Starting phenix.real_space_refine on Fri Apr 5 16:43:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uf7_42185/04_2024/8uf7_42185.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uf7_42185/04_2024/8uf7_42185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uf7_42185/04_2024/8uf7_42185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uf7_42185/04_2024/8uf7_42185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uf7_42185/04_2024/8uf7_42185.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uf7_42185/04_2024/8uf7_42185.pdb" } resolution = 3.2 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= 0.016 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 23 5.16 5 C 2449 2.51 5 N 669 2.21 5 O 786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3927 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1651 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 204} Chain: "B" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1620 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 201} Chain: "C" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 656 Classifications: {'peptide': 84} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 76} Time building chain proxies: 2.65, per 1000 atoms: 0.67 Number of scatterers: 3927 At special positions: 0 Unit cell: (56.212, 62.698, 112.424, 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 23 16.00 O 786 8.00 N 669 7.00 C 2449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 89 " distance=2.04 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 311 " distance=2.04 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 416 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 114 " - pdb=" SG CYS C 138 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.55 Conformation dependent library (CDL) restraints added in 824.7 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 950 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 11 sheets defined 5.1% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 122 through 129 removed outlier: 3.538A pdb=" N GLY A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 190 Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 348 through 352 removed outlier: 3.941A pdb=" N GLN B 352 " --> pdb=" O SER B 349 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.508A pdb=" N MET A 11 " --> pdb=" O GLU A 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.563A pdb=" N MET A 21 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 49 removed outlier: 5.699A pdb=" N LEU A 47 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLN A 38 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 115 through 119 removed outlier: 3.611A pdb=" N PHE A 136 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 134 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 178 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 139 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR A 174 " --> pdb=" O ASN A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 155 removed outlier: 3.638A pdb=" N LYS A 208 " --> pdb=" O CYS A 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AA7, first strand: chain 'B' and resid 233 through 237 removed outlier: 3.513A pdb=" N LEU B 233 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER B 286 " --> pdb=" O TYR B 295 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 274 removed outlier: 3.760A pdb=" N THR B 265 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B 253 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TRP B 251 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR B 265 " --> pdb=" O MET B 249 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET B 249 " --> pdb=" O THR B 265 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 344 through 345 removed outlier: 3.531A pdb=" N LEU B 345 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 400 " --> pdb=" O CYS B 361 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N THR B 397 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ALA B 389 " --> pdb=" O THR B 397 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER B 399 " --> pdb=" O PHE B 387 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 372 through 375 Processing sheet with id=AB2, first strand: chain 'C' and resid 125 through 127 removed outlier: 3.648A pdb=" N GLN C 136 " --> pdb=" O CYS C 126 " (cutoff:3.500A) 77 hydrogen bonds defined for protein. 183 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1266 1.34 - 1.46: 966 1.46 - 1.58: 1760 1.58 - 1.70: 0 1.70 - 1.82: 31 Bond restraints: 4023 Sorted by residual: bond pdb=" C SER A 43 " pdb=" N SER A 44 " ideal model delta sigma weight residual 1.339 1.258 0.082 5.57e-02 3.22e+02 2.15e+00 bond pdb=" CB PRO B 344 " pdb=" CG PRO B 344 " ideal model delta sigma weight residual 1.492 1.551 -0.059 5.00e-02 4.00e+02 1.38e+00 bond pdb=" CG LEU B 260 " pdb=" CD1 LEU B 260 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.15e+00 bond pdb=" CG LEU B 296 " pdb=" CD1 LEU B 296 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.12e+00 bond pdb=" CB VAL B 402 " pdb=" CG2 VAL B 402 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.00e+00 ... (remaining 4018 not shown) Histogram of bond angle deviations from ideal: 98.61 - 105.74: 99 105.74 - 112.87: 2199 112.87 - 120.00: 1272 120.00 - 127.13: 1853 127.13 - 134.25: 58 Bond angle restraints: 5481 Sorted by residual: angle pdb=" N SER A 27 " pdb=" CA SER A 27 " pdb=" CB SER A 27 " ideal model delta sigma weight residual 114.17 110.12 4.05 1.14e+00 7.69e-01 1.26e+01 angle pdb=" C LYS B 426 " pdb=" N VAL B 427 " pdb=" CA VAL B 427 " ideal model delta sigma weight residual 121.97 126.81 -4.84 1.80e+00 3.09e-01 7.22e+00 angle pdb=" N GLY A 42 " pdb=" CA GLY A 42 " pdb=" C GLY A 42 " ideal model delta sigma weight residual 113.18 106.89 6.29 2.37e+00 1.78e-01 7.04e+00 angle pdb=" C ALA B 335 " pdb=" N LYS B 336 " pdb=" CA LYS B 336 " ideal model delta sigma weight residual 121.54 125.88 -4.34 1.91e+00 2.74e-01 5.17e+00 angle pdb=" CA LEU B 235 " pdb=" CB LEU B 235 " pdb=" CG LEU B 235 " ideal model delta sigma weight residual 116.30 124.11 -7.81 3.50e+00 8.16e-02 4.98e+00 ... (remaining 5476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 1975 16.50 - 33.01: 305 33.01 - 49.51: 101 49.51 - 66.01: 26 66.01 - 82.51: 6 Dihedral angle restraints: 2413 sinusoidal: 926 harmonic: 1487 Sorted by residual: dihedral pdb=" CB CYS C 65 " pdb=" SG CYS C 65 " pdb=" SG CYS C 143 " pdb=" CB CYS C 143 " ideal model delta sinusoidal sigma weight residual -86.00 -43.06 -42.94 1 1.00e+01 1.00e-02 2.57e+01 dihedral pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " pdb=" SG CYS C 126 " pdb=" CB CYS C 126 " ideal model delta sinusoidal sigma weight residual -86.00 -44.98 -41.02 1 1.00e+01 1.00e-02 2.36e+01 dihedral pdb=" CA TYR A 37 " pdb=" C TYR A 37 " pdb=" N GLN A 38 " pdb=" CA GLN A 38 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 2410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 322 0.028 - 0.056: 180 0.056 - 0.085: 56 0.085 - 0.113: 44 0.113 - 0.141: 11 Chirality restraints: 613 Sorted by residual: chirality pdb=" CG LEU B 345 " pdb=" CB LEU B 345 " pdb=" CD1 LEU B 345 " pdb=" CD2 LEU B 345 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE A 10 " pdb=" N ILE A 10 " pdb=" C ILE A 10 " pdb=" CB ILE A 10 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE A 151 " pdb=" N ILE A 151 " pdb=" C ILE A 151 " pdb=" CB ILE A 151 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 610 not shown) Planarity restraints: 701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 343 " -0.042 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO B 344 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 344 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 344 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 375 " 0.017 2.00e-02 2.50e+03 1.49e-02 5.56e+00 pdb=" CG TRP B 375 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 375 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 375 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 375 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 375 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 375 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 375 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 375 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 375 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 367 " 0.036 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO B 368 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 368 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 368 " 0.027 5.00e-02 4.00e+02 ... (remaining 698 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 483 2.74 - 3.28: 3907 3.28 - 3.82: 6653 3.82 - 4.36: 7630 4.36 - 4.90: 12989 Nonbonded interactions: 31662 Sorted by model distance: nonbonded pdb=" NH1 ARG A 156 " pdb=" OD1 ASN A 158 " model vdw 2.204 2.520 nonbonded pdb=" NH2 ARG B 282 " pdb=" OD2 ASP B 305 " model vdw 2.206 2.520 nonbonded pdb=" OH TYR A 37 " pdb=" OE1 GLN A 90 " model vdw 2.207 2.440 nonbonded pdb=" OH TYR B 250 " pdb=" NH2 ARG C 90 " model vdw 2.221 2.520 nonbonded pdb=" NZ LYS A 40 " pdb=" O GLU A 82 " model vdw 2.225 2.520 ... (remaining 31657 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 3.580 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.480 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 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 0.082 4023 Z= 0.314 Angle : 0.695 7.814 5481 Z= 0.356 Chirality : 0.045 0.141 613 Planarity : 0.006 0.063 701 Dihedral : 18.207 82.515 1442 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.80 % Favored : 86.61 % Rotamer: Outliers : 0.89 % Allowed : 44.30 % Favored : 54.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.23 (0.37), residues: 508 helix: -0.24 (1.21), residues: 20 sheet: -1.48 (0.41), residues: 160 loop : -1.60 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 375 HIS 0.005 0.001 HIS C 104 PHE 0.008 0.001 PHE A 63 TYR 0.012 0.002 TYR B 366 ARG 0.002 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.429 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 82 average time/residue: 0.1256 time to fit residues: 13.5036 Evaluate side-chains 80 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 244 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.0470 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4023 Z= 0.201 Angle : 0.631 7.202 5481 Z= 0.319 Chirality : 0.043 0.132 613 Planarity : 0.005 0.055 701 Dihedral : 5.536 52.852 562 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.59 % Allowed : 11.22 % Favored : 88.19 % Rotamer: Outliers : 6.04 % Allowed : 38.03 % Favored : 55.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.99 (0.37), residues: 508 helix: 0.25 (1.19), residues: 22 sheet: -1.31 (0.43), residues: 149 loop : -1.47 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 375 HIS 0.003 0.001 HIS A 72 PHE 0.006 0.001 PHE B 387 TYR 0.009 0.001 TYR B 248 ARG 0.002 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 77 time to evaluate : 0.408 Fit side-chains REVERT: A 87 TYR cc_start: 0.7812 (m-80) cc_final: 0.7348 (m-80) outliers start: 27 outliers final: 21 residues processed: 94 average time/residue: 0.1147 time to fit residues: 14.4838 Evaluate side-chains 96 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 139 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.0370 chunk 45 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 0.0470 chunk 44 optimal weight: 0.9990 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4023 Z= 0.188 Angle : 0.608 7.299 5481 Z= 0.304 Chirality : 0.043 0.129 613 Planarity : 0.005 0.055 701 Dihedral : 5.436 56.717 562 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.20 % Favored : 87.20 % Rotamer: Outliers : 7.16 % Allowed : 37.36 % Favored : 55.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.95 (0.37), residues: 508 helix: 0.09 (1.17), residues: 22 sheet: -1.27 (0.43), residues: 150 loop : -1.44 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 375 HIS 0.003 0.001 HIS A 72 PHE 0.006 0.001 PHE A 140 TYR 0.008 0.001 TYR B 248 ARG 0.002 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 79 time to evaluate : 0.450 Fit side-chains REVERT: A 87 TYR cc_start: 0.7793 (m-80) cc_final: 0.7324 (m-80) outliers start: 32 outliers final: 25 residues processed: 102 average time/residue: 0.1104 time to fit residues: 15.0585 Evaluate side-chains 102 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 77 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 4023 Z= 0.340 Angle : 0.684 7.667 5481 Z= 0.345 Chirality : 0.045 0.132 613 Planarity : 0.005 0.057 701 Dihedral : 5.928 59.294 562 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.59 % Allowed : 13.19 % Favored : 86.22 % Rotamer: Outliers : 9.40 % Allowed : 35.12 % Favored : 55.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.07 (0.37), residues: 508 helix: -0.14 (1.14), residues: 22 sheet: -1.27 (0.43), residues: 149 loop : -1.56 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 375 HIS 0.004 0.001 HIS C 104 PHE 0.010 0.002 PHE A 63 TYR 0.014 0.002 TYR B 274 ARG 0.003 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 83 time to evaluate : 0.451 Fit side-chains REVERT: B 306 SER cc_start: 0.8161 (p) cc_final: 0.7933 (p) outliers start: 42 outliers final: 34 residues processed: 113 average time/residue: 0.1133 time to fit residues: 17.4355 Evaluate side-chains 115 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 81 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 139 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 4023 Z= 0.295 Angle : 0.669 6.876 5481 Z= 0.337 Chirality : 0.044 0.131 613 Planarity : 0.005 0.058 701 Dihedral : 5.882 58.522 562 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.99 % Favored : 86.42 % Rotamer: Outliers : 8.72 % Allowed : 34.00 % Favored : 57.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.09 (0.37), residues: 508 helix: -0.06 (1.14), residues: 22 sheet: -1.31 (0.43), residues: 149 loop : -1.57 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 375 HIS 0.004 0.001 HIS C 104 PHE 0.009 0.001 PHE A 63 TYR 0.011 0.002 TYR A 50 ARG 0.003 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 83 time to evaluate : 0.449 Fit side-chains REVERT: B 306 SER cc_start: 0.8143 (p) cc_final: 0.7911 (p) outliers start: 39 outliers final: 35 residues processed: 111 average time/residue: 0.1150 time to fit residues: 17.2255 Evaluate side-chains 113 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 78 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 139 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.0870 chunk 4 optimal weight: 0.0970 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 4023 Z= 0.218 Angle : 0.631 6.961 5481 Z= 0.316 Chirality : 0.043 0.127 613 Planarity : 0.005 0.058 701 Dihedral : 5.626 54.736 562 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.99 % Favored : 86.42 % Rotamer: Outliers : 7.61 % Allowed : 34.90 % Favored : 57.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.04 (0.37), residues: 508 helix: -0.04 (1.13), residues: 22 sheet: -1.31 (0.43), residues: 150 loop : -1.51 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 375 HIS 0.004 0.001 HIS C 104 PHE 0.008 0.001 PHE A 140 TYR 0.009 0.001 TYR B 248 ARG 0.003 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 78 time to evaluate : 0.401 Fit side-chains REVERT: A 87 TYR cc_start: 0.7784 (m-80) cc_final: 0.7204 (m-80) REVERT: B 306 SER cc_start: 0.8180 (p) cc_final: 0.7961 (p) outliers start: 34 outliers final: 29 residues processed: 102 average time/residue: 0.1226 time to fit residues: 16.6155 Evaluate side-chains 108 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 79 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 139 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 4023 Z= 0.231 Angle : 0.639 7.629 5481 Z= 0.318 Chirality : 0.043 0.126 613 Planarity : 0.005 0.058 701 Dihedral : 5.591 52.175 562 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.59 % Allowed : 13.19 % Favored : 86.22 % Rotamer: Outliers : 8.50 % Allowed : 33.78 % Favored : 57.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.05 (0.37), residues: 508 helix: -0.09 (1.11), residues: 22 sheet: -1.34 (0.42), residues: 150 loop : -1.50 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 375 HIS 0.003 0.001 HIS C 104 PHE 0.008 0.001 PHE A 140 TYR 0.009 0.001 TYR A 50 ARG 0.003 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 78 time to evaluate : 0.432 Fit side-chains REVERT: A 87 TYR cc_start: 0.7784 (m-80) cc_final: 0.7105 (m-80) outliers start: 38 outliers final: 33 residues processed: 105 average time/residue: 0.1172 time to fit residues: 16.5139 Evaluate side-chains 111 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 78 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 139 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.4980 chunk 4 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 4023 Z= 0.307 Angle : 0.678 7.151 5481 Z= 0.341 Chirality : 0.044 0.129 613 Planarity : 0.005 0.058 701 Dihedral : 5.815 50.645 562 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.80 % Favored : 86.61 % Rotamer: Outliers : 9.84 % Allowed : 32.21 % Favored : 57.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.17 (0.37), residues: 508 helix: 0.99 (1.23), residues: 16 sheet: -1.41 (0.42), residues: 150 loop : -1.64 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 375 HIS 0.004 0.001 HIS C 104 PHE 0.009 0.002 PHE A 63 TYR 0.011 0.002 TYR A 50 ARG 0.003 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 81 time to evaluate : 0.416 Fit side-chains REVERT: A 87 TYR cc_start: 0.7797 (m-80) cc_final: 0.7008 (m-80) REVERT: B 306 SER cc_start: 0.8179 (p) cc_final: 0.7956 (p) REVERT: C 140 ILE cc_start: 0.4590 (OUTLIER) cc_final: 0.4081 (tp) outliers start: 44 outliers final: 34 residues processed: 114 average time/residue: 0.1111 time to fit residues: 17.1126 Evaluate side-chains 112 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 77 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 140 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.0060 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 39 optimal weight: 0.0980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 4023 Z= 0.221 Angle : 0.651 7.243 5481 Z= 0.325 Chirality : 0.044 0.128 613 Planarity : 0.005 0.060 701 Dihedral : 5.582 48.122 562 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.80 % Favored : 86.61 % Rotamer: Outliers : 7.83 % Allowed : 33.56 % Favored : 58.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.11 (0.37), residues: 508 helix: 1.14 (1.25), residues: 16 sheet: -1.36 (0.43), residues: 150 loop : -1.61 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 375 HIS 0.003 0.001 HIS C 104 PHE 0.008 0.001 PHE A 140 TYR 0.010 0.001 TYR A 88 ARG 0.003 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 81 time to evaluate : 0.552 Fit side-chains REVERT: A 87 TYR cc_start: 0.7768 (m-80) cc_final: 0.6893 (m-80) REVERT: B 306 SER cc_start: 0.8191 (p) cc_final: 0.7947 (p) REVERT: C 140 ILE cc_start: 0.4276 (OUTLIER) cc_final: 0.3800 (tp) outliers start: 35 outliers final: 30 residues processed: 106 average time/residue: 0.1112 time to fit residues: 15.9351 Evaluate side-chains 111 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 80 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 140 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 0.0870 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 4023 Z= 0.218 Angle : 0.649 7.939 5481 Z= 0.324 Chirality : 0.044 0.127 613 Planarity : 0.005 0.059 701 Dihedral : 4.905 19.115 560 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.99 % Favored : 86.42 % Rotamer: Outliers : 7.61 % Allowed : 34.68 % Favored : 57.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.11 (0.37), residues: 508 helix: 1.19 (1.24), residues: 16 sheet: -1.35 (0.43), residues: 150 loop : -1.62 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 375 HIS 0.003 0.001 HIS C 104 PHE 0.009 0.001 PHE A 140 TYR 0.008 0.001 TYR A 50 ARG 0.003 0.000 ARG C 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 75 time to evaluate : 0.430 Fit side-chains REVERT: A 87 TYR cc_start: 0.7758 (m-80) cc_final: 0.6805 (m-80) REVERT: C 140 ILE cc_start: 0.4343 (OUTLIER) cc_final: 0.3877 (tp) outliers start: 34 outliers final: 32 residues processed: 99 average time/residue: 0.1184 time to fit residues: 15.7007 Evaluate side-chains 108 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 75 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 140 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.178267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.161492 restraints weight = 5484.444| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.98 r_work: 0.4005 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 4023 Z= 0.296 Angle : 0.691 7.886 5481 Z= 0.346 Chirality : 0.045 0.128 613 Planarity : 0.005 0.059 701 Dihedral : 5.166 19.564 560 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.59 % Allowed : 13.58 % Favored : 85.83 % Rotamer: Outliers : 7.83 % Allowed : 34.00 % Favored : 58.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 (0.37), residues: 508 helix: 0.94 (1.22), residues: 16 sheet: -1.44 (0.43), residues: 150 loop : -1.65 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 375 HIS 0.004 0.001 HIS C 104 PHE 0.009 0.002 PHE A 140 TYR 0.010 0.002 TYR A 50 ARG 0.003 0.000 ARG C 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1420.32 seconds wall clock time: 26 minutes 27.96 seconds (1587.96 seconds total)