: 0.6589 (tt0) cc_final: 0.6382 (tt0) REVERT: C 452 LEU cc_start: 0.8743 (mp) cc_final: 0.8493 (tp) REVERT: C 505 TYR cc_start: 0.7747 (m-10) cc_final: 0.7490 (m-10) outliers start: 16 outliers final: 11 residues processed: 88 average time/residue: 0.2016 time to fit residues: 21.9648 Evaluate side-chains 74 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain C residue 354 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.0370 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.2980 chunk 58 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN B 6 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.146490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.121431 restraints weight = 11808.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.122158 restraints weight = 8922.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.123422 restraints weight = 6816.892| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4996 Z= 0.268 Angle : 0.666 9.199 6811 Z= 0.335 Chirality : 0.046 0.185 750 Planarity : 0.005 0.086 882 Dihedral : 6.648 57.816 730 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.65 % Favored : 85.35 % Rotamer: Outliers : 4.04 % Allowed : 20.77 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.32), residues: 628 helix: -4.43 (0.71), residues: 18 sheet: -1.47 (0.37), residues: 201 loop : -2.92 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.004 0.001 HIS A 206 PHE 0.018 0.002 PHE C 400 TYR 0.017 0.002 TYR C 489 ARG 0.005 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 29 PHE cc_start: 0.8771 (t80) cc_final: 0.8516 (t80) REVERT: B 131 LEU cc_start: 0.6828 (tt) cc_final: 0.6574 (tp) REVERT: B 176 ASN cc_start: 0.7743 (m-40) cc_final: 0.7301 (t0) REVERT: C 378 LYS cc_start: 0.8845 (mmtm) cc_final: 0.8350 (tptp) REVERT: C 406 GLU cc_start: 0.6738 (tt0) cc_final: 0.6231 (tt0) REVERT: C 452 LEU cc_start: 0.8737 (mp) cc_final: 0.8520 (tp) REVERT: C 505 TYR cc_start: 0.7752 (m-10) cc_final: 0.7431 (m-10) outliers start: 22 outliers final: 20 residues processed: 82 average time/residue: 0.1809 time to fit residues: 18.9305 Evaluate side-chains 79 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 0.0870 chunk 60 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 43 optimal weight: 0.0670 chunk 59 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** 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 = 0.4124 r_free = 0.4124 target = 0.147866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.123205 restraints weight = 11941.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.123695 restraints weight = 9202.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.124851 restraints weight = 7105.017| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4996 Z= 0.202 Angle : 0.638 8.568 6811 Z= 0.321 Chirality : 0.045 0.213 750 Planarity : 0.005 0.082 882 Dihedral : 6.564 58.116 730 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.17 % Favored : 85.83 % Rotamer: Outliers : 4.41 % Allowed : 21.14 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.31), residues: 628 helix: -4.44 (0.73), residues: 18 sheet: -1.25 (0.40), residues: 183 loop : -2.95 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.002 0.001 HIS A 206 PHE 0.016 0.001 PHE C 400 TYR 0.018 0.001 TYR C 489 ARG 0.004 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 29 PHE cc_start: 0.8755 (t80) cc_final: 0.8515 (t80) REVERT: B 176 ASN cc_start: 0.7701 (m-40) cc_final: 0.7067 (t0) REVERT: B 190 GLN cc_start: 0.6610 (mp10) cc_final: 0.6387 (tt0) REVERT: C 378 LYS cc_start: 0.8849 (mmtm) cc_final: 0.8376 (tptp) REVERT: C 406 GLU cc_start: 0.6598 (tt0) cc_final: 0.6173 (tt0) REVERT: C 505 TYR cc_start: 0.7743 (m-10) cc_final: 0.7499 (m-10) outliers start: 24 outliers final: 22 residues processed: 86 average time/residue: 0.2565 time to fit residues: 27.9634 Evaluate side-chains 87 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.142732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.118626 restraints weight = 11789.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.117759 restraints weight = 8402.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.119051 restraints weight = 7045.678| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 4996 Z= 0.351 Angle : 0.742 10.526 6811 Z= 0.375 Chirality : 0.048 0.235 750 Planarity : 0.006 0.079 882 Dihedral : 7.270 59.517 730 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.24 % Favored : 83.76 % Rotamer: Outliers : 4.60 % Allowed : 20.77 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.31), residues: 628 helix: -4.18 (0.93), residues: 18 sheet: -1.49 (0.37), residues: 200 loop : -3.06 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 160 HIS 0.007 0.001 HIS A 206 PHE 0.021 0.002 PHE C 400 TYR 0.020 0.002 TYR C 489 ARG 0.004 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.7504 (mmmt) cc_final: 0.7304 (mmmt) REVERT: A 102 TYR cc_start: 0.9170 (t80) cc_final: 0.8901 (t80) REVERT: A 147 LEU cc_start: 0.6013 (tt) cc_final: 0.5364 (mp) REVERT: B 176 ASN cc_start: 0.7808 (m-40) cc_final: 0.7231 (t0) REVERT: C 378 LYS cc_start: 0.8889 (mmtm) cc_final: 0.8328 (tptp) REVERT: C 505 TYR cc_start: 0.7954 (m-10) cc_final: 0.7694 (m-10) outliers start: 25 outliers final: 21 residues processed: 87 average time/residue: 0.2611 time to fit residues: 29.1529 Evaluate side-chains 85 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 46 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.142237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.118697 restraints weight = 11912.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.117806 restraints weight = 8627.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.119105 restraints weight = 7197.467| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 4996 Z= 0.365 Angle : 0.764 10.865 6811 Z= 0.388 Chirality : 0.049 0.264 750 Planarity : 0.006 0.102 882 Dihedral : 7.436 59.744 730 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.40 % Favored : 83.60 % Rotamer: Outliers : 4.23 % Allowed : 20.77 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.31), residues: 628 helix: -4.40 (0.75), residues: 18 sheet: -1.33 (0.39), residues: 189 loop : -3.12 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 154 HIS 0.006 0.001 HIS A 206 PHE 0.023 0.002 PHE C 400 TYR 0.021 0.002 TYR C 489 ARG 0.004 0.001 ARG A 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 176 ASN cc_start: 0.7910 (m-40) cc_final: 0.7356 (t0) REVERT: C 378 LYS cc_start: 0.8832 (mmtm) cc_final: 0.8306 (tptp) REVERT: C 452 LEU cc_start: 0.8519 (tp) cc_final: 0.8111 (tp) REVERT: C 505 TYR cc_start: 0.7697 (m-10) cc_final: 0.7474 (m-10) outliers start: 23 outliers final: 23 residues processed: 78 average time/residue: 0.1857 time to fit residues: 18.4565 Evaluate side-chains 78 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 27 optimal weight: 0.0030 chunk 40 optimal weight: 0.0570 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.4508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 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 = 0.4093 r_free = 0.4093 target = 0.145287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.121480 restraints weight = 11721.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.121709 restraints weight = 8679.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.122892 restraints weight = 6999.750| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4996 Z= 0.250 Angle : 0.694 10.076 6811 Z= 0.352 Chirality : 0.047 0.247 750 Planarity : 0.006 0.097 882 Dihedral : 7.056 59.351 730 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.45 % Favored : 84.55 % Rotamer: Outliers : 4.04 % Allowed : 21.51 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.31), residues: 628 helix: -4.39 (0.74), residues: 18 sheet: -1.37 (0.38), residues: 195 loop : -3.01 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 154 HIS 0.004 0.001 HIS A 206 PHE 0.018 0.002 PHE C 400 TYR 0.019 0.002 TYR C 489 ARG 0.004 0.001 ARG C 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2832.85 seconds wall clock time: 51 minutes 45.62 seconds (3105.62 seconds total)