Starting phenix.real_space_refine (version: dev) on Thu May 12 16:02:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nrx_12552/05_2022/7nrx_12552.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nrx_12552/05_2022/7nrx_12552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nrx_12552/05_2022/7nrx_12552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nrx_12552/05_2022/7nrx_12552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nrx_12552/05_2022/7nrx_12552.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nrx_12552/05_2022/7nrx_12552.pdb" } resolution = 3.55 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= 0.006 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 None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 5870 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "I" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "F" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "G" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "H" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Time building chain proxies: 3.50, per 1000 atoms: 0.60 Number of scatterers: 5870 At special positions: 0 Unit cell: (132.25, 92, 44.85, 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 10 16.00 O 1110 8.00 N 1080 7.00 C 3670 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 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: 2.06 Conformation dependent library (CDL) restraints added in 840.1 milliseconds 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.516A pdb=" N GLN A 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N TYR F 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL A 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLN F 307 " --> pdb=" O ILE H 308 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N TYR H 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL F 309 " --> pdb=" O TYR H 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.668A pdb=" N VAL A 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL F 313 " --> pdb=" O ASP H 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 322 removed outlier: 6.472A pdb=" N LYS A 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N SER F 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR A 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N CYS F 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LYS A 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS F 317 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N SER H 320 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR F 319 " --> pdb=" O SER H 320 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N CYS H 322 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS F 321 " --> pdb=" O CYS H 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 337 through 340 removed outlier: 6.176A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL A 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LYS B 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 339 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 359 through 362 removed outlier: 6.472A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N HIS D 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASN A 359 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N HIS B 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 371 through 373 removed outlier: 6.223A pdb=" N ILE A 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE F 371 " --> pdb=" O GLU H 372 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 376 through 378 removed outlier: 6.539A pdb=" N LEU B 376 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 376 " --> pdb=" O THR B 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 306 through 310 removed outlier: 6.219A pdb=" N VAL C 306 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL E 309 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE C 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL I 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL C 309 " --> pdb=" O VAL I 306 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE I 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.646A pdb=" N VAL I 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL G 313 " --> pdb=" O ASP J 314 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 317 through 322 removed outlier: 6.496A pdb=" N LYS I 317 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N SER G 320 " --> pdb=" O LYS I 317 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR I 319 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N CYS G 322 " --> pdb=" O THR I 319 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LYS I 321 " --> pdb=" O CYS G 322 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS G 317 " --> pdb=" O VAL J 318 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N SER J 320 " --> pdb=" O LYS G 317 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR G 319 " --> pdb=" O SER J 320 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N CYS J 322 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS G 321 " --> pdb=" O CYS J 322 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 328 through 330 removed outlier: 6.275A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE I 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 336 through 339 removed outlier: 6.553A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL I 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 353 through 354 removed outlier: 6.763A pdb=" N LYS I 353 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS G 353 " --> pdb=" O ILE J 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 359 through 362 removed outlier: 6.760A pdb=" N ILE I 360 " --> pdb=" O THR G 361 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE G 360 " --> pdb=" O THR J 361 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 369 through 371 removed outlier: 6.289A pdb=" N LYS C 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS I 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) 84 hydrogen bonds defined for protein. 249 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: 1.37 Time building geometry restraints manager: 2.27 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: 1836 1.33 - 1.45: 820 1.45 - 1.57: 3294 1.57 - 1.69: 0 1.69 - 1.81: 10 Bond restraints: 5960 Sorted by residual: bond pdb=" CG1 ILE J 354 " pdb=" CD1 ILE J 354 " ideal model delta sigma weight residual 1.513 1.377 0.136 3.90e-02 6.57e+02 1.22e+01 bond pdb=" CG1 ILE G 354 " pdb=" CD1 ILE G 354 " ideal model delta sigma weight residual 1.513 1.377 0.136 3.90e-02 6.57e+02 1.21e+01 bond pdb=" CG1 ILE C 354 " pdb=" CD1 ILE C 354 " ideal model delta sigma weight residual 1.513 1.378 0.135 3.90e-02 6.57e+02 1.20e+01 bond pdb=" CG1 ILE I 354 " pdb=" CD1 ILE I 354 " ideal model delta sigma weight residual 1.513 1.378 0.135 3.90e-02 6.57e+02 1.20e+01 bond pdb=" CG1 ILE E 354 " pdb=" CD1 ILE E 354 " ideal model delta sigma weight residual 1.513 1.378 0.135 3.90e-02 6.57e+02 1.20e+01 ... (remaining 5955 not shown) Histogram of bond angle deviations from ideal: 102.21 - 108.08: 471 108.08 - 113.95: 3185 113.95 - 119.81: 1644 119.81 - 125.68: 2610 125.68 - 131.54: 60 Bond angle restraints: 7970 Sorted by residual: angle pdb=" CA LYS B 311 " pdb=" CB LYS B 311 " pdb=" CG LYS B 311 " ideal model delta sigma weight residual 114.10 123.62 -9.52 2.00e+00 2.50e-01 2.26e+01 angle pdb=" CA LYS H 311 " pdb=" CB LYS H 311 " pdb=" CG LYS H 311 " ideal model delta sigma weight residual 114.10 123.61 -9.51 2.00e+00 2.50e-01 2.26e+01 angle pdb=" CA LYS D 311 " pdb=" CB LYS D 311 " pdb=" CG LYS D 311 " ideal model delta sigma weight residual 114.10 123.58 -9.48 2.00e+00 2.50e-01 2.25e+01 angle pdb=" CA LYS F 311 " pdb=" CB LYS F 311 " pdb=" CG LYS F 311 " ideal model delta sigma weight residual 114.10 123.57 -9.47 2.00e+00 2.50e-01 2.24e+01 angle pdb=" CA LYS A 311 " pdb=" CB LYS A 311 " pdb=" CG LYS A 311 " ideal model delta sigma weight residual 114.10 123.51 -9.41 2.00e+00 2.50e-01 2.21e+01 ... (remaining 7965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.37: 3186 14.37 - 28.74: 329 28.74 - 43.12: 100 43.12 - 57.49: 10 57.49 - 71.86: 5 Dihedral angle restraints: 3630 sinusoidal: 1520 harmonic: 2110 Sorted by residual: dihedral pdb=" CA LYS F 347 " pdb=" C LYS F 347 " pdb=" N ASP F 348 " pdb=" CA ASP F 348 " ideal model delta harmonic sigma weight residual 180.00 -153.66 -26.34 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA LYS D 347 " pdb=" C LYS D 347 " pdb=" N ASP D 348 " pdb=" CA ASP D 348 " ideal model delta harmonic sigma weight residual 180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA LYS H 347 " pdb=" C LYS H 347 " pdb=" N ASP H 348 " pdb=" CA ASP H 348 " ideal model delta harmonic sigma weight residual -180.00 -153.70 -26.30 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 3627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 845 0.144 - 0.289: 35 0.289 - 0.433: 5 0.433 - 0.577: 0 0.577 - 0.722: 5 Chirality restraints: 890 Sorted by residual: chirality pdb=" CB VAL H 306 " pdb=" CA VAL H 306 " pdb=" CG1 VAL H 306 " pdb=" CG2 VAL H 306 " both_signs ideal model delta sigma weight residual False -2.63 -1.91 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CB VAL A 306 " pdb=" CA VAL A 306 " pdb=" CG1 VAL A 306 " pdb=" CG2 VAL A 306 " both_signs ideal model delta sigma weight residual False -2.63 -1.91 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CB VAL B 306 " pdb=" CA VAL B 306 " pdb=" CG1 VAL B 306 " pdb=" CG2 VAL B 306 " both_signs ideal model delta sigma weight residual False -2.63 -1.91 -0.72 2.00e-01 2.50e+01 1.29e+01 ... (remaining 887 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 363 " 0.064 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO D 364 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO D 364 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 364 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 363 " 0.064 5.00e-02 4.00e+02 9.63e-02 1.48e+01 pdb=" N PRO B 364 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO B 364 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 364 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 363 " 0.064 5.00e-02 4.00e+02 9.62e-02 1.48e+01 pdb=" N PRO H 364 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO H 364 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO H 364 " 0.052 5.00e-02 4.00e+02 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1897 2.87 - 3.37: 4466 3.37 - 3.88: 9908 3.88 - 4.39: 10017 4.39 - 4.90: 21866 Nonbonded interactions: 48154 Sorted by model distance: nonbonded pdb=" OE2 GLU G 372 " pdb=" OD2 ASP J 314 " model vdw 2.356 3.040 nonbonded pdb=" OE2 GLU I 372 " pdb=" OD2 ASP G 314 " model vdw 2.372 3.040 nonbonded pdb=" OD2 ASP C 314 " pdb=" OE2 GLU E 372 " model vdw 2.376 3.040 nonbonded pdb=" OD2 ASP I 314 " pdb=" OE2 GLU C 372 " model vdw 2.377 3.040 nonbonded pdb=" NZ LYS A 353 " pdb=" OD2 ASP A 358 " model vdw 2.418 2.520 ... (remaining 48149 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' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 3670 2.51 5 N 1080 2.21 5 O 1110 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 Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.840 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.050 Process input model: 18.550 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 : 0.010 0.136 5960 Z= 0.671 Angle : 1.201 9.516 7970 Z= 0.703 Chirality : 0.092 0.722 890 Planarity : 0.011 0.097 1020 Dihedral : 12.756 71.859 2290 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % 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: -3.60 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.18), residues: 750 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 0.745 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.2413 time to fit residues: 73.7432 Evaluate side-chains 183 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 0.665 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 5960 Z= 0.344 Angle : 0.651 4.669 7970 Z= 0.338 Chirality : 0.050 0.139 890 Planarity : 0.006 0.059 1020 Dihedral : 5.589 21.252 790 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer Outliers : 1.94 % 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: -3.55 (0.25), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.19), residues: 750 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 201 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 209 average time/residue: 0.2134 time to fit residues: 55.4068 Evaluate side-chains 179 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 0.739 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0526 time to fit residues: 2.1812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 52 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 63 optimal weight: 0.0270 chunk 68 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 62 optimal weight: 0.4980 overall best weight: 3.3044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 5960 Z= 0.284 Angle : 0.611 5.887 7970 Z= 0.310 Chirality : 0.050 0.128 890 Planarity : 0.005 0.049 1020 Dihedral : 5.228 22.027 790 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer Outliers : 1.34 % 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: -3.47 (0.25), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.19), residues: 750 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 168 time to evaluate : 0.746 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 174 average time/residue: 0.1625 time to fit residues: 37.1021 Evaluate side-chains 169 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 162 time to evaluate : 0.746 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0565 time to fit residues: 1.7633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 63 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 overall best weight: 4.4986 ------------------------------------------------------------------------------- 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: 0.8313 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 5960 Z= 0.366 Angle : 0.641 5.496 7970 Z= 0.330 Chirality : 0.050 0.137 890 Planarity : 0.005 0.049 1020 Dihedral : 5.213 21.068 790 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.25), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.19), residues: 750 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 166 time to evaluate : 0.742 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 173 average time/residue: 0.1657 time to fit residues: 37.7890 Evaluate side-chains 169 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 159 time to evaluate : 0.746 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0541 time to fit residues: 2.0180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN D 329 HIS ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.051 5960 Z= 0.546 Angle : 0.735 6.111 7970 Z= 0.381 Chirality : 0.053 0.171 890 Planarity : 0.005 0.048 1020 Dihedral : 5.646 23.507 790 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.25), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.19), residues: 750 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 162 time to evaluate : 0.744 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 168 average time/residue: 0.1648 time to fit residues: 36.7267 Evaluate side-chains 163 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0551 time to fit residues: 1.7369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 5960 Z= 0.185 Angle : 0.580 6.186 7970 Z= 0.293 Chirality : 0.050 0.146 890 Planarity : 0.004 0.045 1020 Dihedral : 4.933 20.781 790 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer Outliers : 0.75 % 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: -3.43 (0.25), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.19), residues: 750 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 174 time to evaluate : 0.730 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 177 average time/residue: 0.1526 time to fit residues: 37.1242 Evaluate side-chains 166 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 161 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0728 time to fit residues: 2.0981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 67 optimal weight: 0.0770 chunk 42 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 overall best weight: 5.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.043 5960 Z= 0.439 Angle : 0.677 7.146 7970 Z= 0.349 Chirality : 0.052 0.153 890 Planarity : 0.004 0.046 1020 Dihedral : 5.243 21.398 790 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer Outliers : 1.49 % 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: -3.43 (0.25), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.19), residues: 750 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 time to evaluate : 0.677 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 160 average time/residue: 0.1644 time to fit residues: 34.8409 Evaluate side-chains 156 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0544 time to fit residues: 1.6230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 58 optimal weight: 0.2980 chunk 62 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 5960 Z= 0.175 Angle : 0.583 7.380 7970 Z= 0.296 Chirality : 0.050 0.167 890 Planarity : 0.004 0.044 1020 Dihedral : 4.895 20.442 790 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 0.15 % 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: -3.35 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.20), residues: 750 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 0.774 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 165 average time/residue: 0.1648 time to fit residues: 35.8714 Evaluate side-chains 166 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 0.725 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0555 time to fit residues: 1.1175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 5960 Z= 0.248 Angle : 0.608 7.467 7970 Z= 0.307 Chirality : 0.050 0.164 890 Planarity : 0.004 0.044 1020 Dihedral : 4.832 18.813 790 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer Outliers : 0.60 % 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: -3.29 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.20), residues: 750 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 157 time to evaluate : 0.786 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 158 average time/residue: 0.1788 time to fit residues: 37.0804 Evaluate side-chains 160 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 0.616 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0469 time to fit residues: 1.2483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 5960 Z= 0.218 Angle : 0.612 7.577 7970 Z= 0.307 Chirality : 0.050 0.169 890 Planarity : 0.004 0.043 1020 Dihedral : 4.792 18.179 790 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 0.15 % 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: -3.25 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.20), residues: 750 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 0.742 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 161 average time/residue: 0.1703 time to fit residues: 35.8845 Evaluate side-chains 162 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0570 time to fit residues: 1.1153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 40.0000 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 63 optimal weight: 0.1980 chunk 37 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.121721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.100135 restraints weight = 9141.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.102883 restraints weight = 3779.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.104574 restraints weight = 2146.998| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5960 Z= 0.232 Angle : 0.616 7.974 7970 Z= 0.307 Chirality : 0.050 0.168 890 Planarity : 0.004 0.043 1020 Dihedral : 4.738 18.229 790 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 0.15 % 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: -3.21 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.20), residues: 750 =============================================================================== Job complete usr+sys time: 1408.28 seconds wall clock time: 26 minutes 29.57 seconds (1589.57 seconds total)