Starting phenix.real_space_refine on Tue Feb 11 09:09:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wo7_32641/02_2025/7wo7_32641.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wo7_32641/02_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_32641/02_2025/7wo7_32641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wo7_32641/02_2025/7wo7_32641.map" model { file = "/net/cci-nas-00/data/ceres_data/7wo7_32641/02_2025/7wo7_32641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wo7_32641/02_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-5592/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: 4.50, per 1000 atoms: 0.92 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: 1.16 Conformation dependent library (CDL) restraints added in 572.4 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: 0.54 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: 1.18 Time building geometry restraints manager: 1.38 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: 5.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.150 Find NCS groups from input model: 0.060 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.630 ------------------------------------------------------------------------------- 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 : 0.542 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: 0.1987 time to fit residues: 42.8511 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 : 0.540 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.5038 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.150104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.124529 restraints weight = 11945.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.123125 restraints weight = 8307.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.124542 restraints weight = 6298.976| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4996 Z= 0.248 Angle : 0.616 7.215 6811 Z= 0.321 Chirality : 0.046 0.278 750 Planarity : 0.006 0.081 882 Dihedral : 9.657 82.879 767 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.74 % Favored : 87.26 % Rotamer: Outliers : 7.72 % Allowed : 11.76 % Favored : 80.51 % 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: -4.20 (0.29), residues: 628 helix: -4.46 (0.70), residues: 18 sheet: -2.30 (0.36), residues: 189 loop : -3.14 (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 0.016 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: 42 poor density : 100 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7237 (t0) cc_final: 0.6607 (t70) REVERT: A 102 TYR cc_start: 0.9263 (t80) cc_final: 0.8997 (t80) REVERT: A 123 LYS cc_start: 0.8378 (pttt) cc_final: 0.8131 (pttm) REVERT: A 147 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.5778 (mp) REVERT: A 184 LEU cc_start: 0.6829 (tp) cc_final: 0.6611 (tp) REVERT: B 154 TRP cc_start: 0.6553 (m-90) cc_final: 0.6311 (m-90) REVERT: B 189 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7772 (mm-30) REVERT: B 194 HIS cc_start: 0.6630 (OUTLIER) cc_final: 0.6382 (m90) REVERT: B 195 ARG cc_start: 0.6499 (mmm160) cc_final: 0.5373 (mpp-170) REVERT: C 378 LYS cc_start: 0.9017 (mmtm) cc_final: 0.8324 (tptp) REVERT: C 406 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6461 (tt0) REVERT: C 461 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5867 (tp) REVERT: C 517 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7952 (tm) outliers start: 42 outliers final: 21 residues processed: 130 average time/residue: 0.2025 time to fit residues: 32.4967 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 : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN 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 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: 0.0980 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 53 optimal weight: 0.0570 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4153 r_free = 0.4153 target = 0.149878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.125097 restraints weight = 12252.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.127192 restraints weight = 8494.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.128193 restraints weight = 5664.288| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4996 Z= 0.255 Angle : 0.626 6.534 6811 Z= 0.326 Chirality : 0.047 0.290 750 Planarity : 0.005 0.088 882 Dihedral : 8.581 83.181 747 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.69 % Favored : 86.31 % Rotamer: Outliers : 6.80 % Allowed : 15.26 % Favored : 77.94 % 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: -4.09 (0.30), residues: 628 helix: -4.44 (0.78), residues: 18 sheet: -2.19 (0.34), residues: 203 loop : -3.08 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 47 HIS 0.007 0.001 HIS B 203 PHE 0.020 0.002 PHE C 400 TYR 0.013 0.002 TYR A 151 ARG 0.003 0.001 ARG B 55 *********************** 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 112 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 75 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7150 (t0) cc_final: 0.6806 (t70) REVERT: A 76 LYS cc_start: 0.8187 (pttp) cc_final: 0.7903 (pttm) REVERT: B 189 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7747 (mm-30) REVERT: B 194 HIS cc_start: 0.6730 (OUTLIER) cc_final: 0.6503 (m90) REVERT: B 195 ARG cc_start: 0.6536 (mmm160) cc_final: 0.5457 (mpp-170) REVERT: C 378 LYS cc_start: 0.8933 (mmtm) cc_final: 0.8632 (mmtm) REVERT: C 452 LEU cc_start: 0.8833 (mp) cc_final: 0.8544 (mt) REVERT: C 465 GLU cc_start: 0.6499 (pt0) cc_final: 0.6298 (pt0) REVERT: C 525 CYS cc_start: 0.4425 (t) cc_final: 0.3812 (t) outliers start: 37 outliers final: 23 residues processed: 104 average time/residue: 0.1987 time to fit residues: 25.7453 Evaluate side-chains 96 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 TYR 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 192 LYS Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 510 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 3 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 16 optimal weight: 0.0010 chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 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 = 0.4152 r_free = 0.4152 target = 0.148416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.121241 restraints weight = 12187.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.122427 restraints weight = 8473.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.123579 restraints weight = 5820.854| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4996 Z= 0.283 Angle : 0.647 6.917 6811 Z= 0.333 Chirality : 0.046 0.252 750 Planarity : 0.005 0.085 882 Dihedral : 8.355 83.323 742 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.45 % Favored : 84.55 % Rotamer: Outliers : 6.43 % Allowed : 16.54 % Favored : 77.02 % 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: -3.92 (0.30), residues: 628 helix: -4.50 (0.72), residues: 18 sheet: -2.03 (0.34), residues: 206 loop : -2.98 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.005 0.002 HIS A 206 PHE 0.016 0.002 PHE C 400 TYR 0.013 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 108 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 73 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8241 (pttp) cc_final: 0.8018 (pttm) REVERT: B 195 ARG cc_start: 0.6310 (mmm160) cc_final: 0.5193 (mpp-170) REVERT: C 378 LYS cc_start: 0.8914 (mmtm) cc_final: 0.8575 (mmtm) REVERT: C 406 GLU cc_start: 0.6501 (tt0) cc_final: 0.6199 (tt0) outliers start: 35 outliers final: 22 residues processed: 101 average time/residue: 0.1787 time to fit residues: 23.1336 Evaluate side-chains 85 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 126 SER 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 57 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 130 GLU 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 Chi-restraints excluded: chain C residue 433 VAL 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: 0.8980 chunk 60 optimal weight: 0.0970 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.0070 chunk 13 optimal weight: 4.9990 chunk 43 optimal weight: 0.0870 chunk 22 optimal weight: 0.0870 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.2352 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.152380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.121601 restraints weight = 12216.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.124448 restraints weight = 6632.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.126212 restraints weight = 4554.124| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4996 Z= 0.185 Angle : 0.596 6.345 6811 Z= 0.307 Chirality : 0.045 0.217 750 Planarity : 0.005 0.090 882 Dihedral : 6.942 64.446 733 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer: Outliers : 4.41 % Allowed : 19.67 % Favored : 75.92 % 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: -3.73 (0.31), residues: 628 helix: -4.51 (0.69), residues: 18 sheet: -1.76 (0.36), residues: 201 loop : -2.92 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.006 0.001 HIS B 194 PHE 0.020 0.001 PHE A 152 TYR 0.010 0.001 TYR B 50 ARG 0.002 0.000 ARG C 457 *********************** 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: 24 poor density : 75 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 LYS cc_start: 0.5793 (pttp) cc_final: 0.5271 (pttp) REVERT: B 114 GLN cc_start: 0.7251 (mp10) cc_final: 0.6881 (mp10) REVERT: B 116 LYS cc_start: 0.6388 (tmtt) cc_final: 0.6137 (tptt) REVERT: B 195 ARG cc_start: 0.6247 (mmm160) cc_final: 0.5088 (mpp-170) REVERT: C 378 LYS cc_start: 0.8879 (mmtm) cc_final: 0.8320 (tptp) REVERT: C 406 GLU cc_start: 0.6588 (tt0) cc_final: 0.6279 (tt0) REVERT: C 452 LEU cc_start: 0.8729 (mp) cc_final: 0.8475 (tp) outliers start: 24 outliers final: 18 residues processed: 94 average time/residue: 0.1809 time to fit residues: 21.5491 Evaluate side-chains 81 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL 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 130 GLU 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 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: 0.0870 chunk 43 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 5 optimal weight: 0.0070 chunk 20 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.0980 chunk 25 optimal weight: 0.9990 overall best weight: 0.2576 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.148119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.123187 restraints weight = 11847.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.122782 restraints weight = 8569.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.124267 restraints weight = 6959.534| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4996 Z= 0.194 Angle : 0.613 9.037 6811 Z= 0.312 Chirality : 0.045 0.198 750 Planarity : 0.005 0.093 882 Dihedral : 6.870 64.381 733 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.85 % Favored : 86.15 % Rotamer: Outliers : 3.68 % Allowed : 20.22 % 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: -3.64 (0.31), residues: 628 helix: -4.50 (0.68), residues: 18 sheet: -1.59 (0.37), residues: 201 loop : -2.92 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.003 0.001 HIS B 203 PHE 0.018 0.001 PHE C 400 TYR 0.010 0.001 TYR C 473 ARG 0.002 0.000 ARG C 408 *********************** 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 89 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 215 LYS cc_start: 0.5903 (pttp) cc_final: 0.5219 (pttp) REVERT: B 195 ARG cc_start: 0.6340 (mmm160) cc_final: 0.5169 (mpp-170) REVERT: C 378 LYS cc_start: 0.8842 (mmtm) cc_final: 0.8310 (tptp) REVERT: C 406 GLU cc_start: 0.6603 (tt0) cc_final: 0.6299 (tt0) REVERT: C 452 LEU cc_start: 0.8684 (mp) cc_final: 0.8431 (tp) outliers start: 20 outliers final: 18 residues processed: 85 average time/residue: 0.2114 time to fit residues: 22.8764 Evaluate side-chains 79 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 126 SER 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 130 GLU Chi-restraints excluded: chain B residue 141 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 chunk 56 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.146593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.122351 restraints weight = 11823.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.122576 restraints weight = 8679.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.123680 restraints weight = 7163.613| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4996 Z= 0.222 Angle : 0.623 9.197 6811 Z= 0.316 Chirality : 0.045 0.187 750 Planarity : 0.006 0.094 882 Dihedral : 6.978 66.565 733 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.97 % Favored : 85.03 % Rotamer: Outliers : 4.23 % Allowed : 19.67 % 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: -3.55 (0.32), residues: 628 helix: -4.48 (0.69), residues: 18 sheet: -1.46 (0.38), residues: 201 loop : -2.90 (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 0.001 PHE C 400 TYR 0.016 0.002 TYR C 489 ARG 0.002 0.000 ARG B 55 *********************** 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 91 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 LYS cc_start: 0.6076 (pttp) cc_final: 0.5396 (pttp) REVERT: B 195 ARG cc_start: 0.6504 (mmm160) cc_final: 0.5270 (mpp-170) REVERT: C 378 LYS cc_start: 0.8904 (mmtm) cc_final: 0.8373 (tptp) REVERT: C 452 LEU cc_start: 0.8721 (mp) cc_final: 0.8488 (tp) outliers start: 23 outliers final: 22 residues processed: 87 average time/residue: 0.2032 time to fit residues: 22.4047 Evaluate side-chains 82 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 126 SER 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 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 ASP 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 59 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.144013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.120637 restraints weight = 12039.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.119090 restraints weight = 10367.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.120592 restraints weight = 7867.652| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4996 Z= 0.294 Angle : 0.685 8.832 6811 Z= 0.349 Chirality : 0.046 0.195 750 Planarity : 0.006 0.095 882 Dihedral : 7.251 66.128 733 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.08 % Favored : 83.92 % Rotamer: Outliers : 4.78 % Allowed : 19.49 % Favored : 75.74 % 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: -3.61 (0.31), residues: 628 helix: -4.42 (0.72), residues: 18 sheet: -1.50 (0.37), residues: 200 loop : -2.95 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.005 0.001 HIS A 206 PHE 0.021 0.002 PHE C 400 TYR 0.020 0.002 TYR C 489 ARG 0.003 0.001 ARG B 55 *********************** 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 92 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 LYS cc_start: 0.6145 (pttp) cc_final: 0.5281 (pttp) REVERT: B 195 ARG cc_start: 0.6522 (mmm160) cc_final: 0.5274 (mpp-170) REVERT: C 378 LYS cc_start: 0.8892 (mmtm) cc_final: 0.8570 (tptp) REVERT: C 452 LEU cc_start: 0.8797 (mp) cc_final: 0.8576 (tp) outliers start: 26 outliers final: 23 residues processed: 88 average time/residue: 0.2026 time to fit residues: 22.7373 Evaluate side-chains 81 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 116 THR Chi-restraints excluded: chain A residue 126 SER 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 93 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 ASP 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 433 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.143380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.118838 restraints weight = 11764.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.117669 restraints weight = 9296.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.119073 restraints weight = 7830.955| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4996 Z= 0.310 Angle : 0.687 8.462 6811 Z= 0.353 Chirality : 0.047 0.240 750 Planarity : 0.006 0.095 882 Dihedral : 7.386 64.191 733 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.08 % Favored : 83.92 % Rotamer: Outliers : 4.96 % Allowed : 20.77 % Favored : 74.26 % 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: -3.63 (0.31), residues: 628 helix: -4.49 (0.70), residues: 18 sheet: -1.48 (0.38), residues: 200 loop : -2.98 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 154 HIS 0.005 0.002 HIS A 206 PHE 0.022 0.002 PHE C 400 TYR 0.020 0.002 TYR C 489 ARG 0.003 0.001 ARG A 98 *********************** 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 90 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: B 195 ARG cc_start: 0.6517 (mmm160) cc_final: 0.5271 (mpp-170) REVERT: C 378 LYS cc_start: 0.8884 (mmtm) cc_final: 0.8331 (tptp) outliers start: 27 outliers final: 25 residues processed: 84 average time/residue: 0.1794 time to fit residues: 19.2580 Evaluate side-chains 85 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 116 THR Chi-restraints excluded: chain A residue 126 SER 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 57 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 46 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS ** 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 = 0.4065 r_free = 0.4065 target = 0.143582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.120628 restraints weight = 11930.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.119104 restraints weight = 8914.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.120447 restraints weight = 7504.623| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4996 Z= 0.305 Angle : 0.704 8.559 6811 Z= 0.362 Chirality : 0.048 0.252 750 Planarity : 0.006 0.096 882 Dihedral : 7.435 63.503 733 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.40 % Favored : 83.60 % Rotamer: Outliers : 4.78 % Allowed : 20.77 % 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: -3.59 (0.32), residues: 628 helix: -4.39 (0.78), residues: 18 sheet: -1.48 (0.38), residues: 200 loop : -2.94 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 154 HIS 0.006 0.001 HIS A 206 PHE 0.031 0.002 PHE A 29 TYR 0.022 0.002 TYR C 489 ARG 0.003 0.001 ARG B 55 ********************** 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 83 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.7534 (mmmt) cc_final: 0.7322 (mmmt) REVERT: B 195 ARG cc_start: 0.6579 (mmm160) cc_final: 0.5289 (mpp-170) REVERT: C 378 LYS cc_start: 0.8835 (mmtm) cc_final: 0.8290 (tptp) REVERT: C 406 GLU cc_start: 0.5992 (tt0) cc_final: 0.5375 (tt0) outliers start: 26 outliers final: 26 residues processed: 78 average time/residue: 0.1895 time to fit residues: 18.8637 Evaluate side-chains 79 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 53 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 126 SER 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 57 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 27 optimal weight: 0.0000 chunk 40 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4099 r_free = 0.4099 target = 0.146193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.121904 restraints weight = 11878.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.120953 restraints weight = 8781.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.122440 restraints weight = 7344.742| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4996 Z= 0.208 Angle : 0.644 8.045 6811 Z= 0.330 Chirality : 0.046 0.210 750 Planarity : 0.006 0.097 882 Dihedral : 6.996 60.764 733 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.49 % Favored : 85.51 % 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: -3.40 (0.32), residues: 628 helix: -4.55 (0.64), residues: 18 sheet: -1.22 (0.39), residues: 194 loop : -2.86 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 154 HIS 0.003 0.001 HIS A 206 PHE 0.016 0.001 PHE C 400 TYR 0.019 0.001 TYR C 489 ARG 0.002 0.000 ARG B 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2140.01 seconds wall clock time: 40 minutes 30.68 seconds (2430.68 seconds total)