Starting phenix.real_space_refine on Tue Mar 11 14:31:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jva_36672/03_2025/8jva_36672.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jva_36672/03_2025/8jva_36672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jva_36672/03_2025/8jva_36672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jva_36672/03_2025/8jva_36672.map" model { file = "/net/cci-nas-00/data/ceres_data/8jva_36672/03_2025/8jva_36672.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jva_36672/03_2025/8jva_36672.cif" } resolution = 2.81 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= -0.002 sd= 0.015 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 3862 2.51 5 N 1002 2.21 5 O 1187 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-5624/modules/chem_data/mon_lib" Total number of atoms: 6071 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "A" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1652 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "B" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1455 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 1 Chain: "F" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1972 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 15, 'TRANS': 227} Chain breaks: 6 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.02, per 1000 atoms: 0.83 Number of scatterers: 6071 At special positions: 0 Unit cell: (76.68, 73.44, 147.96, 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 1187 8.00 N 1002 7.00 C 3862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " 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 F 401 " - " ASN F 122 " " NAG F 402 " - " ASN F 165 " " NAG F 403 " - " ASN F 282 " " NAG F 404 " - " ASN F 234 " " NAG F 405 " - " ASN F 61 " Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 806.1 milliseconds 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 16 sheets defined 5.9% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 61 through 65 removed outlier: 3.929A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.676A pdb=" N THR D 91 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 103 removed outlier: 4.016A pdb=" N GLN D 103 " --> pdb=" O PRO D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 103' Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.904A pdb=" N SER B 31 " --> pdb=" O THR B 28 " (cutoff:3.500A) removed outlier: 3.726A 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 86 through 90 removed outlier: 3.689A pdb=" N THR B 90 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 303 removed outlier: 3.635A pdb=" N LYS F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.548A pdb=" N ASN D 97 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.613A pdb=" N ASP A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 10 through 13 Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 49 removed outlier: 6.665A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 33 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 114 through 118 removed outlier: 3.935A pdb=" N ASN A 137 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 145 through 150 removed outlier: 4.066A pdb=" N TYR A 192 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.177A pdb=" N GLY B 10 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET B 34 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 52 " --> pdb=" O ASN B 56 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.177A pdb=" N GLY B 10 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.821A pdb=" N VAL B 152 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 27 through 30 removed outlier: 4.097A pdb=" N ALA F 27 " --> pdb=" O TRP F 64 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR F 63 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL F 227 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER F 205 " --> pdb=" O PRO F 225 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 47 through 55 removed outlier: 3.561A pdb=" N VAL F 47 " --> pdb=" O TYR F 279 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.994A pdb=" N SER F 162 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.547A pdb=" N SER F 172 " --> pdb=" O VAL F 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 141 through 145 removed outlier: 5.924A pdb=" N LEU F 141 " --> pdb=" O LEU F 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 215 hydrogen bonds defined for protein. 531 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: 1.53 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1923 1.34 - 1.46: 1599 1.46 - 1.58: 2671 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 6219 Sorted by residual: bond pdb=" C1 NAG F 402 " pdb=" O5 NAG F 402 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 NAG F 405 " pdb=" O5 NAG F 405 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C1 NAG F 403 " pdb=" O5 NAG F 403 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" C5 NAG F 405 " pdb=" O5 NAG F 405 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.33e+00 bond pdb=" C5 NAG F 403 " pdb=" O5 NAG F 403 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.20e+00 ... (remaining 6214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 8234 1.69 - 3.37: 193 3.37 - 5.06: 21 5.06 - 6.75: 3 6.75 - 8.44: 1 Bond angle restraints: 8452 Sorted by residual: angle pdb=" N ILE F 100 " pdb=" CA ILE F 100 " pdb=" C ILE F 100 " ideal model delta sigma weight residual 112.96 108.70 4.26 1.00e+00 1.00e+00 1.81e+01 angle pdb=" C TYR B 103 " pdb=" CA TYR B 103 " pdb=" CB TYR B 103 " ideal model delta sigma weight residual 117.23 111.53 5.70 1.36e+00 5.41e-01 1.76e+01 angle pdb=" C PHE F 32 " pdb=" CA PHE F 32 " pdb=" CB PHE F 32 " ideal model delta sigma weight residual 115.89 110.98 4.91 1.32e+00 5.74e-01 1.38e+01 angle pdb=" N GLY B 149 " pdb=" CA GLY B 149 " pdb=" C GLY B 149 " ideal model delta sigma weight residual 110.87 115.91 -5.04 1.54e+00 4.22e-01 1.07e+01 angle pdb=" CA GLY A 66 " pdb=" C GLY A 66 " pdb=" O GLY A 66 " ideal model delta sigma weight residual 122.45 120.16 2.29 7.20e-01 1.93e+00 1.01e+01 ... (remaining 8447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 3391 16.77 - 33.54: 290 33.54 - 50.32: 53 50.32 - 67.09: 8 67.09 - 83.86: 4 Dihedral angle restraints: 3746 sinusoidal: 1516 harmonic: 2230 Sorted by residual: dihedral pdb=" CB CYS A 134 " pdb=" SG CYS A 134 " pdb=" SG CYS A 194 " pdb=" CB CYS A 194 " ideal model delta sinusoidal sigma weight residual 93.00 169.35 -76.35 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 134.15 -41.15 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" CA ASP A 167 " pdb=" C ASP A 167 " pdb=" N SER A 168 " pdb=" CA SER A 168 " ideal model delta harmonic sigma weight residual -180.00 -162.52 -17.48 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 3743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 627 0.036 - 0.071: 207 0.071 - 0.107: 78 0.107 - 0.142: 32 0.142 - 0.178: 2 Chirality restraints: 946 Sorted by residual: chirality pdb=" C1 NAG F 403 " pdb=" ND2 ASN F 282 " pdb=" C2 NAG F 403 " pdb=" O5 NAG F 403 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CA GLU B 158 " pdb=" N GLU B 158 " pdb=" C GLU B 158 " pdb=" CB GLU B 158 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" C1 NAG F 402 " pdb=" ND2 ASN F 165 " pdb=" C2 NAG F 402 " pdb=" O5 NAG F 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 943 not shown) Planarity restraints: 1085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 53 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO D 54 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 54 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 54 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 126 " -0.034 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO B 127 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 127 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 127 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 58 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO A 59 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 59 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 59 " 0.024 5.00e-02 4.00e+02 ... (remaining 1082 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 700 2.75 - 3.29: 5199 3.29 - 3.83: 8847 3.83 - 4.36: 10352 4.36 - 4.90: 19171 Nonbonded interactions: 44269 Sorted by model distance: nonbonded pdb=" OG SER F 94 " pdb=" OE1 GLU F 96 " model vdw 2.217 3.040 nonbonded pdb=" OG SER D 35 " pdb=" O ALA D 49 " model vdw 2.251 3.040 nonbonded pdb=" OD2 ASP F 40 " pdb=" NH2 ARG F 44 " model vdw 2.304 3.120 nonbonded pdb=" O ARG B 52 " pdb=" NH1 ARG B 71 " model vdw 2.310 3.120 nonbonded pdb=" O SER A 114 " pdb=" OG SER A 114 " model vdw 2.321 3.040 ... (remaining 44264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.500 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.060 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:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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 0.038 6219 Z= 0.246 Angle : 0.630 8.436 8452 Z= 0.349 Chirality : 0.044 0.178 946 Planarity : 0.005 0.063 1080 Dihedral : 12.608 83.859 2298 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.47 (0.30), residues: 747 helix: 0.33 (1.21), residues: 16 sheet: 0.87 (0.32), residues: 283 loop : -1.18 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.016 0.001 PHE F 220 TYR 0.016 0.001 TYR A 140 ARG 0.003 0.000 ARG D 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 90 ASP cc_start: 0.6254 (m-30) cc_final: 0.5410 (m-30) REVERT: F 158 ARG cc_start: 0.8370 (mtt-85) cc_final: 0.7841 (tmt170) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 1.3777 time to fit residues: 207.7442 Evaluate side-chains 78 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 0.0870 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.089809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.059456 restraints weight = 16576.784| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 4.03 r_work: 0.2948 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6219 Z= 0.272 Angle : 0.654 8.247 8452 Z= 0.339 Chirality : 0.045 0.186 946 Planarity : 0.005 0.055 1080 Dihedral : 5.822 49.729 934 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.50 % Allowed : 12.28 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.32 (0.30), residues: 747 helix: 0.36 (1.24), residues: 16 sheet: 1.15 (0.32), residues: 280 loop : -1.21 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.004 0.001 HIS B 35 PHE 0.017 0.002 PHE A 118 TYR 0.015 0.001 TYR A 140 ARG 0.006 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1 GLN cc_start: 0.8419 (pt0) cc_final: 0.7878 (pp30) REVERT: D 73 ASP cc_start: 0.8417 (t0) cc_final: 0.8087 (t0) REVERT: A 195 GLU cc_start: 0.8140 (tt0) cc_final: 0.7929 (tm-30) REVERT: B 89 ASP cc_start: 0.8868 (m-30) cc_final: 0.8618 (m-30) REVERT: F 158 ARG cc_start: 0.8812 (mtt-85) cc_final: 0.7478 (tmt170) REVERT: F 169 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8414 (tp30) REVERT: F 298 GLU cc_start: 0.8163 (tp30) cc_final: 0.7949 (tp30) outliers start: 10 outliers final: 5 residues processed: 95 average time/residue: 1.2831 time to fit residues: 127.6277 Evaluate side-chains 80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain F residue 169 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.089665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.059340 restraints weight = 16843.671| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 4.09 r_work: 0.2942 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6219 Z= 0.207 Angle : 0.618 8.237 8452 Z= 0.316 Chirality : 0.045 0.181 946 Planarity : 0.005 0.051 1080 Dihedral : 5.108 34.413 934 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.25 % Allowed : 13.62 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.14 (0.30), residues: 747 helix: 1.00 (1.40), residues: 16 sheet: 1.23 (0.32), residues: 280 loop : -1.08 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.014 0.001 PHE A 118 TYR 0.014 0.001 TYR A 192 ARG 0.005 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 73 ASP cc_start: 0.8519 (t0) cc_final: 0.7550 (t0) REVERT: D 76 LYS cc_start: 0.9285 (mtmt) cc_final: 0.8859 (pttm) REVERT: D 90 ASP cc_start: 0.8230 (t70) cc_final: 0.8000 (t70) REVERT: A 108 ARG cc_start: 0.8270 (tmm-80) cc_final: 0.7896 (tpt-90) REVERT: A 147 GLN cc_start: 0.7706 (tp40) cc_final: 0.7425 (tp-100) REVERT: A 195 GLU cc_start: 0.8158 (tt0) cc_final: 0.7914 (tm-30) REVERT: B 89 ASP cc_start: 0.8867 (m-30) cc_final: 0.8495 (m-30) REVERT: F 100 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8323 (mp) REVERT: F 158 ARG cc_start: 0.8791 (mtt-85) cc_final: 0.7463 (tmt170) REVERT: F 169 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8382 (tp30) REVERT: F 298 GLU cc_start: 0.8164 (tp30) cc_final: 0.7916 (tp30) outliers start: 15 outliers final: 7 residues processed: 90 average time/residue: 1.2135 time to fit residues: 114.5449 Evaluate side-chains 84 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 169 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 57 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN F 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.089386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059511 restraints weight = 16943.242| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 4.04 r_work: 0.2934 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6219 Z= 0.189 Angle : 0.610 9.621 8452 Z= 0.309 Chirality : 0.044 0.181 946 Planarity : 0.005 0.050 1080 Dihedral : 4.763 32.732 934 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.40 % Allowed : 15.42 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.06 (0.31), residues: 747 helix: 0.96 (1.41), residues: 16 sheet: 1.23 (0.32), residues: 282 loop : -0.98 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.016 0.001 PHE A 118 TYR 0.012 0.001 TYR B 94 ARG 0.007 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 73 ASP cc_start: 0.8569 (t0) cc_final: 0.8053 (t0) REVERT: A 147 GLN cc_start: 0.7719 (tp40) cc_final: 0.7423 (tp-100) REVERT: A 192 TYR cc_start: 0.5914 (m-80) cc_final: 0.5122 (m-80) REVERT: A 195 GLU cc_start: 0.8188 (tt0) cc_final: 0.7942 (tm-30) REVERT: B 89 ASP cc_start: 0.8894 (m-30) cc_final: 0.8450 (m-30) REVERT: F 158 ARG cc_start: 0.8789 (mtt-85) cc_final: 0.7488 (tmt170) REVERT: F 169 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8379 (tp30) REVERT: F 298 GLU cc_start: 0.8127 (tp30) cc_final: 0.7875 (tp30) outliers start: 16 outliers final: 7 residues processed: 87 average time/residue: 1.2365 time to fit residues: 112.7690 Evaluate side-chains 76 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain F residue 169 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 0.0970 chunk 50 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 75 optimal weight: 0.3980 chunk 51 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN F 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.089280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.059240 restraints weight = 16828.921| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 4.04 r_work: 0.2953 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6219 Z= 0.229 Angle : 0.617 8.511 8452 Z= 0.316 Chirality : 0.044 0.176 946 Planarity : 0.005 0.049 1080 Dihedral : 4.637 32.327 934 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.40 % Allowed : 15.87 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.09 (0.31), residues: 747 helix: 0.92 (1.40), residues: 16 sheet: 1.17 (0.32), residues: 284 loop : -0.97 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.004 0.001 HIS B 35 PHE 0.011 0.001 PHE A 118 TYR 0.014 0.001 TYR B 94 ARG 0.009 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ASP cc_start: 0.8819 (t0) cc_final: 0.8262 (t0) REVERT: D 76 LYS cc_start: 0.9296 (mtmt) cc_final: 0.8961 (pttp) REVERT: A 108 ARG cc_start: 0.8226 (tmm-80) cc_final: 0.7795 (tpt-90) REVERT: A 147 GLN cc_start: 0.7743 (tp40) cc_final: 0.7445 (tp-100) REVERT: A 195 GLU cc_start: 0.8231 (tt0) cc_final: 0.7983 (tm-30) REVERT: B 89 ASP cc_start: 0.8963 (m-30) cc_final: 0.8542 (m-30) REVERT: F 24 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8130 (mp) REVERT: F 100 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8433 (mp) REVERT: F 158 ARG cc_start: 0.8801 (mtt-85) cc_final: 0.7498 (tmt170) REVERT: F 169 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8428 (tp30) REVERT: F 298 GLU cc_start: 0.8050 (tp30) cc_final: 0.7809 (tp30) outliers start: 16 outliers final: 8 residues processed: 86 average time/residue: 1.3437 time to fit residues: 120.8720 Evaluate side-chains 77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 197 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 12 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.088782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.059021 restraints weight = 16600.093| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.97 r_work: 0.2952 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6219 Z= 0.238 Angle : 0.625 9.782 8452 Z= 0.319 Chirality : 0.044 0.181 946 Planarity : 0.005 0.049 1080 Dihedral : 4.621 32.374 934 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.69 % Allowed : 17.07 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.08 (0.31), residues: 747 helix: 0.89 (1.43), residues: 16 sheet: 1.18 (0.32), residues: 284 loop : -0.97 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.004 0.001 HIS B 35 PHE 0.012 0.001 PHE A 118 TYR 0.014 0.001 TYR B 94 ARG 0.009 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 73 ASP cc_start: 0.8839 (t0) cc_final: 0.8278 (t0) REVERT: D 76 LYS cc_start: 0.9306 (mtmt) cc_final: 0.9068 (mtmt) REVERT: A 105 ASP cc_start: 0.8062 (m-30) cc_final: 0.7828 (p0) REVERT: A 108 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7816 (tpt-90) REVERT: A 147 GLN cc_start: 0.7811 (tp40) cc_final: 0.7489 (tp-100) REVERT: A 183 LYS cc_start: 0.5418 (OUTLIER) cc_final: 0.4845 (ttmm) REVERT: A 195 GLU cc_start: 0.8297 (tt0) cc_final: 0.8039 (tm-30) REVERT: B 89 ASP cc_start: 0.8988 (m-30) cc_final: 0.8555 (m-30) REVERT: B 125 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8388 (tmmm) REVERT: B 154 ASP cc_start: 0.8291 (m-30) cc_final: 0.7710 (m-30) REVERT: F 24 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8145 (mp) REVERT: F 158 ARG cc_start: 0.8755 (mtt-85) cc_final: 0.7479 (tmt170) REVERT: F 298 GLU cc_start: 0.8010 (tp30) cc_final: 0.7776 (tp30) outliers start: 18 outliers final: 10 residues processed: 82 average time/residue: 1.3374 time to fit residues: 114.9838 Evaluate side-chains 79 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain F residue 24 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 71 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 3 GLN F 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.089382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059464 restraints weight = 16782.652| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 4.02 r_work: 0.2959 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6219 Z= 0.203 Angle : 0.625 9.075 8452 Z= 0.320 Chirality : 0.044 0.180 946 Planarity : 0.005 0.057 1080 Dihedral : 4.544 31.388 934 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.54 % Allowed : 17.96 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.02 (0.31), residues: 747 helix: 1.01 (1.42), residues: 16 sheet: 1.22 (0.32), residues: 284 loop : -0.93 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.016 0.001 PHE B 130 TYR 0.013 0.001 TYR B 94 ARG 0.014 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7819 (mmt90) REVERT: D 73 ASP cc_start: 0.8847 (t0) cc_final: 0.8393 (t0) REVERT: A 105 ASP cc_start: 0.8069 (m-30) cc_final: 0.7848 (p0) REVERT: A 108 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7838 (tpt-90) REVERT: A 147 GLN cc_start: 0.7778 (tp40) cc_final: 0.7466 (tp-100) REVERT: A 195 GLU cc_start: 0.8341 (tt0) cc_final: 0.8089 (tm-30) REVERT: B 89 ASP cc_start: 0.8978 (m-30) cc_final: 0.8534 (m-30) REVERT: B 125 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8380 (tmmm) REVERT: B 154 ASP cc_start: 0.8227 (m-30) cc_final: 0.7618 (m-30) REVERT: F 24 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8153 (mp) REVERT: F 158 ARG cc_start: 0.8750 (mtt-85) cc_final: 0.7440 (tpt170) REVERT: F 298 GLU cc_start: 0.7993 (tp30) cc_final: 0.7763 (tp30) outliers start: 17 outliers final: 9 residues processed: 84 average time/residue: 1.4231 time to fit residues: 124.9501 Evaluate side-chains 78 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain F residue 24 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 26 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.089070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.059364 restraints weight = 16631.306| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.96 r_work: 0.2955 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6219 Z= 0.229 Angle : 0.660 10.734 8452 Z= 0.333 Chirality : 0.044 0.181 946 Planarity : 0.005 0.050 1080 Dihedral : 4.523 30.986 934 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.25 % Allowed : 18.71 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.02 (0.31), residues: 747 helix: 1.34 (1.44), residues: 16 sheet: 1.20 (0.32), residues: 284 loop : -0.93 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.014 0.001 PHE A 118 TYR 0.013 0.001 TYR B 94 ARG 0.012 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ASP cc_start: 0.8890 (t0) cc_final: 0.8497 (t0) REVERT: A 105 ASP cc_start: 0.8058 (m-30) cc_final: 0.7856 (p0) REVERT: A 108 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7879 (tpt-90) REVERT: A 147 GLN cc_start: 0.7837 (tp40) cc_final: 0.7512 (tp-100) REVERT: A 195 GLU cc_start: 0.8484 (tt0) cc_final: 0.8229 (tm-30) REVERT: B 89 ASP cc_start: 0.9004 (m-30) cc_final: 0.8564 (m-30) REVERT: B 125 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8374 (tmmm) REVERT: B 154 ASP cc_start: 0.8263 (m-30) cc_final: 0.7642 (m-30) REVERT: F 24 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8134 (mp) REVERT: F 158 ARG cc_start: 0.8733 (mtt-85) cc_final: 0.7429 (tpt170) outliers start: 15 outliers final: 9 residues processed: 81 average time/residue: 1.3436 time to fit residues: 113.8270 Evaluate side-chains 80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain F residue 24 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 14 optimal weight: 0.0040 chunk 61 optimal weight: 0.5980 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.089158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059270 restraints weight = 16938.626| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 4.03 r_work: 0.2953 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6219 Z= 0.224 Angle : 0.657 9.866 8452 Z= 0.334 Chirality : 0.044 0.185 946 Planarity : 0.005 0.048 1080 Dihedral : 4.472 30.670 934 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.80 % Allowed : 19.31 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.00 (0.31), residues: 747 helix: 1.41 (1.48), residues: 16 sheet: 1.20 (0.32), residues: 284 loop : -0.92 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.014 0.001 PHE A 118 TYR 0.013 0.001 TYR B 94 ARG 0.009 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ASP cc_start: 0.8913 (t0) cc_final: 0.8617 (t0) REVERT: A 105 ASP cc_start: 0.8034 (m-30) cc_final: 0.7807 (p0) REVERT: A 108 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7906 (tpt-90) REVERT: A 147 GLN cc_start: 0.7821 (tp40) cc_final: 0.7498 (tp-100) REVERT: A 195 GLU cc_start: 0.8491 (tt0) cc_final: 0.8231 (tm-30) REVERT: B 89 ASP cc_start: 0.9010 (m-30) cc_final: 0.8564 (m-30) REVERT: B 125 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8378 (tmmm) REVERT: B 154 ASP cc_start: 0.8254 (m-30) cc_final: 0.7649 (m-30) REVERT: F 24 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8139 (mp) REVERT: F 158 ARG cc_start: 0.8737 (mtt-85) cc_final: 0.7438 (tpt170) outliers start: 12 outliers final: 6 residues processed: 80 average time/residue: 1.3909 time to fit residues: 116.2798 Evaluate side-chains 78 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain F residue 24 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 0.0270 chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.089788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.059636 restraints weight = 16992.375| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 4.05 r_work: 0.2970 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6219 Z= 0.212 Angle : 0.671 9.987 8452 Z= 0.339 Chirality : 0.044 0.178 946 Planarity : 0.004 0.048 1080 Dihedral : 4.303 29.138 934 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.80 % Allowed : 19.91 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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 (0.31), residues: 747 helix: 1.42 (1.48), residues: 16 sheet: 1.24 (0.32), residues: 284 loop : -0.91 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.011 0.001 PHE A 118 TYR 0.012 0.001 TYR B 94 ARG 0.014 0.001 ARG D 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 73 ASP cc_start: 0.8899 (t0) cc_final: 0.8550 (t0) REVERT: A 108 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7958 (tpt-90) REVERT: A 147 GLN cc_start: 0.7818 (tp40) cc_final: 0.7486 (tp-100) REVERT: A 161 GLU cc_start: 0.8831 (pm20) cc_final: 0.8523 (mm-30) REVERT: A 183 LYS cc_start: 0.5383 (OUTLIER) cc_final: 0.5166 (mptt) REVERT: A 195 GLU cc_start: 0.8515 (tt0) cc_final: 0.8272 (tm-30) REVERT: B 89 ASP cc_start: 0.8989 (m-30) cc_final: 0.8531 (m-30) REVERT: B 125 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8356 (tmmm) REVERT: B 154 ASP cc_start: 0.8234 (m-30) cc_final: 0.7614 (m-30) REVERT: F 24 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8143 (mp) REVERT: F 158 ARG cc_start: 0.8724 (mtt-85) cc_final: 0.7413 (tpt170) outliers start: 12 outliers final: 6 residues processed: 80 average time/residue: 1.4063 time to fit residues: 117.4698 Evaluate side-chains 74 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain F residue 24 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 14 optimal weight: 0.0470 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 55 optimal weight: 0.0670 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN F 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.089201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.059357 restraints weight = 17147.011| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.98 r_work: 0.2971 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6219 Z= 0.226 Angle : 0.677 9.199 8452 Z= 0.343 Chirality : 0.044 0.178 946 Planarity : 0.005 0.076 1080 Dihedral : 4.361 29.056 934 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.50 % Allowed : 20.06 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.02 (0.31), residues: 747 helix: 1.26 (1.46), residues: 16 sheet: 1.27 (0.32), residues: 282 loop : -0.92 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.012 0.001 PHE F 220 TYR 0.034 0.001 TYR A 186 ARG 0.018 0.001 ARG D 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5481.43 seconds wall clock time: 93 minutes 54.25 seconds (5634.25 seconds total)