Starting phenix.real_space_refine on Wed Feb 12 16:11:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cr0_30443/02_2025/7cr0_30443.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cr0_30443/02_2025/7cr0_30443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cr0_30443/02_2025/7cr0_30443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cr0_30443/02_2025/7cr0_30443.map" model { file = "/net/cci-nas-00/data/ceres_data/7cr0_30443/02_2025/7cr0_30443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cr0_30443/02_2025/7cr0_30443.cif" } resolution = 3.1 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= 0.003 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 36 5.16 5 C 5436 2.51 5 N 1380 2.21 5 O 1336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8188 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2047 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Chain: "B" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2047 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Chain: "C" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2047 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Chain: "D" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2047 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Time building chain proxies: 5.41, per 1000 atoms: 0.66 Number of scatterers: 8188 At special positions: 0 Unit cell: (132.834, 132.834, 77.064, 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 36 16.00 O 1336 8.00 N 1380 7.00 C 5436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 1.1 seconds 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 85.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 91 through 114 removed outlier: 4.178A pdb=" N TYR A 95 " --> pdb=" O TRP A 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 4.715A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 165 Processing helix chain 'A' and resid 166 through 183 Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 254 Processing helix chain 'A' and resid 263 through 276 removed outlier: 3.570A pdb=" N ALA A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 330 removed outlier: 3.718A pdb=" N ARG A 291 " --> pdb=" O THR A 287 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix removed outlier: 4.105A pdb=" N GLU A 330 " --> pdb=" O GLN A 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 91 through 114 removed outlier: 4.178A pdb=" N TYR B 95 " --> pdb=" O TRP B 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 removed outlier: 4.715A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 Processing helix chain 'B' and resid 166 through 183 Processing helix chain 'B' and resid 196 through 211 Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'B' and resid 228 through 254 Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.570A pdb=" N ALA B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 330 removed outlier: 3.718A pdb=" N ARG B 291 " --> pdb=" O THR B 287 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix removed outlier: 4.105A pdb=" N GLU B 330 " --> pdb=" O GLN B 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 91 through 114 removed outlier: 4.177A pdb=" N TYR C 95 " --> pdb=" O TRP C 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 148 removed outlier: 4.715A pdb=" N ILE C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 165 Processing helix chain 'C' and resid 166 through 183 Processing helix chain 'C' and resid 196 through 211 Processing helix chain 'C' and resid 215 through 228 Processing helix chain 'C' and resid 228 through 254 Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.570A pdb=" N ALA C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 330 removed outlier: 3.718A pdb=" N ARG C 291 " --> pdb=" O THR C 287 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Proline residue: C 308 - end of helix removed outlier: 4.105A pdb=" N GLU C 330 " --> pdb=" O GLN C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 91 through 114 removed outlier: 4.178A pdb=" N TYR D 95 " --> pdb=" O TRP D 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 removed outlier: 4.715A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 165 Processing helix chain 'D' and resid 166 through 183 Processing helix chain 'D' and resid 196 through 211 Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 254 Processing helix chain 'D' and resid 263 through 276 removed outlier: 3.570A pdb=" N ALA D 267 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 330 removed outlier: 3.718A pdb=" N ARG D 291 " --> pdb=" O THR D 287 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix removed outlier: 4.105A pdb=" N GLU D 330 " --> pdb=" O GLN D 326 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1935 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: 2.39 Time building geometry restraints manager: 2.12 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: 2480 1.34 - 1.46: 2350 1.46 - 1.58: 3534 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 8412 Sorted by residual: bond pdb=" CD2 TYR B 280 " pdb=" CE2 TYR B 280 " ideal model delta sigma weight residual 1.382 1.352 0.030 3.00e-02 1.11e+03 9.69e-01 bond pdb=" CD2 TYR D 280 " pdb=" CE2 TYR D 280 " ideal model delta sigma weight residual 1.382 1.352 0.030 3.00e-02 1.11e+03 9.69e-01 bond pdb=" CD2 TYR A 280 " pdb=" CE2 TYR A 280 " ideal model delta sigma weight residual 1.382 1.352 0.030 3.00e-02 1.11e+03 9.69e-01 bond pdb=" CD2 TYR C 280 " pdb=" CE2 TYR C 280 " ideal model delta sigma weight residual 1.382 1.352 0.030 3.00e-02 1.11e+03 9.69e-01 bond pdb=" CB THR C 274 " pdb=" CG2 THR C 274 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.60e-01 ... (remaining 8407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 10421 1.05 - 2.10: 812 2.10 - 3.15: 123 3.15 - 4.20: 24 4.20 - 5.25: 8 Bond angle restraints: 11388 Sorted by residual: angle pdb=" N ARG B 87 " pdb=" CA ARG B 87 " pdb=" C ARG B 87 " ideal model delta sigma weight residual 109.81 114.52 -4.71 2.21e+00 2.05e-01 4.54e+00 angle pdb=" N ARG C 87 " pdb=" CA ARG C 87 " pdb=" C ARG C 87 " ideal model delta sigma weight residual 109.81 114.52 -4.71 2.21e+00 2.05e-01 4.54e+00 angle pdb=" N ARG D 87 " pdb=" CA ARG D 87 " pdb=" C ARG D 87 " ideal model delta sigma weight residual 109.81 114.52 -4.71 2.21e+00 2.05e-01 4.54e+00 angle pdb=" N ARG A 87 " pdb=" CA ARG A 87 " pdb=" C ARG A 87 " ideal model delta sigma weight residual 109.81 114.52 -4.71 2.21e+00 2.05e-01 4.54e+00 angle pdb=" C ASP A 212 " pdb=" N ARG A 213 " pdb=" CA ARG A 213 " ideal model delta sigma weight residual 121.54 125.46 -3.92 1.91e+00 2.74e-01 4.22e+00 ... (remaining 11383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4272 17.87 - 35.74: 428 35.74 - 53.61: 80 53.61 - 71.48: 8 71.48 - 89.35: 4 Dihedral angle restraints: 4792 sinusoidal: 1884 harmonic: 2908 Sorted by residual: dihedral pdb=" CA GLU A 86 " pdb=" C GLU A 86 " pdb=" N ARG A 87 " pdb=" CA ARG A 87 " ideal model delta harmonic sigma weight residual -180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA GLU D 86 " pdb=" C GLU D 86 " pdb=" N ARG D 87 " pdb=" CA ARG D 87 " ideal model delta harmonic sigma weight residual 180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLU C 86 " pdb=" C GLU C 86 " pdb=" N ARG C 87 " pdb=" CA ARG C 87 " ideal model delta harmonic sigma weight residual 180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 4789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 712 0.031 - 0.063: 422 0.063 - 0.094: 90 0.094 - 0.125: 20 0.125 - 0.157: 8 Chirality restraints: 1252 Sorted by residual: chirality pdb=" CA ARG B 87 " pdb=" N ARG B 87 " pdb=" C ARG B 87 " pdb=" CB ARG B 87 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA ARG C 87 " pdb=" N ARG C 87 " pdb=" C ARG C 87 " pdb=" CB ARG C 87 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA ARG D 87 " pdb=" N ARG D 87 " pdb=" C ARG D 87 " pdb=" CB ARG D 87 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 1249 not shown) Planarity restraints: 1380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 298 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C THR A 298 " -0.028 2.00e-02 2.50e+03 pdb=" O THR A 298 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 299 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 298 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C THR D 298 " -0.028 2.00e-02 2.50e+03 pdb=" O THR D 298 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU D 299 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 298 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C THR B 298 " 0.028 2.00e-02 2.50e+03 pdb=" O THR B 298 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU B 299 " -0.009 2.00e-02 2.50e+03 ... (remaining 1377 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1403 2.75 - 3.29: 7751 3.29 - 3.82: 13206 3.82 - 4.36: 15284 4.36 - 4.90: 26020 Nonbonded interactions: 63664 Sorted by model distance: nonbonded pdb=" OE1 GLU C 86 " pdb=" NH2 ARG C 214 " model vdw 2.212 3.120 nonbonded pdb=" OE1 GLU D 86 " pdb=" NH2 ARG D 214 " model vdw 2.212 3.120 nonbonded pdb=" OE1 GLU A 86 " pdb=" NH2 ARG A 214 " model vdw 2.212 3.120 nonbonded pdb=" OE1 GLU B 86 " pdb=" NH2 ARG B 214 " model vdw 2.212 3.120 nonbonded pdb=" O SER B 110 " pdb=" NH2 ARG B 201 " model vdw 2.262 3.120 ... (remaining 63659 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 1.180 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 22.120 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.005 0.032 8412 Z= 0.327 Angle : 0.627 5.250 11388 Z= 0.378 Chirality : 0.040 0.157 1252 Planarity : 0.005 0.029 1380 Dihedral : 14.379 89.345 2936 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.17), residues: 988 helix: -2.96 (0.11), residues: 824 sheet: None (None), residues: 0 loop : -3.65 (0.39), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 269 HIS 0.003 0.001 HIS A 96 PHE 0.013 0.001 PHE B 73 TYR 0.024 0.002 TYR C 98 ARG 0.004 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.983 Fit side-chains REVERT: A 78 GLN cc_start: 0.7956 (tt0) cc_final: 0.7568 (tt0) REVERT: B 78 GLN cc_start: 0.7954 (tt0) cc_final: 0.7568 (tt0) REVERT: C 78 GLN cc_start: 0.7953 (tt0) cc_final: 0.7569 (tt0) REVERT: D 78 GLN cc_start: 0.7954 (tt0) cc_final: 0.7568 (tt0) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2394 time to fit residues: 52.5683 Evaluate side-chains 150 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS A 323 GLN A 326 GLN B 228 HIS B 323 GLN B 326 GLN C 228 HIS C 323 GLN C 326 GLN D 228 HIS D 323 GLN D 326 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.157267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.111248 restraints weight = 10342.062| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.90 r_work: 0.3212 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8412 Z= 0.208 Angle : 0.540 5.537 11388 Z= 0.304 Chirality : 0.037 0.119 1252 Planarity : 0.004 0.023 1380 Dihedral : 4.254 12.921 1124 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.38 % Allowed : 15.00 % Favored : 82.62 % 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: -0.65 (0.24), residues: 988 helix: 0.12 (0.16), residues: 816 sheet: None (None), residues: 0 loop : -2.69 (0.39), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 146 HIS 0.002 0.001 HIS B 96 PHE 0.011 0.002 PHE A 163 TYR 0.012 0.002 TYR D 280 ARG 0.002 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.946 Fit side-chains REVERT: A 78 GLN cc_start: 0.7834 (tt0) cc_final: 0.7543 (tt0) REVERT: A 102 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8114 (tp) REVERT: A 129 LEU cc_start: 0.8365 (tp) cc_final: 0.7984 (tt) REVERT: A 202 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7940 (t80) REVERT: B 78 GLN cc_start: 0.7814 (tt0) cc_final: 0.7566 (tt0) REVERT: B 102 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8115 (tp) REVERT: B 129 LEU cc_start: 0.8367 (tp) cc_final: 0.7989 (tt) REVERT: B 202 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7934 (t80) REVERT: C 78 GLN cc_start: 0.7804 (tt0) cc_final: 0.7557 (tt0) REVERT: C 102 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8113 (tp) REVERT: C 129 LEU cc_start: 0.8358 (tp) cc_final: 0.7967 (tt) REVERT: C 202 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7939 (t80) REVERT: D 78 GLN cc_start: 0.7815 (tt0) cc_final: 0.7568 (tt0) REVERT: D 102 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8112 (tp) REVERT: D 129 LEU cc_start: 0.8371 (tp) cc_final: 0.7978 (tt) REVERT: D 202 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7939 (t80) outliers start: 20 outliers final: 12 residues processed: 176 average time/residue: 0.2130 time to fit residues: 51.1927 Evaluate side-chains 188 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN A 326 GLN B 323 GLN B 326 GLN C 323 GLN C 326 GLN D 323 GLN D 326 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.159251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113214 restraints weight = 10505.397| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.94 r_work: 0.3237 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 8412 Z= 0.168 Angle : 0.476 4.822 11388 Z= 0.262 Chirality : 0.036 0.115 1252 Planarity : 0.003 0.022 1380 Dihedral : 3.810 11.965 1124 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.33 % Allowed : 15.24 % Favored : 81.43 % 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: 0.95 (0.26), residues: 988 helix: 1.29 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.90 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 146 HIS 0.002 0.001 HIS B 96 PHE 0.009 0.001 PHE B 163 TYR 0.010 0.001 TYR B 237 ARG 0.001 0.000 ARG C 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.862 Fit side-chains REVERT: A 78 GLN cc_start: 0.7857 (tt0) cc_final: 0.7594 (tt0) REVERT: A 129 LEU cc_start: 0.8310 (tp) cc_final: 0.7954 (tt) REVERT: A 201 ARG cc_start: 0.8183 (ttm170) cc_final: 0.6445 (ttp80) REVERT: A 202 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.8053 (t80) REVERT: A 257 GLU cc_start: 0.8299 (mp0) cc_final: 0.7987 (mp0) REVERT: B 78 GLN cc_start: 0.7905 (tt0) cc_final: 0.7661 (tt0) REVERT: B 129 LEU cc_start: 0.8313 (tp) cc_final: 0.7957 (tt) REVERT: B 201 ARG cc_start: 0.8232 (ttm170) cc_final: 0.6443 (ttp80) REVERT: B 202 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.8044 (t80) REVERT: B 257 GLU cc_start: 0.8299 (mp0) cc_final: 0.7988 (mp0) REVERT: C 78 GLN cc_start: 0.7893 (tt0) cc_final: 0.7653 (tt0) REVERT: C 129 LEU cc_start: 0.8296 (tp) cc_final: 0.7892 (tt) REVERT: C 201 ARG cc_start: 0.8202 (ttm170) cc_final: 0.6447 (ttp80) REVERT: C 202 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.8065 (t80) REVERT: D 78 GLN cc_start: 0.7896 (tt0) cc_final: 0.7656 (tt0) REVERT: D 129 LEU cc_start: 0.8309 (tp) cc_final: 0.7907 (tt) REVERT: D 201 ARG cc_start: 0.8198 (ttm170) cc_final: 0.6439 (ttp80) REVERT: D 202 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.8048 (t80) REVERT: D 257 GLU cc_start: 0.8308 (mp0) cc_final: 0.7996 (mp0) outliers start: 28 outliers final: 20 residues processed: 184 average time/residue: 0.2010 time to fit residues: 50.1842 Evaluate side-chains 187 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 0.0570 chunk 34 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.0970 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 323 GLN C 323 GLN D 79 ASN D 323 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.160038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.113808 restraints weight = 10423.299| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.94 r_work: 0.3247 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 8412 Z= 0.156 Angle : 0.463 5.660 11388 Z= 0.248 Chirality : 0.035 0.113 1252 Planarity : 0.002 0.019 1380 Dihedral : 3.666 10.971 1124 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.29 % Allowed : 14.29 % Favored : 81.43 % 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: 1.78 (0.27), residues: 988 helix: 1.84 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.58 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 146 HIS 0.002 0.001 HIS C 96 PHE 0.008 0.001 PHE C 240 TYR 0.010 0.001 TYR B 237 ARG 0.003 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 0.948 Fit side-chains REVERT: A 78 GLN cc_start: 0.7859 (tt0) cc_final: 0.7604 (tt0) REVERT: A 129 LEU cc_start: 0.8242 (tp) cc_final: 0.7969 (tp) REVERT: A 201 ARG cc_start: 0.8175 (ttm170) cc_final: 0.6426 (ttp80) REVERT: A 202 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.8084 (t80) REVERT: A 257 GLU cc_start: 0.8294 (mp0) cc_final: 0.7949 (mp0) REVERT: B 78 GLN cc_start: 0.7873 (tt0) cc_final: 0.7608 (tt0) REVERT: B 129 LEU cc_start: 0.8239 (tp) cc_final: 0.7849 (tt) REVERT: B 201 ARG cc_start: 0.8169 (ttm170) cc_final: 0.6417 (ttp80) REVERT: B 202 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.8071 (t80) REVERT: B 207 ARG cc_start: 0.7918 (mmt90) cc_final: 0.7717 (mmt90) REVERT: B 257 GLU cc_start: 0.8282 (mp0) cc_final: 0.7936 (mp0) REVERT: C 78 GLN cc_start: 0.7874 (tt0) cc_final: 0.7611 (tt0) REVERT: C 129 LEU cc_start: 0.8225 (tp) cc_final: 0.7952 (tp) REVERT: C 201 ARG cc_start: 0.8169 (ttm170) cc_final: 0.6422 (ttp80) REVERT: C 202 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.8072 (t80) REVERT: D 78 GLN cc_start: 0.7877 (tt0) cc_final: 0.7613 (tt0) REVERT: D 129 LEU cc_start: 0.8241 (tp) cc_final: 0.7972 (tp) REVERT: D 201 ARG cc_start: 0.8163 (ttm170) cc_final: 0.6417 (ttp80) REVERT: D 202 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.8062 (t80) REVERT: D 257 GLU cc_start: 0.8297 (mp0) cc_final: 0.7950 (mp0) outliers start: 36 outliers final: 20 residues processed: 188 average time/residue: 0.1978 time to fit residues: 50.6112 Evaluate side-chains 186 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 323 GLN C 323 GLN D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.159404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.112618 restraints weight = 10337.504| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.93 r_work: 0.3231 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 8412 Z= 0.184 Angle : 0.498 6.852 11388 Z= 0.260 Chirality : 0.036 0.115 1252 Planarity : 0.002 0.019 1380 Dihedral : 3.625 10.989 1124 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.81 % Allowed : 15.24 % Favored : 80.95 % 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: 2.20 (0.27), residues: 988 helix: 2.14 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.51 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 146 HIS 0.002 0.001 HIS D 96 PHE 0.008 0.001 PHE D 240 TYR 0.010 0.001 TYR A 237 ARG 0.002 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 129 LEU cc_start: 0.8240 (tp) cc_final: 0.7990 (tp) REVERT: A 202 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7990 (t80) REVERT: A 257 GLU cc_start: 0.8281 (mp0) cc_final: 0.7930 (mp0) REVERT: B 78 GLN cc_start: 0.7821 (tt0) cc_final: 0.7562 (tt0) REVERT: B 129 LEU cc_start: 0.8259 (tp) cc_final: 0.8007 (tp) REVERT: B 202 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.8016 (t80) REVERT: B 257 GLU cc_start: 0.8273 (mp0) cc_final: 0.7922 (mp0) REVERT: C 78 GLN cc_start: 0.7817 (tt0) cc_final: 0.7562 (tt0) REVERT: C 129 LEU cc_start: 0.8221 (tp) cc_final: 0.7969 (tp) REVERT: C 202 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.8012 (t80) REVERT: D 78 GLN cc_start: 0.7781 (tt0) cc_final: 0.7563 (tt0) REVERT: D 129 LEU cc_start: 0.8243 (tp) cc_final: 0.7995 (tp) REVERT: D 202 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7999 (t80) REVERT: D 257 GLU cc_start: 0.8280 (mp0) cc_final: 0.7930 (mp0) outliers start: 32 outliers final: 20 residues processed: 172 average time/residue: 0.1880 time to fit residues: 45.0669 Evaluate side-chains 174 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 10.0000 chunk 88 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 323 GLN C 323 GLN D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.159550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113123 restraints weight = 10297.291| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.94 r_work: 0.3236 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8412 Z= 0.175 Angle : 0.480 6.643 11388 Z= 0.253 Chirality : 0.036 0.114 1252 Planarity : 0.002 0.018 1380 Dihedral : 3.579 10.981 1124 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.81 % Allowed : 15.71 % Favored : 80.48 % 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: 2.43 (0.27), residues: 988 helix: 2.30 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.45 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 146 HIS 0.002 0.001 HIS B 96 PHE 0.010 0.001 PHE B 163 TYR 0.009 0.001 TYR A 237 ARG 0.005 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.8224 (tp) cc_final: 0.7968 (tp) REVERT: A 202 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.8001 (t80) REVERT: A 257 GLU cc_start: 0.8284 (mp0) cc_final: 0.7934 (mp0) REVERT: B 129 LEU cc_start: 0.8247 (tp) cc_final: 0.7994 (tp) REVERT: B 202 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.8013 (t80) REVERT: B 257 GLU cc_start: 0.8280 (mp0) cc_final: 0.7935 (mp0) REVERT: C 129 LEU cc_start: 0.8212 (tp) cc_final: 0.7956 (tp) REVERT: C 202 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.8009 (t80) REVERT: D 78 GLN cc_start: 0.7757 (tt0) cc_final: 0.7547 (tt0) REVERT: D 129 LEU cc_start: 0.8228 (tp) cc_final: 0.7974 (tp) REVERT: D 202 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7992 (t80) REVERT: D 257 GLU cc_start: 0.8281 (mp0) cc_final: 0.7928 (mp0) outliers start: 32 outliers final: 16 residues processed: 168 average time/residue: 0.1796 time to fit residues: 41.8502 Evaluate side-chains 168 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 323 GLN C 323 GLN D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.160756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.114051 restraints weight = 10262.017| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.94 r_work: 0.3251 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8412 Z= 0.156 Angle : 0.477 7.417 11388 Z= 0.247 Chirality : 0.035 0.112 1252 Planarity : 0.002 0.019 1380 Dihedral : 3.515 10.644 1124 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.33 % Allowed : 16.43 % Favored : 80.24 % 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: 2.66 (0.27), residues: 988 helix: 2.48 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -2.41 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 146 HIS 0.002 0.001 HIS C 96 PHE 0.011 0.001 PHE B 163 TYR 0.010 0.001 TYR D 237 ARG 0.005 0.000 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.8210 (tp) cc_final: 0.7993 (tp) REVERT: A 202 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.8082 (t80) REVERT: B 129 LEU cc_start: 0.8218 (tp) cc_final: 0.7983 (tp) REVERT: B 202 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.8028 (t80) REVERT: C 129 LEU cc_start: 0.8198 (tp) cc_final: 0.7979 (tp) REVERT: C 202 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.8094 (t80) REVERT: D 129 LEU cc_start: 0.8206 (tp) cc_final: 0.7989 (tp) REVERT: D 202 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.8087 (t80) outliers start: 28 outliers final: 21 residues processed: 168 average time/residue: 0.1813 time to fit residues: 42.5039 Evaluate side-chains 174 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 45 optimal weight: 0.0870 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.0270 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 323 GLN B 323 GLN C 323 GLN D 323 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.161766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115649 restraints weight = 10325.159| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.96 r_work: 0.3273 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8412 Z= 0.144 Angle : 0.495 7.758 11388 Z= 0.253 Chirality : 0.034 0.112 1252 Planarity : 0.002 0.017 1380 Dihedral : 3.443 10.484 1124 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.21 % Allowed : 17.14 % Favored : 79.64 % 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: 2.75 (0.27), residues: 988 helix: 2.55 (0.17), residues: 828 sheet: None (None), residues: 0 loop : -2.42 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 146 HIS 0.001 0.000 HIS B 96 PHE 0.012 0.001 PHE D 163 TYR 0.011 0.001 TYR A 74 ARG 0.005 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.844 Fit side-chains REVERT: A 129 LEU cc_start: 0.8215 (tp) cc_final: 0.7970 (tp) REVERT: A 201 ARG cc_start: 0.8168 (ttm170) cc_final: 0.6363 (ttp80) REVERT: B 129 LEU cc_start: 0.8199 (tp) cc_final: 0.7960 (tp) REVERT: B 201 ARG cc_start: 0.8159 (ttm170) cc_final: 0.6366 (ttp80) REVERT: C 129 LEU cc_start: 0.8208 (tp) cc_final: 0.7962 (tp) REVERT: C 201 ARG cc_start: 0.8174 (ttm170) cc_final: 0.6361 (ttp80) REVERT: D 129 LEU cc_start: 0.8216 (tp) cc_final: 0.7971 (tp) REVERT: D 201 ARG cc_start: 0.8171 (ttm170) cc_final: 0.6359 (ttp80) outliers start: 27 outliers final: 23 residues processed: 169 average time/residue: 0.1968 time to fit residues: 45.0343 Evaluate side-chains 175 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 15 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 16 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 79 ASN B 323 GLN C 79 ASN C 323 GLN D 323 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.159106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.111603 restraints weight = 10484.637| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.96 r_work: 0.3216 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8412 Z= 0.209 Angle : 0.531 8.925 11388 Z= 0.272 Chirality : 0.036 0.117 1252 Planarity : 0.003 0.017 1380 Dihedral : 3.527 10.728 1124 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.10 % Allowed : 17.86 % Favored : 79.05 % 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: 2.74 (0.27), residues: 988 helix: 2.56 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -2.52 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 146 HIS 0.002 0.001 HIS C 96 PHE 0.008 0.001 PHE D 240 TYR 0.009 0.001 TYR D 237 ARG 0.006 0.000 ARG D 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.882 Fit side-chains REVERT: A 129 LEU cc_start: 0.8258 (tp) cc_final: 0.8002 (tp) REVERT: B 129 LEU cc_start: 0.8260 (tp) cc_final: 0.8006 (tp) REVERT: C 129 LEU cc_start: 0.8248 (tp) cc_final: 0.8008 (tp) REVERT: D 129 LEU cc_start: 0.8254 (tp) cc_final: 0.7997 (tp) outliers start: 26 outliers final: 24 residues processed: 170 average time/residue: 0.1945 time to fit residues: 45.4122 Evaluate side-chains 174 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 68 optimal weight: 0.0970 chunk 83 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 0.0980 chunk 84 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 323 GLN C 323 GLN D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.162850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.116362 restraints weight = 10182.735| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.94 r_work: 0.3289 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8412 Z= 0.141 Angle : 0.512 8.896 11388 Z= 0.257 Chirality : 0.034 0.108 1252 Planarity : 0.002 0.018 1380 Dihedral : 3.430 10.479 1124 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.86 % Allowed : 17.62 % Favored : 79.52 % 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: 2.83 (0.27), residues: 988 helix: 2.66 (0.17), residues: 824 sheet: None (None), residues: 0 loop : -2.61 (0.41), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 146 HIS 0.001 0.000 HIS C 96 PHE 0.013 0.001 PHE C 163 TYR 0.010 0.001 TYR A 237 ARG 0.004 0.000 ARG B 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.925 Fit side-chains REVERT: A 201 ARG cc_start: 0.8104 (ttm170) cc_final: 0.6368 (ttp80) REVERT: A 257 GLU cc_start: 0.8302 (mp0) cc_final: 0.8059 (mm-30) REVERT: B 201 ARG cc_start: 0.8092 (ttm170) cc_final: 0.6348 (ttp80) REVERT: B 257 GLU cc_start: 0.8275 (mp0) cc_final: 0.8012 (mp0) REVERT: C 201 ARG cc_start: 0.8115 (ttm170) cc_final: 0.6382 (ttp80) REVERT: D 201 ARG cc_start: 0.8143 (ttm170) cc_final: 0.6394 (ttp80) REVERT: D 257 GLU cc_start: 0.8286 (mp0) cc_final: 0.8030 (mp0) outliers start: 24 outliers final: 22 residues processed: 179 average time/residue: 0.2152 time to fit residues: 51.6948 Evaluate side-chains 180 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.1980 chunk 30 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 75 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 323 GLN C 323 GLN D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.162584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.115483 restraints weight = 10327.199| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.96 r_work: 0.3274 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8412 Z= 0.152 Angle : 0.515 9.414 11388 Z= 0.259 Chirality : 0.035 0.112 1252 Planarity : 0.002 0.019 1380 Dihedral : 3.398 10.269 1124 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.21 % Allowed : 18.21 % Favored : 78.57 % 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: 2.97 (0.27), residues: 988 helix: 2.70 (0.17), residues: 828 sheet: None (None), residues: 0 loop : -2.35 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 146 HIS 0.002 0.001 HIS A 96 PHE 0.008 0.001 PHE A 240 TYR 0.010 0.001 TYR D 237 ARG 0.002 0.000 ARG D 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4874.92 seconds wall clock time: 86 minutes 52.73 seconds (5212.73 seconds total)