Starting phenix.real_space_refine on Tue Feb 11 09:41:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qtk_14143/02_2025/7qtk_14143.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qtk_14143/02_2025/7qtk_14143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qtk_14143/02_2025/7qtk_14143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qtk_14143/02_2025/7qtk_14143.map" model { file = "/net/cci-nas-00/data/ceres_data/7qtk_14143/02_2025/7qtk_14143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qtk_14143/02_2025/7qtk_14143.cif" } resolution = 3.84 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= 0.029 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 19 5.16 5 C 3171 2.51 5 N 845 2.21 5 O 974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5009 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "C" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.69, per 1000 atoms: 0.94 Number of scatterers: 5009 At special positions: 0 Unit cell: (71.9316, 103.747, 125.88, 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 19 16.00 O 974 8.00 N 845 7.00 C 3171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.05 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " 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 BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN D 343 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 709.0 milliseconds 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1194 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 13 sheets defined 11.7% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.320A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 372 removed outlier: 3.875A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 removed outlier: 4.035A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.756A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.766A pdb=" N ASP B 31 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.853A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 removed outlier: 3.654A pdb=" N LYS C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 189 removed outlier: 3.731A pdb=" N HIS C 189 " --> pdb=" O ASP C 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 354 through 358 removed outlier: 4.132A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'D' and resid 473 through 474 removed outlier: 4.001A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.334A pdb=" N GLY B 10 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 50 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 59 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.334A pdb=" N GLY B 10 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE B 114 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 136 removed outlier: 3.547A pdb=" N GLY B 151 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 144 Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 166 removed outlier: 3.650A pdb=" N THR B 163 " --> pdb=" O ASN B 211 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR B 206 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.665A pdb=" N VAL C 19 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 13 removed outlier: 7.135A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 114 through 118 removed outlier: 3.804A pdb=" N VAL C 133 " --> pdb=" O PHE C 118 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 153 through 155 removed outlier: 4.260A pdb=" N TRP C 148 " --> pdb=" O GLN C 155 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS C 145 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 207 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL C 196 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 205 " --> pdb=" O VAL C 196 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 408 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: 1.71 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 859 1.32 - 1.45: 1457 1.45 - 1.57: 2798 1.57 - 1.69: 0 1.69 - 1.82: 20 Bond restraints: 5134 Sorted by residual: bond pdb=" N VAL C 96 " pdb=" CA VAL C 96 " ideal model delta sigma weight residual 1.457 1.509 -0.052 1.32e-02 5.74e+03 1.53e+01 bond pdb=" CA SER C 93 " pdb=" CB SER C 93 " ideal model delta sigma weight residual 1.530 1.470 0.060 1.69e-02 3.50e+03 1.26e+01 bond pdb=" N THR C 109 " pdb=" CA THR C 109 " ideal model delta sigma weight residual 1.455 1.498 -0.042 1.33e-02 5.65e+03 1.00e+01 bond pdb=" N VAL C 110 " pdb=" CA VAL C 110 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.22e-02 6.72e+03 9.37e+00 bond pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.45e+00 ... (remaining 5129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 6696 1.64 - 3.28: 220 3.28 - 4.92: 50 4.92 - 6.57: 13 6.57 - 8.21: 4 Bond angle restraints: 6983 Sorted by residual: angle pdb=" C VAL C 96 " pdb=" N THR C 97 " pdb=" CA THR C 97 " ideal model delta sigma weight residual 122.39 115.93 6.46 1.48e+00 4.57e-01 1.90e+01 angle pdb=" N PRO C 95 " pdb=" CA PRO C 95 " pdb=" C PRO C 95 " ideal model delta sigma weight residual 112.47 104.26 8.21 2.06e+00 2.36e-01 1.59e+01 angle pdb=" N TYR C 94 " pdb=" CA TYR C 94 " pdb=" CB TYR C 94 " ideal model delta sigma weight residual 110.37 117.38 -7.01 1.78e+00 3.16e-01 1.55e+01 angle pdb=" CA TYR C 94 " pdb=" C TYR C 94 " pdb=" N PRO C 95 " ideal model delta sigma weight residual 118.44 124.39 -5.95 1.59e+00 3.96e-01 1.40e+01 angle pdb=" CA LYS B 129 " pdb=" C LYS B 129 " pdb=" O LYS B 129 " ideal model delta sigma weight residual 121.40 117.32 4.08 1.11e+00 8.12e-01 1.35e+01 ... (remaining 6978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 2781 16.64 - 33.28: 240 33.28 - 49.92: 47 49.92 - 66.56: 13 66.56 - 83.20: 4 Dihedral angle restraints: 3085 sinusoidal: 1216 harmonic: 1869 Sorted by residual: dihedral pdb=" N TYR C 94 " pdb=" C TYR C 94 " pdb=" CA TYR C 94 " pdb=" CB TYR C 94 " ideal model delta harmonic sigma weight residual 122.80 138.48 -15.68 0 2.50e+00 1.60e-01 3.93e+01 dihedral pdb=" C TYR C 94 " pdb=" N TYR C 94 " pdb=" CA TYR C 94 " pdb=" CB TYR C 94 " ideal model delta harmonic sigma weight residual -122.60 -135.93 13.33 0 2.50e+00 1.60e-01 2.84e+01 dihedral pdb=" CB CYS D 391 " pdb=" SG CYS D 391 " pdb=" SG CYS D 525 " pdb=" CB CYS D 525 " ideal model delta sinusoidal sigma weight residual 93.00 50.33 42.67 1 1.00e+01 1.00e-02 2.54e+01 ... (remaining 3082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 755 0.122 - 0.245: 18 0.245 - 0.367: 1 0.367 - 0.489: 0 0.489 - 0.611: 1 Chirality restraints: 775 Sorted by residual: chirality pdb=" CA TYR C 94 " pdb=" N TYR C 94 " pdb=" C TYR C 94 " pdb=" CB TYR C 94 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.34e+00 chirality pdb=" CA VAL B 123 " pdb=" N VAL B 123 " pdb=" C VAL B 123 " pdb=" CB VAL B 123 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA LYS B 129 " pdb=" N LYS B 129 " pdb=" C LYS B 129 " pdb=" CB LYS B 129 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 772 not shown) Planarity restraints: 899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS C 92 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C HIS C 92 " 0.047 2.00e-02 2.50e+03 pdb=" O HIS C 92 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 93 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 97 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C THR C 97 " -0.033 2.00e-02 2.50e+03 pdb=" O THR C 97 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE C 98 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 94 " 0.018 2.00e-02 2.50e+03 1.06e-02 2.23e+00 pdb=" CG TYR C 94 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 94 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 94 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 94 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 94 " 0.005 2.00e-02 2.50e+03 ... (remaining 896 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 260 2.73 - 3.27: 4783 3.27 - 3.81: 7745 3.81 - 4.36: 9078 4.36 - 4.90: 15883 Nonbonded interactions: 37749 Sorted by model distance: nonbonded pdb=" OD1 ASP B 99 " pdb=" N ARG B 100 " model vdw 2.182 3.120 nonbonded pdb=" OG SER C 14 " pdb=" OD2 ASP C 17 " model vdw 2.210 3.040 nonbonded pdb=" OE2 GLU D 406 " pdb=" NE2 GLN D 409 " model vdw 2.279 3.120 nonbonded pdb=" O TYR C 192 " pdb=" OG SER C 208 " model vdw 2.287 3.040 nonbonded pdb=" OG SER B 17 " pdb=" ND2 ASN B 84 " model vdw 2.299 3.120 ... (remaining 37744 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: 2.500 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: 0.040 Set scattering table: 0.040 Process input model: 17.990 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:0.010 Internal consistency checks: 0.000 Total: 23.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 : 0.004 0.060 5134 Z= 0.264 Angle : 0.731 8.208 6983 Z= 0.420 Chirality : 0.054 0.611 775 Planarity : 0.004 0.033 898 Dihedral : 13.163 83.203 1864 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.87 % Favored : 94.98 % Rotamer: Outliers : 0.54 % Allowed : 1.44 % Favored : 98.02 % Cbeta Deviations : 0.17 % 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: -0.03 (0.34), residues: 637 helix: -2.54 (0.93), residues: 22 sheet: 0.89 (0.34), residues: 244 loop : -0.47 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 115 HIS 0.003 0.001 HIS C 189 PHE 0.019 0.001 PHE D 392 TYR 0.023 0.002 TYR C 94 ARG 0.010 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.534 Fit side-chains REVERT: B 89 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7709 (mp0) REVERT: B 152 CYS cc_start: 0.3391 (m) cc_final: 0.3030 (m) REVERT: B 216 ASN cc_start: 0.7341 (m-40) cc_final: 0.6990 (p0) REVERT: C 49 TYR cc_start: 0.8696 (p90) cc_final: 0.8487 (p90) outliers start: 3 outliers final: 0 residues processed: 84 average time/residue: 0.2285 time to fit residues: 23.4081 Evaluate side-chains 61 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 57 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN B 183 GLN B 209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.121933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.096936 restraints weight = 11828.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.098586 restraints weight = 8253.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.099493 restraints weight = 6539.536| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5134 Z= 0.296 Angle : 0.686 10.526 6983 Z= 0.353 Chirality : 0.049 0.392 775 Planarity : 0.004 0.034 898 Dihedral : 6.216 53.332 744 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.81 % Favored : 94.03 % Rotamer: Outliers : 1.08 % Allowed : 9.91 % Favored : 89.01 % 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: -0.35 (0.34), residues: 637 helix: -2.51 (0.81), residues: 28 sheet: 0.74 (0.34), residues: 243 loop : -0.71 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 115 HIS 0.005 0.002 HIS C 198 PHE 0.018 0.002 PHE B 29 TYR 0.020 0.002 TYR D 369 ARG 0.007 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.908 Fit side-chains REVERT: D 406 GLU cc_start: 0.8078 (pt0) cc_final: 0.7819 (pt0) REVERT: B 29 PHE cc_start: 0.8145 (t80) cc_final: 0.7936 (t80) REVERT: B 89 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7754 (mp0) REVERT: B 114 ILE cc_start: 0.9068 (mm) cc_final: 0.8772 (mm) REVERT: B 216 ASN cc_start: 0.7166 (m-40) cc_final: 0.6336 (p0) REVERT: C 48 ILE cc_start: 0.9368 (tp) cc_final: 0.9121 (tp) outliers start: 6 outliers final: 2 residues processed: 73 average time/residue: 0.3252 time to fit residues: 29.7698 Evaluate side-chains 64 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 59 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 0.0970 chunk 33 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 422 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 = 0.3832 r_free = 0.3832 target = 0.123229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.098106 restraints weight = 11818.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.099905 restraints weight = 8085.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.101095 restraints weight = 6304.191| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5134 Z= 0.185 Angle : 0.624 11.444 6983 Z= 0.315 Chirality : 0.047 0.365 775 Planarity : 0.004 0.033 898 Dihedral : 5.654 47.511 744 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.55 % Favored : 95.29 % Rotamer: Outliers : 0.54 % Allowed : 13.15 % Favored : 86.31 % 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: -0.26 (0.34), residues: 637 helix: -2.28 (0.94), residues: 26 sheet: 0.76 (0.34), residues: 245 loop : -0.66 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 115 HIS 0.003 0.001 HIS B 101 PHE 0.015 0.001 PHE D 515 TYR 0.030 0.001 TYR C 49 ARG 0.005 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.550 Fit side-chains REVERT: D 378 LYS cc_start: 0.8916 (ttpt) cc_final: 0.8499 (pttm) REVERT: B 28 ARG cc_start: 0.7482 (ttp80) cc_final: 0.7075 (ttp80) REVERT: B 29 PHE cc_start: 0.8025 (t80) cc_final: 0.7730 (t80) REVERT: B 89 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7722 (mp0) REVERT: B 114 ILE cc_start: 0.9050 (mm) cc_final: 0.8783 (mm) REVERT: B 206 TYR cc_start: 0.5207 (m-80) cc_final: 0.5002 (m-80) REVERT: C 18 ARG cc_start: 0.6829 (tpp80) cc_final: 0.6548 (mmm-85) REVERT: C 48 ILE cc_start: 0.9343 (tp) cc_final: 0.9089 (tp) outliers start: 3 outliers final: 2 residues processed: 68 average time/residue: 0.2412 time to fit residues: 20.1233 Evaluate side-chains 62 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 0.0270 chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 overall best weight: 2.0044 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.120614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.095151 restraints weight = 11996.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.096946 restraints weight = 8127.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.098036 restraints weight = 6343.371| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5134 Z= 0.255 Angle : 0.642 11.131 6983 Z= 0.325 Chirality : 0.047 0.358 775 Planarity : 0.004 0.033 898 Dihedral : 5.693 48.290 744 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.66 % Rotamer: Outliers : 1.98 % Allowed : 13.87 % Favored : 84.14 % 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: -0.37 (0.34), residues: 637 helix: -2.10 (1.00), residues: 26 sheet: 0.63 (0.34), residues: 239 loop : -0.69 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 115 HIS 0.004 0.001 HIS B 101 PHE 0.023 0.002 PHE D 515 TYR 0.026 0.002 TYR C 49 ARG 0.005 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.510 Fit side-chains REVERT: D 378 LYS cc_start: 0.8978 (ttpt) cc_final: 0.8738 (pttm) REVERT: B 28 ARG cc_start: 0.7632 (ttp80) cc_final: 0.7083 (ttp80) REVERT: B 29 PHE cc_start: 0.8132 (t80) cc_final: 0.7781 (t80) REVERT: B 32 TYR cc_start: 0.8707 (m-80) cc_final: 0.8047 (m-80) REVERT: B 89 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7756 (mp0) REVERT: B 183 GLN cc_start: 0.7557 (tt0) cc_final: 0.7195 (tt0) REVERT: B 185 SER cc_start: 0.7808 (p) cc_final: 0.7590 (p) REVERT: B 206 TYR cc_start: 0.5105 (m-80) cc_final: 0.4867 (m-80) REVERT: B 209 ASN cc_start: 0.6809 (OUTLIER) cc_final: 0.6443 (m-40) REVERT: C 18 ARG cc_start: 0.6936 (tpp80) cc_final: 0.6701 (mmm-85) REVERT: C 48 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.8979 (mm) outliers start: 11 outliers final: 5 residues processed: 77 average time/residue: 0.2296 time to fit residues: 21.9703 Evaluate side-chains 67 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 46 optimal weight: 0.0370 chunk 42 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.121235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.096110 restraints weight = 12091.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.097905 restraints weight = 8342.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.099097 restraints weight = 6502.119| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5134 Z= 0.185 Angle : 0.639 11.529 6983 Z= 0.316 Chirality : 0.047 0.368 775 Planarity : 0.004 0.033 898 Dihedral : 5.563 46.440 744 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.08 % Favored : 95.76 % Rotamer: Outliers : 1.80 % Allowed : 14.77 % Favored : 83.42 % 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: -0.41 (0.34), residues: 637 helix: -2.44 (0.83), residues: 32 sheet: 0.67 (0.34), residues: 232 loop : -0.68 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 115 HIS 0.003 0.001 HIS B 101 PHE 0.020 0.001 PHE D 515 TYR 0.028 0.001 TYR C 49 ARG 0.004 0.000 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.596 Fit side-chains REVERT: D 378 LYS cc_start: 0.8929 (ttpt) cc_final: 0.8727 (pttm) REVERT: D 402 ILE cc_start: 0.8122 (mm) cc_final: 0.7811 (pt) REVERT: B 29 PHE cc_start: 0.8074 (t80) cc_final: 0.7824 (t80) REVERT: B 89 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7689 (mp0) REVERT: B 156 ASP cc_start: 0.5925 (m-30) cc_final: 0.4970 (t0) REVERT: B 162 VAL cc_start: 0.7212 (OUTLIER) cc_final: 0.6907 (p) REVERT: B 183 GLN cc_start: 0.7345 (tt0) cc_final: 0.6996 (tt0) REVERT: B 185 SER cc_start: 0.7825 (p) cc_final: 0.7572 (p) REVERT: C 1 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7866 (p0) REVERT: C 48 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8965 (mm) outliers start: 10 outliers final: 4 residues processed: 71 average time/residue: 0.2250 time to fit residues: 19.7303 Evaluate side-chains 68 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 417 ASN Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 36 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 21 optimal weight: 0.0570 chunk 44 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 29 optimal weight: 0.3980 chunk 58 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.122291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.097017 restraints weight = 12189.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.098894 restraints weight = 8305.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.099940 restraints weight = 6440.896| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5134 Z= 0.161 Angle : 0.615 10.545 6983 Z= 0.302 Chirality : 0.046 0.361 775 Planarity : 0.003 0.033 898 Dihedral : 5.459 50.928 744 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.40 % Favored : 95.45 % Rotamer: Outliers : 1.98 % Allowed : 15.32 % Favored : 82.70 % 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: -0.31 (0.34), residues: 637 helix: -2.32 (0.83), residues: 32 sheet: 0.83 (0.34), residues: 239 loop : -0.71 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 115 HIS 0.003 0.001 HIS B 101 PHE 0.019 0.001 PHE D 515 TYR 0.027 0.001 TYR C 49 ARG 0.003 0.000 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.602 Fit side-chains REVERT: D 378 LYS cc_start: 0.8938 (ttpt) cc_final: 0.8712 (pttm) REVERT: D 402 ILE cc_start: 0.7890 (mm) cc_final: 0.7612 (pt) REVERT: D 418 ILE cc_start: 0.8401 (mp) cc_final: 0.7878 (mt) REVERT: B 29 PHE cc_start: 0.8147 (t80) cc_final: 0.7860 (t80) REVERT: B 83 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.6892 (mtp) REVERT: B 89 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7723 (mp0) REVERT: B 156 ASP cc_start: 0.5836 (m-30) cc_final: 0.4981 (t0) REVERT: C 1 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7912 (p0) REVERT: C 48 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.8986 (mm) outliers start: 11 outliers final: 6 residues processed: 73 average time/residue: 0.2430 time to fit residues: 21.8235 Evaluate side-chains 74 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 89 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 61 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 38 optimal weight: 0.0070 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 overall best weight: 3.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.116333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.094377 restraints weight = 12199.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.093098 restraints weight = 10232.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.093564 restraints weight = 9741.570| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 5134 Z= 0.394 Angle : 0.762 12.047 6983 Z= 0.386 Chirality : 0.050 0.389 775 Planarity : 0.005 0.039 898 Dihedral : 5.996 41.493 744 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.91 % Favored : 92.94 % Rotamer: Outliers : 3.06 % Allowed : 15.50 % Favored : 81.44 % 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: -0.78 (0.33), residues: 637 helix: -2.58 (0.77), residues: 32 sheet: 0.45 (0.34), residues: 232 loop : -0.97 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 115 HIS 0.006 0.001 HIS B 101 PHE 0.026 0.002 PHE D 515 TYR 0.017 0.002 TYR C 87 ARG 0.006 0.001 ARG D 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: B 29 PHE cc_start: 0.8279 (t80) cc_final: 0.7947 (t80) REVERT: B 32 TYR cc_start: 0.8757 (m-80) cc_final: 0.8212 (m-80) REVERT: B 83 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.7377 (mmm) REVERT: B 162 VAL cc_start: 0.7333 (OUTLIER) cc_final: 0.7018 (p) REVERT: C 48 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.8996 (mm) outliers start: 17 outliers final: 7 residues processed: 77 average time/residue: 0.2246 time to fit residues: 21.3706 Evaluate side-chains 68 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain C residue 48 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 0.0370 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.120653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.098197 restraints weight = 12211.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.097544 restraints weight = 10090.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.097965 restraints weight = 8771.430| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5134 Z= 0.171 Angle : 0.665 11.765 6983 Z= 0.329 Chirality : 0.047 0.369 775 Planarity : 0.004 0.035 898 Dihedral : 5.500 42.279 744 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.87 % Favored : 94.98 % Rotamer: Outliers : 2.88 % Allowed : 15.68 % Favored : 81.44 % 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: -0.55 (0.34), residues: 637 helix: -2.22 (0.86), residues: 32 sheet: 0.56 (0.35), residues: 227 loop : -0.78 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 115 HIS 0.002 0.001 HIS B 101 PHE 0.019 0.001 PHE D 515 TYR 0.026 0.001 TYR C 49 ARG 0.004 0.001 ARG D 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.554 Fit side-chains REVERT: B 29 PHE cc_start: 0.8144 (t80) cc_final: 0.7860 (t80) REVERT: B 32 TYR cc_start: 0.8626 (m-80) cc_final: 0.8095 (m-80) REVERT: B 83 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7259 (mtm) REVERT: B 156 ASP cc_start: 0.5693 (m-30) cc_final: 0.5117 (t0) REVERT: B 162 VAL cc_start: 0.7237 (OUTLIER) cc_final: 0.6933 (p) REVERT: C 1 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7807 (p0) REVERT: C 48 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.8976 (mm) outliers start: 16 outliers final: 8 residues processed: 78 average time/residue: 0.2151 time to fit residues: 20.8677 Evaluate side-chains 72 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 89 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 0.0270 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.121048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.096040 restraints weight = 12080.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.097796 restraints weight = 8320.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.098976 restraints weight = 6516.115| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5134 Z= 0.169 Angle : 0.670 13.568 6983 Z= 0.329 Chirality : 0.047 0.352 775 Planarity : 0.004 0.035 898 Dihedral : 5.090 27.724 744 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.71 % Favored : 95.13 % Rotamer: Outliers : 2.16 % Allowed : 15.86 % Favored : 81.98 % 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: -0.36 (0.34), residues: 637 helix: -2.11 (0.89), residues: 32 sheet: 0.79 (0.35), residues: 234 loop : -0.75 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 115 HIS 0.002 0.001 HIS B 101 PHE 0.018 0.001 PHE D 515 TYR 0.024 0.001 TYR C 49 ARG 0.005 0.001 ARG D 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.521 Fit side-chains REVERT: B 29 PHE cc_start: 0.8168 (t80) cc_final: 0.7961 (t80) REVERT: B 32 TYR cc_start: 0.8574 (m-80) cc_final: 0.7982 (m-80) REVERT: B 83 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.6896 (mtp) REVERT: B 156 ASP cc_start: 0.5877 (m-30) cc_final: 0.5002 (t0) REVERT: B 162 VAL cc_start: 0.7228 (OUTLIER) cc_final: 0.6912 (p) REVERT: C 1 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7842 (p0) REVERT: C 48 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.8979 (mm) outliers start: 12 outliers final: 6 residues processed: 71 average time/residue: 0.2473 time to fit residues: 21.7391 Evaluate side-chains 67 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 7 optimal weight: 0.3980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.119748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.094630 restraints weight = 12401.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.096092 restraints weight = 8756.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.097330 restraints weight = 7059.510| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5134 Z= 0.204 Angle : 0.677 12.945 6983 Z= 0.334 Chirality : 0.047 0.371 775 Planarity : 0.004 0.034 898 Dihedral : 5.168 32.119 744 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.02 % Favored : 94.82 % Rotamer: Outliers : 1.80 % Allowed : 16.40 % Favored : 81.80 % 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: -0.37 (0.34), residues: 637 helix: -2.19 (0.86), residues: 32 sheet: 0.76 (0.35), residues: 233 loop : -0.73 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 115 HIS 0.005 0.001 HIS B 101 PHE 0.019 0.001 PHE D 515 TYR 0.021 0.001 TYR C 49 ARG 0.004 0.001 ARG C 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.614 Fit side-chains REVERT: B 29 PHE cc_start: 0.8204 (t80) cc_final: 0.8001 (t80) REVERT: B 32 TYR cc_start: 0.8563 (m-80) cc_final: 0.7926 (m-80) REVERT: B 62 GLU cc_start: 0.6621 (mp0) cc_final: 0.6404 (mp0) REVERT: B 83 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.6860 (mtp) REVERT: B 156 ASP cc_start: 0.5934 (m-30) cc_final: 0.5009 (t0) REVERT: B 162 VAL cc_start: 0.7232 (OUTLIER) cc_final: 0.6924 (p) REVERT: C 1 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7685 (p0) REVERT: C 48 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8960 (mm) outliers start: 10 outliers final: 6 residues processed: 66 average time/residue: 0.2420 time to fit residues: 19.7585 Evaluate side-chains 68 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 26 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.119023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.094220 restraints weight = 12521.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.095646 restraints weight = 9292.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.096621 restraints weight = 7610.282| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5134 Z= 0.234 Angle : 0.689 12.641 6983 Z= 0.341 Chirality : 0.047 0.377 775 Planarity : 0.004 0.031 898 Dihedral : 5.350 35.477 744 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.02 % Favored : 94.82 % Rotamer: Outliers : 2.52 % Allowed : 15.68 % Favored : 81.80 % 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: -0.45 (0.34), residues: 637 helix: -2.34 (0.83), residues: 32 sheet: 0.71 (0.35), residues: 233 loop : -0.78 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 115 HIS 0.004 0.001 HIS B 101 PHE 0.021 0.001 PHE D 515 TYR 0.020 0.001 TYR C 49 ARG 0.005 0.001 ARG C 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1895.89 seconds wall clock time: 35 minutes 0.66 seconds (2100.66 seconds total)