Starting phenix.real_space_refine on Tue Mar 3 18:45:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cr0_30443/03_2026/7cr0_30443.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cr0_30443/03_2026/7cr0_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 { model { file = "/net/cci-nas-00/data/ceres_data/7cr0_30443/03_2026/7cr0_30443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cr0_30443/03_2026/7cr0_30443.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cr0_30443/03_2026/7cr0_30443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cr0_30443/03_2026/7cr0_30443.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.70, per 1000 atoms: 0.21 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: 0.68 Conformation dependent library (CDL) restraints added in 198.7 milliseconds 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: 0.15 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: 0.91 Time building geometry restraints manager: 0.89 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 1.170 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.640 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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= 0.228 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.001 ARG D 201 TYR 0.024 0.002 TYR C 98 PHE 0.013 0.001 PHE B 73 TRP 0.011 0.002 TRP D 269 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 8412) covalent geometry : angle 0.62667 (11388) hydrogen bonds : bond 0.16259 ( 645) hydrogen bonds : angle 6.97841 ( 1935) *********************** 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 : 0.245 Fit side-chains REVERT: A 78 GLN cc_start: 0.7955 (tt0) cc_final: 0.7568 (tt0) REVERT: B 78 GLN cc_start: 0.7953 (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: 0.0982 time to fit residues: 21.6503 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 : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3949 r_free = 0.3949 target = 0.158968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113191 restraints weight = 10466.938| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.91 r_work: 0.3239 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 8412 Z= 0.131 Angle : 0.518 5.158 11388 Z= 0.290 Chirality : 0.036 0.118 1252 Planarity : 0.004 0.023 1380 Dihedral : 4.197 12.808 1124 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.86 % Allowed : 13.57 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.23), residues: 988 helix: 0.08 (0.16), residues: 824 sheet: None (None), residues: 0 loop : -2.93 (0.39), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 325 TYR 0.013 0.002 TYR A 141 PHE 0.014 0.002 PHE A 163 TRP 0.009 0.001 TRP C 146 HIS 0.001 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8412) covalent geometry : angle 0.51818 (11388) hydrogen bonds : bond 0.05326 ( 645) hydrogen bonds : angle 4.17198 ( 1935) *********************** 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 197 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.271 Fit side-chains REVERT: A 78 GLN cc_start: 0.7826 (tt0) cc_final: 0.7613 (tt0) REVERT: A 102 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8087 (tp) REVERT: A 129 LEU cc_start: 0.8316 (tp) cc_final: 0.7913 (tt) REVERT: A 201 ARG cc_start: 0.8245 (ttm170) cc_final: 0.6488 (ttp80) REVERT: A 202 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7998 (t80) REVERT: A 211 MET cc_start: 0.8913 (mmm) cc_final: 0.8601 (mmm) REVERT: B 78 GLN cc_start: 0.7788 (tt0) cc_final: 0.7546 (tt0) REVERT: B 102 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8086 (tp) REVERT: B 129 LEU cc_start: 0.8316 (tp) cc_final: 0.7929 (tt) REVERT: B 201 ARG cc_start: 0.8238 (ttm170) cc_final: 0.6479 (ttp80) REVERT: B 202 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7990 (t80) REVERT: C 78 GLN cc_start: 0.7773 (tt0) cc_final: 0.7534 (tt0) REVERT: C 102 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8090 (tp) REVERT: C 129 LEU cc_start: 0.8304 (tp) cc_final: 0.7896 (tt) REVERT: C 201 ARG cc_start: 0.8237 (ttm170) cc_final: 0.6484 (ttp80) REVERT: C 202 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7997 (t80) REVERT: C 211 MET cc_start: 0.8928 (mmm) cc_final: 0.8621 (mmm) REVERT: D 78 GLN cc_start: 0.7785 (tt0) cc_final: 0.7547 (tt0) REVERT: D 102 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8082 (tp) REVERT: D 129 LEU cc_start: 0.8318 (tp) cc_final: 0.7915 (tt) REVERT: D 201 ARG cc_start: 0.8236 (ttm170) cc_final: 0.6486 (ttp80) REVERT: D 202 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.8002 (t80) outliers start: 24 outliers final: 16 residues processed: 185 average time/residue: 0.0828 time to fit residues: 21.0111 Evaluate side-chains 184 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 244 ILE 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 244 ILE 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 244 ILE 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 244 ILE 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 29 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 22 optimal weight: 0.0060 overall best weight: 1.1800 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.157789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.111401 restraints weight = 10339.583| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.93 r_work: 0.3210 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2161 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= 0.147 Angle : 0.495 4.939 11388 Z= 0.272 Chirality : 0.036 0.119 1252 Planarity : 0.003 0.023 1380 Dihedral : 3.872 12.125 1124 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.33 % Allowed : 16.55 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.26), residues: 988 helix: 1.29 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -3.00 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 201 TYR 0.010 0.001 TYR C 237 PHE 0.008 0.001 PHE C 240 TRP 0.009 0.001 TRP B 146 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8412) covalent geometry : angle 0.49502 (11388) hydrogen bonds : bond 0.05102 ( 645) hydrogen bonds : angle 3.86055 ( 1935) *********************** 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 181 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.269 Fit side-chains REVERT: A 78 GLN cc_start: 0.7780 (tt0) cc_final: 0.7532 (tt0) REVERT: A 129 LEU cc_start: 0.8338 (tp) cc_final: 0.7980 (tt) REVERT: A 202 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7990 (t80) REVERT: A 257 GLU cc_start: 0.8316 (mp0) cc_final: 0.7984 (mp0) REVERT: B 78 GLN cc_start: 0.7892 (tt0) cc_final: 0.7590 (tt0) REVERT: B 201 ARG cc_start: 0.8255 (ttm170) cc_final: 0.6474 (ttp80) REVERT: B 202 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.8052 (t80) REVERT: B 257 GLU cc_start: 0.8296 (mp0) cc_final: 0.7964 (mp0) REVERT: C 78 GLN cc_start: 0.7906 (tt0) cc_final: 0.7603 (tt0) REVERT: C 129 LEU cc_start: 0.8325 (tp) cc_final: 0.8099 (tp) REVERT: C 202 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7997 (t80) REVERT: C 257 GLU cc_start: 0.8316 (mp0) cc_final: 0.7984 (mp0) REVERT: D 78 GLN cc_start: 0.7914 (tt0) cc_final: 0.7618 (tt0) REVERT: D 129 LEU cc_start: 0.8348 (tp) cc_final: 0.7963 (tt) REVERT: D 202 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7987 (t80) REVERT: D 257 GLU cc_start: 0.8317 (mp0) cc_final: 0.7985 (mp0) outliers start: 28 outliers final: 19 residues processed: 169 average time/residue: 0.0732 time to fit residues: 17.2954 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 : 0.286 ------------------------------------------------------------------------------- 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 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 202 PHE 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 10.0000 chunk 83 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 94 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 79 ASN C 323 GLN D 79 ASN D 323 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.160596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.114304 restraints weight = 10542.006| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.96 r_work: 0.3255 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8412 Z= 0.115 Angle : 0.483 9.283 11388 Z= 0.250 Chirality : 0.035 0.111 1252 Planarity : 0.002 0.022 1380 Dihedral : 3.658 11.319 1124 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.93 % Allowed : 15.71 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.27), residues: 988 helix: 1.87 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.72 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 207 TYR 0.010 0.001 TYR C 237 PHE 0.009 0.001 PHE B 163 TRP 0.010 0.001 TRP A 146 HIS 0.002 0.000 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8412) covalent geometry : angle 0.48300 (11388) hydrogen bonds : bond 0.04378 ( 645) hydrogen bonds : angle 3.62720 ( 1935) *********************** 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 201 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.281 Fit side-chains REVERT: A 78 GLN cc_start: 0.7859 (tt0) cc_final: 0.7614 (tt0) REVERT: A 129 LEU cc_start: 0.8211 (tp) cc_final: 0.7964 (tp) REVERT: A 201 ARG cc_start: 0.8191 (ttm170) cc_final: 0.6431 (ttp80) REVERT: A 202 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.8059 (t80) REVERT: A 257 GLU cc_start: 0.8265 (mp0) cc_final: 0.7937 (mp0) REVERT: B 78 GLN cc_start: 0.7804 (tt0) cc_final: 0.7588 (tt0) REVERT: B 129 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7916 (tt) REVERT: B 201 ARG cc_start: 0.8178 (ttm170) cc_final: 0.6443 (ttp80) REVERT: B 202 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.8040 (t80) REVERT: B 257 GLU cc_start: 0.8242 (mp0) cc_final: 0.7912 (mp0) REVERT: C 78 GLN cc_start: 0.7811 (tt0) cc_final: 0.7598 (tt0) REVERT: C 129 LEU cc_start: 0.8197 (tp) cc_final: 0.7949 (tp) REVERT: C 201 ARG cc_start: 0.8180 (ttm170) cc_final: 0.6436 (ttp80) REVERT: C 202 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.8049 (t80) REVERT: C 257 GLU cc_start: 0.8251 (mp0) cc_final: 0.7914 (mp0) REVERT: D 78 GLN cc_start: 0.7817 (tt0) cc_final: 0.7604 (tt0) REVERT: D 129 LEU cc_start: 0.8216 (tp) cc_final: 0.7970 (tp) REVERT: D 201 ARG cc_start: 0.8180 (ttm170) cc_final: 0.6439 (ttp80) REVERT: D 202 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.8045 (t80) REVERT: D 257 GLU cc_start: 0.8262 (mp0) cc_final: 0.7933 (mp0) outliers start: 33 outliers final: 20 residues processed: 189 average time/residue: 0.0784 time to fit residues: 20.4048 Evaluate side-chains 189 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 129 LEU 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 1 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.160362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.114024 restraints weight = 10378.683| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.95 r_work: 0.3251 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 8412 Z= 0.121 Angle : 0.480 6.180 11388 Z= 0.251 Chirality : 0.035 0.113 1252 Planarity : 0.002 0.020 1380 Dihedral : 3.577 11.134 1124 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.93 % Allowed : 15.95 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.27), residues: 988 helix: 2.20 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.59 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 201 TYR 0.010 0.001 TYR D 237 PHE 0.009 0.001 PHE D 163 TRP 0.010 0.001 TRP A 146 HIS 0.002 0.001 HIS C 96 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8412) covalent geometry : angle 0.48005 (11388) hydrogen bonds : bond 0.04412 ( 645) hydrogen bonds : angle 3.59335 ( 1935) *********************** 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 189 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.8220 (tp) cc_final: 0.7968 (tp) REVERT: A 201 ARG cc_start: 0.8171 (ttm170) cc_final: 0.6444 (ttp80) REVERT: A 202 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.8047 (t80) REVERT: B 129 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7871 (tt) REVERT: B 201 ARG cc_start: 0.8153 (ttm170) cc_final: 0.6427 (ttp80) REVERT: B 202 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.8075 (t80) REVERT: C 78 GLN cc_start: 0.7777 (tt0) cc_final: 0.7571 (tt0) REVERT: C 129 LEU cc_start: 0.8204 (tp) cc_final: 0.7951 (tp) REVERT: C 201 ARG cc_start: 0.8182 (ttm170) cc_final: 0.6459 (ttp80) REVERT: C 202 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.8059 (t80) REVERT: C 257 GLU cc_start: 0.8274 (mp0) cc_final: 0.7910 (mp0) REVERT: D 78 GLN cc_start: 0.7787 (tt0) cc_final: 0.7581 (tt0) REVERT: D 129 LEU cc_start: 0.8230 (tp) cc_final: 0.7979 (tp) REVERT: D 201 ARG cc_start: 0.8186 (ttm170) cc_final: 0.6461 (ttp80) REVERT: D 202 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.8051 (t80) outliers start: 33 outliers final: 20 residues processed: 177 average time/residue: 0.0794 time to fit residues: 19.2786 Evaluate side-chains 181 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 129 LEU 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 49 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.158396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.111298 restraints weight = 10339.794| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.95 r_work: 0.3210 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8412 Z= 0.152 Angle : 0.502 7.036 11388 Z= 0.266 Chirality : 0.037 0.121 1252 Planarity : 0.003 0.020 1380 Dihedral : 3.643 11.340 1124 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.45 % Allowed : 16.55 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.27), residues: 988 helix: 2.33 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -2.62 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 207 TYR 0.010 0.001 TYR D 237 PHE 0.010 0.001 PHE C 163 TRP 0.012 0.001 TRP A 146 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8412) covalent geometry : angle 0.50203 (11388) hydrogen bonds : bond 0.04849 ( 645) hydrogen bonds : angle 3.69463 ( 1935) *********************** 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 182 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.8276 (tp) cc_final: 0.8043 (tp) REVERT: A 219 LYS cc_start: 0.8503 (mttt) cc_final: 0.8201 (mmtp) REVERT: B 129 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7971 (tt) REVERT: C 78 GLN cc_start: 0.7847 (tt0) cc_final: 0.7577 (tt0) REVERT: C 129 LEU cc_start: 0.8266 (tp) cc_final: 0.8030 (tp) REVERT: D 78 GLN cc_start: 0.7848 (tt0) cc_final: 0.7579 (tt0) REVERT: D 129 LEU cc_start: 0.8277 (tp) cc_final: 0.8045 (tp) outliers start: 29 outliers final: 20 residues processed: 174 average time/residue: 0.0728 time to fit residues: 17.7441 Evaluate side-chains 174 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 312 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 150 CYS 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 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 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 37 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.159979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113198 restraints weight = 10378.440| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.96 r_work: 0.3239 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8412 Z= 0.126 Angle : 0.498 8.052 11388 Z= 0.257 Chirality : 0.036 0.113 1252 Planarity : 0.002 0.021 1380 Dihedral : 3.546 11.035 1124 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.45 % Allowed : 17.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.27), residues: 988 helix: 2.45 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -2.59 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 207 TYR 0.010 0.001 TYR C 237 PHE 0.010 0.001 PHE D 163 TRP 0.012 0.001 TRP A 146 HIS 0.002 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8412) covalent geometry : angle 0.49838 (11388) hydrogen bonds : bond 0.04451 ( 645) hydrogen bonds : angle 3.60138 ( 1935) *********************** 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 182 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.8220 (tp) cc_final: 0.7965 (tp) REVERT: A 202 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.8001 (t80) REVERT: B 129 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7971 (tt) REVERT: B 201 ARG cc_start: 0.8173 (ttm170) cc_final: 0.6405 (ttp80) REVERT: B 202 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.8088 (t80) REVERT: C 129 LEU cc_start: 0.8204 (tp) cc_final: 0.7948 (tp) REVERT: C 202 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.8015 (t80) REVERT: D 129 LEU cc_start: 0.8218 (tp) cc_final: 0.7964 (tp) REVERT: D 202 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.8002 (t80) outliers start: 29 outliers final: 16 residues processed: 170 average time/residue: 0.0763 time to fit residues: 18.1434 Evaluate side-chains 170 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 129 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 8 optimal weight: 0.0270 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 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 = 0.3984 r_free = 0.3984 target = 0.161843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.115666 restraints weight = 10289.088| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.94 r_work: 0.3273 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3043 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= 0.112 Angle : 0.495 8.269 11388 Z= 0.251 Chirality : 0.035 0.112 1252 Planarity : 0.002 0.019 1380 Dihedral : 3.447 10.400 1124 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.45 % Allowed : 16.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.27), residues: 988 helix: 2.56 (0.17), residues: 828 sheet: None (None), residues: 0 loop : -2.52 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 207 TYR 0.010 0.001 TYR D 237 PHE 0.011 0.001 PHE A 163 TRP 0.013 0.001 TRP A 146 HIS 0.001 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 8412) covalent geometry : angle 0.49490 (11388) hydrogen bonds : bond 0.04104 ( 645) hydrogen bonds : angle 3.50027 ( 1935) *********************** 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 182 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.8197 (tp) cc_final: 0.7955 (tp) REVERT: A 201 ARG cc_start: 0.8147 (ttm170) cc_final: 0.6380 (ttp80) REVERT: B 129 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7946 (tt) REVERT: B 201 ARG cc_start: 0.8140 (ttm170) cc_final: 0.6417 (ttp80) REVERT: C 129 LEU cc_start: 0.8210 (tp) cc_final: 0.7961 (tp) REVERT: C 201 ARG cc_start: 0.8154 (ttm170) cc_final: 0.6374 (ttp80) REVERT: D 129 LEU cc_start: 0.8220 (tp) cc_final: 0.7974 (tp) REVERT: D 201 ARG cc_start: 0.8159 (ttm170) cc_final: 0.6390 (ttp80) outliers start: 29 outliers final: 22 residues processed: 171 average time/residue: 0.0889 time to fit residues: 20.5726 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 : 0.283 ------------------------------------------------------------------------------- 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 129 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.161634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.114691 restraints weight = 10264.297| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.96 r_work: 0.3260 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3136 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= 0.117 Angle : 0.507 9.553 11388 Z= 0.257 Chirality : 0.035 0.111 1252 Planarity : 0.002 0.020 1380 Dihedral : 3.421 10.198 1124 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.86 % Allowed : 18.21 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.27), residues: 988 helix: 2.61 (0.17), residues: 828 sheet: None (None), residues: 0 loop : -2.50 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 207 TYR 0.011 0.001 TYR A 74 PHE 0.013 0.001 PHE B 163 TRP 0.013 0.001 TRP A 146 HIS 0.002 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8412) covalent geometry : angle 0.50718 (11388) hydrogen bonds : bond 0.04179 ( 645) hydrogen bonds : angle 3.50479 ( 1935) *********************** 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 184 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.8230 (tp) cc_final: 0.7985 (tp) REVERT: A 201 ARG cc_start: 0.8104 (ttm170) cc_final: 0.6354 (ttp80) REVERT: A 322 GLU cc_start: 0.8506 (pp20) cc_final: 0.8243 (pp20) REVERT: B 129 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7920 (tt) REVERT: B 201 ARG cc_start: 0.8142 (ttm170) cc_final: 0.6433 (ttp80) REVERT: B 322 GLU cc_start: 0.8511 (pp20) cc_final: 0.8242 (pp20) REVERT: C 129 LEU cc_start: 0.8229 (tp) cc_final: 0.7982 (tp) REVERT: C 201 ARG cc_start: 0.8128 (ttm170) cc_final: 0.6368 (ttp80) REVERT: C 322 GLU cc_start: 0.8526 (pp20) cc_final: 0.8258 (pp20) REVERT: D 129 LEU cc_start: 0.8237 (tp) cc_final: 0.7991 (tp) REVERT: D 201 ARG cc_start: 0.8119 (ttm170) cc_final: 0.6376 (ttp80) REVERT: D 322 GLU cc_start: 0.8515 (pp20) cc_final: 0.8255 (pp20) outliers start: 24 outliers final: 22 residues processed: 176 average time/residue: 0.0901 time to fit residues: 21.3655 Evaluate side-chains 181 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 129 LEU 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 4 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 0.0470 overall best weight: 0.6680 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.161510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.115004 restraints weight = 10274.203| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.95 r_work: 0.3266 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3230 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= 0.115 Angle : 0.517 9.805 11388 Z= 0.260 Chirality : 0.035 0.110 1252 Planarity : 0.002 0.019 1380 Dihedral : 3.415 10.176 1124 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.86 % Allowed : 18.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.27), residues: 988 helix: 2.63 (0.17), residues: 828 sheet: None (None), residues: 0 loop : -2.48 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 207 TYR 0.010 0.001 TYR D 237 PHE 0.013 0.001 PHE B 163 TRP 0.013 0.001 TRP A 146 HIS 0.002 0.001 HIS C 96 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8412) covalent geometry : angle 0.51670 (11388) hydrogen bonds : bond 0.04110 ( 645) hydrogen bonds : angle 3.48278 ( 1935) ********************** 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 186 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.8219 (tp) cc_final: 0.7978 (tp) REVERT: A 201 ARG cc_start: 0.8137 (ttm170) cc_final: 0.6378 (ttp80) REVERT: A 257 GLU cc_start: 0.8284 (mp0) cc_final: 0.7980 (mm-30) REVERT: A 322 GLU cc_start: 0.8499 (pp20) cc_final: 0.8233 (pp20) REVERT: B 129 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7940 (tt) REVERT: B 201 ARG cc_start: 0.8149 (ttm170) cc_final: 0.6418 (ttp80) REVERT: B 257 GLU cc_start: 0.8251 (mp0) cc_final: 0.7987 (mm-30) REVERT: B 322 GLU cc_start: 0.8492 (pp20) cc_final: 0.8228 (pp20) REVERT: C 129 LEU cc_start: 0.8214 (tp) cc_final: 0.7971 (tp) REVERT: C 201 ARG cc_start: 0.8149 (ttm170) cc_final: 0.6382 (ttp80) REVERT: C 322 GLU cc_start: 0.8503 (pp20) cc_final: 0.8240 (pp20) REVERT: D 129 LEU cc_start: 0.8226 (tp) cc_final: 0.7986 (tp) REVERT: D 201 ARG cc_start: 0.8155 (ttm170) cc_final: 0.6395 (ttp80) REVERT: D 257 GLU cc_start: 0.8295 (mp0) cc_final: 0.7982 (mm-30) REVERT: D 322 GLU cc_start: 0.8506 (pp20) cc_final: 0.8240 (pp20) outliers start: 24 outliers final: 23 residues processed: 178 average time/residue: 0.0863 time to fit residues: 21.0382 Evaluate side-chains 184 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 129 LEU 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 29 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 45 optimal weight: 0.0000 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.161770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.114819 restraints weight = 10345.845| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.96 r_work: 0.3263 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3261 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= 0.119 Angle : 0.519 9.841 11388 Z= 0.261 Chirality : 0.035 0.110 1252 Planarity : 0.002 0.026 1380 Dihedral : 3.411 10.150 1124 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.10 % Allowed : 18.45 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.27), residues: 988 helix: 2.65 (0.17), residues: 828 sheet: None (None), residues: 0 loop : -2.46 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 207 TYR 0.010 0.001 TYR D 237 PHE 0.013 0.001 PHE B 163 TRP 0.013 0.001 TRP A 146 HIS 0.002 0.001 HIS C 96 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8412) covalent geometry : angle 0.51928 (11388) hydrogen bonds : bond 0.04143 ( 645) hydrogen bonds : angle 3.48347 ( 1935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2315.55 seconds wall clock time: 40 minutes 9.93 seconds (2409.93 seconds total)