Starting phenix.real_space_refine (version: 1.19rc7) on Tue Jan 5 10:27:32 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjm_4564/01_2021/6qjm_4564.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjm_4564/01_2021/6qjm_4564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjm_4564/01_2021/6qjm_4564.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjm_4564/01_2021/6qjm_4564.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjm_4564/01_2021/6qjm_4564.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjm_4564/01_2021/6qjm_4564.pdb" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.014 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 846 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain breaks: 1 Chain: "B" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain breaks: 1 Chain: "C" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain breaks: 1 Time building chain proxies: 0.80, per 1000 atoms: 0.95 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Number of scatterers: 846 At special positions: 0 Unit cell: (59.34, 57.96, 38.64, 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 3 16.00 O 159 8.00 N 147 7.00 C 537 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 - 3.50 Amimo 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: 0.29 Conformation dependent library (CDL) restraints added in 133.2 milliseconds 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 210 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 45.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 275 through 280 removed outlier: 6.853A pdb=" N VAL A 275 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE B 278 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 277 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LYS B 280 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASN A 279 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLN A 276 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ASN C 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE A 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 283 through 288 removed outlier: 6.903A pdb=" N LEU A 284 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER B 285 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ASP A 283 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N ASN C 286 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N SER A 285 " --> pdb=" O ASN C 286 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLN C 288 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL A 287 " --> pdb=" O GLN C 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.095A pdb=" N VAL A 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL C 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 313 through 314 removed outlier: 7.116A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 318 through 320 removed outlier: 5.893A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) 10 hydrogen bonds defined for protein. 30 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: 0.20 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 219 1.33 - 1.45: 101 1.45 - 1.57: 523 1.57 - 1.69: 0 1.69 - 1.81: 3 Bond restraints: 846 Sorted by residual: bond pdb=" CA SER C 285 " pdb=" CB SER C 285 " ideal model delta sigma weight residual 1.530 1.511 0.019 1.24e-02 6.50e+03 2.36e+00 bond pdb=" CA SER B 285 " pdb=" CB SER B 285 " ideal model delta sigma weight residual 1.530 1.511 0.019 1.24e-02 6.50e+03 2.23e+00 bond pdb=" CA SER A 285 " pdb=" CB SER A 285 " ideal model delta sigma weight residual 1.530 1.512 0.018 1.24e-02 6.50e+03 2.17e+00 bond pdb=" CG ASN B 279 " pdb=" ND2 ASN B 279 " ideal model delta sigma weight residual 1.328 1.303 0.025 2.10e-02 2.27e+03 1.46e+00 bond pdb=" CA SER C 316 " pdb=" CB SER C 316 " ideal model delta sigma weight residual 1.534 1.513 0.021 1.72e-02 3.38e+03 1.46e+00 ... (remaining 841 not shown) Histogram of bond angle deviations from ideal: 103.43 - 108.53: 54 108.53 - 113.62: 489 113.62 - 118.71: 186 118.71 - 123.80: 384 123.80 - 128.89: 12 Bond angle restraints: 1125 Sorted by residual: angle pdb=" C TYR A 310 " pdb=" N LYS A 311 " pdb=" CA LYS A 311 " ideal model delta sigma weight residual 121.80 126.66 -4.86 2.44e+00 1.68e-01 3.98e+00 angle pdb=" C TYR B 310 " pdb=" N LYS B 311 " pdb=" CA LYS B 311 " ideal model delta sigma weight residual 121.80 126.65 -4.85 2.44e+00 1.68e-01 3.95e+00 angle pdb=" C TYR C 310 " pdb=" N LYS C 311 " pdb=" CA LYS C 311 " ideal model delta sigma weight residual 121.80 126.64 -4.84 2.44e+00 1.68e-01 3.94e+00 angle pdb=" C LYS C 281 " pdb=" N LEU C 282 " pdb=" CA LEU C 282 " ideal model delta sigma weight residual 122.07 118.85 3.22 1.71e+00 3.42e-01 3.54e+00 angle pdb=" C LYS B 281 " pdb=" N LEU B 282 " pdb=" CA LEU B 282 " ideal model delta sigma weight residual 122.07 118.86 3.21 1.71e+00 3.42e-01 3.52e+00 ... (remaining 1120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.03: 382 5.03 - 10.07: 107 10.07 - 15.10: 33 15.10 - 20.13: 9 20.13 - 25.16: 12 Dihedral angle restraints: 543 sinusoidal: 225 harmonic: 318 Sorted by residual: dihedral pdb=" CA SER B 316 " pdb=" C SER B 316 " pdb=" N LYS B 317 " pdb=" CA LYS B 317 " ideal model delta harmonic sigma weight residual 180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA SER A 316 " pdb=" C SER A 316 " pdb=" N LYS A 317 " pdb=" CA LYS A 317 " ideal model delta harmonic sigma weight residual 180.00 -162.78 -17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA SER C 316 " pdb=" C SER C 316 " pdb=" N LYS C 317 " pdb=" CA LYS C 317 " ideal model delta harmonic sigma weight residual 180.00 -162.79 -17.21 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 540 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.038: 40 0.038 - 0.072: 51 0.072 - 0.105: 29 0.105 - 0.139: 21 0.139 - 0.172: 3 Chirality restraints: 144 Sorted by residual: chirality pdb=" CG LEU A 284 " pdb=" CB LEU A 284 " pdb=" CD1 LEU A 284 " pdb=" CD2 LEU A 284 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CG LEU C 284 " pdb=" CB LEU C 284 " pdb=" CD1 LEU C 284 " pdb=" CD2 LEU C 284 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CG LEU B 284 " pdb=" CB LEU B 284 " pdb=" CD1 LEU B 284 " pdb=" CD2 LEU B 284 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.24e-01 ... (remaining 141 not shown) Planarity restraints: 132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 279 " 0.008 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" CG ASN A 279 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 279 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 279 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 279 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.25e+00 pdb=" CG ASN C 279 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 279 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 279 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 279 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" CG ASN B 279 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 279 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 279 " 0.009 2.00e-02 2.50e+03 ... (remaining 129 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 310 2.91 - 3.40: 693 3.40 - 3.90: 1259 3.90 - 4.40: 1147 4.40 - 4.90: 2511 Nonbonded interactions: 5920 Sorted by model distance: nonbonded pdb=" OG SER A 285 " pdb=" O SER B 285 " model vdw 2.408 2.440 nonbonded pdb=" O SER A 285 " pdb=" OG SER C 285 " model vdw 2.408 2.440 nonbonded pdb=" O LYS A 321 " pdb=" O SER C 320 " model vdw 2.516 3.040 nonbonded pdb=" OG SER A 285 " pdb=" N ASN A 286 " model vdw 2.521 2.520 nonbonded pdb=" OG SER B 285 " pdb=" N ASN B 286 " model vdw 2.521 2.520 ... (remaining 5915 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 846 846 False True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 3 5.16 5 C 537 2.51 5 N 147 2.21 5 O 159 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.680 Set model interpretation parameters: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.540 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.010 Process input model: 8.750 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 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:2.570 Internal consistency checks: 0.000 Total: 15.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.010 0.031 846 Angle : 1.006 5.731 1125 Chirality : 0.073 0.172 144 Planarity : 0.006 0.024 132 Dihedral : 8.063 25.161 333 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.36 (0.83), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.63), residues: 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.127 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1824 time to fit residues: 5.1271 Evaluate side-chains 11 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.117 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.0870 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6703 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 288 GLN B 276 GLN B 279 ASN C 276 GLN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.011 846 Angle : 0.504 3.590 1125 Chirality : 0.053 0.126 144 Planarity : 0.003 0.016 132 Dihedral : 5.228 12.223 108 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.39 (0.80), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.61), residues: 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.120 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1379 time to fit residues: 3.2249 Evaluate side-chains 14 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.111 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.0050 chunk 7 optimal weight: 0.0670 chunk 8 optimal weight: 4.9990 overall best weight: 0.4420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.011 846 Angle : 0.456 3.539 1125 Chirality : 0.052 0.123 144 Planarity : 0.002 0.011 132 Dihedral : 4.598 10.809 108 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.18 (0.81), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.62), residues: 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.123 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1069 time to fit residues: 2.1256 Evaluate side-chains 14 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.123 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 1.2235 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.017 846 Angle : 0.546 3.741 1125 Chirality : 0.055 0.143 144 Planarity : 0.002 0.011 132 Dihedral : 4.911 12.122 108 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.40 (0.76), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.58), residues: 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.125 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1044 time to fit residues: 2.1826 Evaluate side-chains 15 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 overall best weight: 0.7733 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.018 846 Angle : 0.510 3.572 1125 Chirality : 0.054 0.129 144 Planarity : 0.002 0.015 132 Dihedral : 4.623 11.235 108 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.26 (0.77), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.59), residues: 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.125 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0782 time to fit residues: 1.5392 Evaluate side-chains 12 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.138 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 overall best weight: 0.8730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.011 846 Angle : 0.502 3.517 1125 Chirality : 0.054 0.132 144 Planarity : 0.002 0.009 132 Dihedral : 4.551 11.173 108 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.29 (0.76), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.58), residues: 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.125 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0821 time to fit residues: 1.5936 Evaluate side-chains 13 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.126 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.0070 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.9258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.013 846 Angle : 0.491 3.512 1125 Chirality : 0.053 0.132 144 Planarity : 0.002 0.007 132 Dihedral : 4.580 12.517 108 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.21 (0.77), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.59), residues: 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.130 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0765 time to fit residues: 1.4804 Evaluate side-chains 12 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.119 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.010 846 Angle : 0.459 3.423 1125 Chirality : 0.053 0.128 144 Planarity : 0.002 0.007 132 Dihedral : 4.386 10.892 108 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.18 (0.78), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.60), residues: 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.131 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0804 time to fit residues: 1.5670 Evaluate side-chains 12 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.121 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.0020 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.010 846 Angle : 0.476 3.435 1125 Chirality : 0.053 0.127 144 Planarity : 0.002 0.007 132 Dihedral : 4.284 10.900 108 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.15 (0.79), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.60), residues: 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.117 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0479 time to fit residues: 0.9583 Evaluate side-chains 12 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.108 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.010 846 Angle : 0.466 3.426 1125 Chirality : 0.053 0.128 144 Planarity : 0.002 0.008 132 Dihedral : 4.236 10.865 108 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.13 (0.79), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.60), residues: 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 198 Ramachandran restraints generated. 99 Oldfield and 0 Emsley and 99 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.126 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0535 time to fit residues: 0.9801 Evaluate side-chains 10 residues out of total 105 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.119 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.0870 overall best weight: 0.5453 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5941 r_free = 0.5941 target = 0.280431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5771 r_free = 0.5771 target = 0.253764 restraints weight = 1071.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5798 r_free = 0.5798 target = 0.258740 restraints weight = 636.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5818 r_free = 0.5818 target = 0.261943 restraints weight = 447.155| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.002 0.010 846 ANGLE : 0.448 3.372 1125 CHIRALITY : 0.053 0.126 144 PLANARITY : 0.002 0.008 132 DIHEDRAL : 4.117 10.445 108 MIN NONBONDED DISTANCE : 2.142 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 5.05 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 3.03 % FAVORED : 96.97 % ROTAMER OUTLIERS : 0.00 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (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: -2.10 (0.80), RESIDUES: 99 HELIX: NONE (NONE), RESIDUES: 0 SHEET: NONE (NONE), RESIDUES: 0 LOOP : -1.59 (0.61), RESIDUES: 99 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.010 846 Angle : 0.448 3.372 1125 Chirality : 0.053 0.126 144 Planarity : 0.002 0.008 132 Dihedral : 4.117 10.445 108 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.10 (0.80), residues: 99 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.61), residues: 99 =============================================================================== Job complete usr+sys time: 720.29 seconds wall clock time: 13 minutes 32.34 seconds (812.34 seconds total)