Starting phenix.real_space_refine (version: dev) on Mon Apr 4 11:58:13 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkk_14045/04_2022/7qkk_14045.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkk_14045/04_2022/7qkk_14045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkk_14045/04_2022/7qkk_14045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkk_14045/04_2022/7qkk_14045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkk_14045/04_2022/7qkk_14045.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkk_14045/04_2022/7qkk_14045.pdb" } resolution = 2.8 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= 0.000 sd= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 3537 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 1.99, per 1000 atoms: 0.56 Number of scatterers: 3537 At special positions: 0 Unit cell: (85.696, 72.512, 37.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 O 324 8.00 N 321 7.00 C 1086 6.00 H 1803 1.00 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 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: 2.56 Conformation dependent library (CDL) restraints added in 273.8 milliseconds 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 396 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 36.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.569A pdb=" N VAL B 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL C 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE B 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN B 307 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N TYR A 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL B 309 " --> pdb=" O TYR A 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.963A pdb=" N VAL B 313 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.238A pdb=" N VAL B 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LYS C 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N SER B 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS B 317 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N SER A 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR B 319 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N CYS A 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS B 321 " --> pdb=" O CYS A 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 327 through 330 removed outlier: 6.706A pdb=" N ILE B 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN B 327 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HIS A 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS B 329 " --> pdb=" O HIS A 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.598A pdb=" N GLN B 336 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL A 339 " --> pdb=" O GLN B 336 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU B 338 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.472A pdb=" N LYS B 343 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N PHE A 346 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP B 345 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 351 through 353 removed outlier: 6.635A pdb=" N SER B 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 356 through 361 removed outlier: 6.758A pdb=" N SER B 356 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ASN A 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 358 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N THR A 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B 360 " --> pdb=" O THR A 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 374 through 375 16 hydrogen bonds defined for protein. 48 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: 1.17 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 1800 1.12 - 1.29: 289 1.29 - 1.46: 513 1.46 - 1.64: 959 1.64 - 1.81: 3 Bond restraints: 3564 Sorted by residual: bond pdb=" ND2 ASN B 368 " pdb="HD21 ASN B 368 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" ND2 ASN A 368 " pdb="HD21 ASN A 368 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LYS A 375 " pdb=" H LYS A 375 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" ND2 ASN B 368 " pdb="HD22 ASN B 368 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LYS A 369 " pdb=" H LYS A 369 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 3559 not shown) Histogram of bond angle deviations from ideal: 96.91 - 103.27: 26 103.27 - 109.62: 2854 109.62 - 115.98: 1733 115.98 - 122.33: 1511 122.33 - 128.69: 368 Bond angle restraints: 6492 Sorted by residual: angle pdb=" CA HIS C 374 " pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 113.80 123.66 -9.86 1.00e+00 1.00e+00 9.73e+01 angle pdb=" CA HIS A 374 " pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 113.80 122.99 -9.19 1.00e+00 1.00e+00 8.45e+01 angle pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 131.20 120.20 11.00 1.30e+00 5.92e-01 7.16e+01 angle pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " pdb=" CD2 HIS C 374 " ideal model delta sigma weight residual 131.20 121.33 9.87 1.30e+00 5.92e-01 5.76e+01 angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 119.26 -6.66 1.00e+00 1.00e+00 4.44e+01 ... (remaining 6487 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 14.05: 1172 14.05 - 28.10: 117 28.10 - 42.15: 37 42.15 - 56.20: 15 56.20 - 70.25: 30 Dihedral angle restraints: 1371 sinusoidal: 669 harmonic: 702 Sorted by residual: dihedral pdb=" CA LYS B 375 " pdb=" C LYS B 375 " pdb=" N LEU B 376 " pdb=" CA LEU B 376 " ideal model delta harmonic sigma weight residual 180.00 149.29 30.71 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" C VAL A 363 " pdb=" N VAL A 363 " pdb=" CA VAL A 363 " pdb=" CB VAL A 363 " ideal model delta harmonic sigma weight residual -122.00 -136.61 14.61 0 2.50e+00 1.60e-01 3.42e+01 dihedral pdb=" CA LYS C 375 " pdb=" C LYS C 375 " pdb=" N LEU C 376 " pdb=" CA LEU C 376 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 1368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 155 0.091 - 0.182: 80 0.182 - 0.274: 20 0.274 - 0.365: 7 0.365 - 0.456: 2 Chirality restraints: 264 Sorted by residual: chirality pdb=" CA PRO B 364 " pdb=" N PRO B 364 " pdb=" C PRO B 364 " pdb=" CB PRO B 364 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.46 2.00e-01 2.50e+01 5.20e+00 chirality pdb=" CA VAL B 363 " pdb=" N VAL B 363 " pdb=" C VAL B 363 " pdb=" CB VAL B 363 " both_signs ideal model delta sigma weight residual False 2.44 2.08 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CA VAL A 363 " pdb=" N VAL A 363 " pdb=" C VAL A 363 " pdb=" CB VAL A 363 " both_signs ideal model delta sigma weight residual False 2.44 2.08 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 261 not shown) Planarity restraints: 516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 374 " -0.321 2.00e-02 2.50e+03 1.68e-01 6.35e+02 pdb=" CG HIS A 374 " 0.219 2.00e-02 2.50e+03 pdb=" ND1 HIS A 374 " 0.162 2.00e-02 2.50e+03 pdb=" CD2 HIS A 374 " 0.167 2.00e-02 2.50e+03 pdb=" CE1 HIS A 374 " 0.022 2.00e-02 2.50e+03 pdb=" NE2 HIS A 374 " 0.056 2.00e-02 2.50e+03 pdb=" HD2 HIS A 374 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 HIS A 374 " -0.147 2.00e-02 2.50e+03 pdb=" HE2 HIS A 374 " -0.153 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 374 " -0.249 2.00e-02 2.50e+03 1.30e-01 3.83e+02 pdb=" CG HIS C 374 " 0.181 2.00e-02 2.50e+03 pdb=" ND1 HIS C 374 " 0.124 2.00e-02 2.50e+03 pdb=" CD2 HIS C 374 " 0.129 2.00e-02 2.50e+03 pdb=" CE1 HIS C 374 " 0.008 2.00e-02 2.50e+03 pdb=" NE2 HIS C 374 " 0.039 2.00e-02 2.50e+03 pdb=" HD2 HIS C 374 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 HIS C 374 " -0.113 2.00e-02 2.50e+03 pdb=" HE2 HIS C 374 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 374 " 0.151 2.00e-02 2.50e+03 8.51e-02 1.63e+02 pdb=" CG HIS B 374 " -0.120 2.00e-02 2.50e+03 pdb=" ND1 HIS B 374 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 HIS B 374 " -0.078 2.00e-02 2.50e+03 pdb=" CE1 HIS B 374 " -0.026 2.00e-02 2.50e+03 pdb=" NE2 HIS B 374 " -0.040 2.00e-02 2.50e+03 pdb=" HD2 HIS B 374 " 0.027 2.00e-02 2.50e+03 pdb=" HE1 HIS B 374 " 0.094 2.00e-02 2.50e+03 pdb=" HE2 HIS B 374 " 0.066 2.00e-02 2.50e+03 ... (remaining 513 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 185 2.14 - 2.76: 5632 2.76 - 3.37: 9537 3.37 - 3.99: 12229 3.99 - 4.60: 17889 Nonbonded interactions: 45472 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.525 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.571 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.642 1.850 nonbonded pdb=" OD2 ASP B 314 " pdb=" HZ1 LYS B 370 " model vdw 1.674 1.850 nonbonded pdb=" OD2 ASP A 314 " pdb=" HZ2 LYS A 370 " model vdw 1.693 1.850 ... (remaining 45467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 3 5.16 5 C 1086 2.51 5 N 321 2.21 5 O 324 1.98 5 H 1803 0.53 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 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: 2.380 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: 0.060 Extract box with map and model: 11.290 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 16.350 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.012 0.086 1761 Z= 0.799 Angle : 2.170 11.001 2355 Z= 1.448 Chirality : 0.118 0.456 264 Planarity : 0.017 0.155 300 Dihedral : 13.175 70.250 675 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 2.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -3.44 (0.40), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.30), residues: 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 1.8491 time to fit residues: 133.9113 Evaluate side-chains 32 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.301 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 1761 Z= 0.220 Angle : 0.810 7.979 2355 Z= 0.425 Chirality : 0.052 0.130 264 Planarity : 0.004 0.035 300 Dihedral : 8.043 29.316 234 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer Outliers : 5.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.41), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.31), residues: 222 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 47 average time/residue: 1.4859 time to fit residues: 71.7750 Evaluate side-chains 32 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.319 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1935 time to fit residues: 0.6153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.6769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 1761 Z= 0.183 Angle : 0.685 5.649 2355 Z= 0.361 Chirality : 0.050 0.128 264 Planarity : 0.004 0.044 300 Dihedral : 6.789 22.954 234 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer Outliers : 4.55 % 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: -3.14 (0.41), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.31), residues: 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 38 average time/residue: 1.5179 time to fit residues: 59.2818 Evaluate side-chains 29 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.287 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1800 time to fit residues: 0.5690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.7114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 1761 Z= 0.164 Angle : 0.626 4.282 2355 Z= 0.328 Chirality : 0.049 0.127 264 Planarity : 0.004 0.039 300 Dihedral : 6.038 21.650 234 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer Outliers : 3.03 % 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: -3.09 (0.42), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.32), residues: 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 29 average time/residue: 1.9612 time to fit residues: 58.2632 Evaluate side-chains 27 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.302 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.2114 time to fit residues: 0.6300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.7319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 1761 Z= 0.171 Angle : 0.616 5.983 2355 Z= 0.318 Chirality : 0.049 0.122 264 Planarity : 0.004 0.039 300 Dihedral : 5.750 20.168 234 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer Outliers : 2.53 % 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: -3.20 (0.42), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.32), residues: 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 32 average time/residue: 1.7559 time to fit residues: 57.6350 Evaluate side-chains 26 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 22 time to evaluate : 0.297 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1986 time to fit residues: 0.6038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.0040 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.7461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 1761 Z= 0.153 Angle : 0.595 4.834 2355 Z= 0.303 Chirality : 0.048 0.127 264 Planarity : 0.003 0.031 300 Dihedral : 5.357 20.078 234 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 2.53 % 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: -3.11 (0.42), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.32), residues: 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 26 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 29 average time/residue: 1.8446 time to fit residues: 54.8511 Evaluate side-chains 24 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.308 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1174 time to fit residues: 0.5310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.0070 chunk 5 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.7653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.138 1761 Z= 0.344 Angle : 0.736 12.120 2355 Z= 0.390 Chirality : 0.048 0.122 264 Planarity : 0.004 0.034 300 Dihedral : 5.355 21.341 234 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer Outliers : 2.02 % 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: -3.14 (0.42), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.32), residues: 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 18 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 22 average time/residue: 2.0925 time to fit residues: 47.2897 Evaluate side-chains 20 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 17 time to evaluate : 0.257 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.3263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7833 moved from start: 0.7676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 1761 Z= 0.198 Angle : 0.612 4.913 2355 Z= 0.316 Chirality : 0.049 0.124 264 Planarity : 0.005 0.054 300 Dihedral : 5.417 20.193 234 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer Outliers : 2.02 % 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: -3.26 (0.43), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.33), residues: 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 23 average time/residue: 1.9841 time to fit residues: 46.8067 Evaluate side-chains 24 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.322 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.1601 time to fit residues: 0.7802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7820 moved from start: 0.7689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 1761 Z= 0.243 Angle : 0.602 6.732 2355 Z= 0.319 Chirality : 0.049 0.122 264 Planarity : 0.008 0.126 300 Dihedral : 5.343 20.175 234 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer Outliers : 1.01 % 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: -3.32 (0.43), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.33), residues: 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 2.0083 time to fit residues: 47.4147 Evaluate side-chains 21 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.312 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.3690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7793 moved from start: 0.7941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.020 0.809 1761 Z= 1.808 Angle : 1.323 42.679 2355 Z= 0.765 Chirality : 0.048 0.122 264 Planarity : 0.005 0.042 300 Dihedral : 5.213 19.718 234 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.43), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.33), residues: 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 2.1785 time to fit residues: 55.6333 Evaluate side-chains 22 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.247 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0997 time to fit residues: 0.4382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.130841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.116819 restraints weight = 7445.648| |-----------------------------------------------------------------------------| r_work (start): 0.4444 rms_B_bonded: 2.75 r_work: 0.4434 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4424 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work: 0.4414 rms_B_bonded: 2.58 restraints_weight: 0.1250 r_work: 0.4403 rms_B_bonded: 2.72 restraints_weight: 0.0625 r_work: 0.4392 rms_B_bonded: 2.91 restraints_weight: 0.0312 r_work: 0.4379 rms_B_bonded: 3.16 restraints_weight: 0.0156 r_work: 0.4365 rms_B_bonded: 3.47 restraints_weight: 0.0078 r_work: 0.4349 rms_B_bonded: 3.84 restraints_weight: 0.0039 r_work: 0.4332 rms_B_bonded: 4.28 restraints_weight: 0.0020 r_work: 0.4313 rms_B_bonded: 4.81 restraints_weight: 0.0010 r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.7950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.207 1761 Z= 0.575 Angle : 0.778 15.514 2355 Z= 0.424 Chirality : 0.048 0.125 264 Planarity : 0.004 0.051 300 Dihedral : 5.160 19.592 234 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer Outliers : 2.02 % 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: -3.24 (0.44), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.33), residues: 222 =============================================================================== Job complete usr+sys time: 2757.53 seconds wall clock time: 48 minutes 58.32 seconds (2938.32 seconds total)