Starting phenix.real_space_refine on Tue May 7 03:32:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q99_18272/05_2024/8q99_18272.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q99_18272/05_2024/8q99_18272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q99_18272/05_2024/8q99_18272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q99_18272/05_2024/8q99_18272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q99_18272/05_2024/8q99_18272.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q99_18272/05_2024/8q99_18272.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2046 2.51 5 N 588 2.21 5 O 606 1.98 5 H 3396 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 6642 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "D" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "C" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "B" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "E" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "F" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Time building chain proxies: 5.76, per 1000 atoms: 0.87 Number of scatterers: 6642 At special positions: 0 Unit cell: (114.536, 96.408, 37.904, 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 6 16.00 O 606 8.00 N 588 7.00 C 2046 6.00 H 3396 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: 4.58 Conformation dependent library (CDL) restraints added in 1.1 seconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 309 through 310 removed outlier: 6.695A pdb=" N VAL A 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.710A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.288A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.500A pdb=" N ILE A 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.538A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.531A pdb=" N ASP A 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.560A pdb=" N GLN A 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ILE D 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS A 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 357 through 361 removed outlier: 6.711A pdb=" N LEU A 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE C 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 368 through 377 removed outlier: 6.562A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLU D 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N HIS D 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR A 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU D 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS A 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 309 through 310 removed outlier: 6.431A pdb=" N VAL B 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.633A pdb=" N VAL B 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 317 through 325 removed outlier: 6.319A pdb=" N VAL B 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS F 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N SER B 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLY F 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N CYS B 322 " --> pdb=" O GLY F 323 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU F 325 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N SER B 324 " --> pdb=" O LEU F 325 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 328 through 330 removed outlier: 6.654A pdb=" N ILE B 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 337 through 342 Processing sheet with id=AB6, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.614A pdb=" N ASP B 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 350 through 354 removed outlier: 6.513A pdb=" N GLN B 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ILE E 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LYS B 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 357 through 361 Processing sheet with id=AB9, first strand: chain 'E' and resid 368 through 377 removed outlier: 6.537A pdb=" N LYS B 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLU E 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE B 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N HIS E 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR B 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU E 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS B 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) 79 hydrogen bonds defined for protein. 237 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: 2.26 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 2.22: 6681 2.22 - 3.49: 3 3.49 - 4.76: 6 4.76 - 6.03: 3 6.03 - 7.29: 3 Warning: very large bond lengths. Bond restraints: 6696 Sorted by residual: bond pdb=" N LYS B 343 " pdb=" H BLYS B 343 " ideal model delta sigma weight residual 0.860 7.294 -6.434 2.00e-02 2.50e+03 1.04e+05 bond pdb=" N LYS F 343 " pdb=" H BLYS F 343 " ideal model delta sigma weight residual 0.860 7.174 -6.314 2.00e-02 2.50e+03 9.97e+04 bond pdb=" N LYS E 343 " pdb=" H BLYS E 343 " ideal model delta sigma weight residual 0.860 7.088 -6.228 2.00e-02 2.50e+03 9.70e+04 bond pdb=" N SER B 341 " pdb=" H BSER B 341 " ideal model delta sigma weight residual 0.860 5.496 -4.636 2.00e-02 2.50e+03 5.37e+04 bond pdb=" N SER F 341 " pdb=" H BSER F 341 " ideal model delta sigma weight residual 0.860 5.442 -4.582 2.00e-02 2.50e+03 5.25e+04 ... (remaining 6691 not shown) Histogram of bond angle deviations from ideal: 25.10 - 45.99: 10 45.99 - 66.88: 7 66.88 - 87.77: 7 87.77 - 108.66: 3024 108.66 - 129.55: 9174 Bond angle restraints: 12222 Sorted by residual: angle pdb=" C LYS A 340 " pdb=" N SER A 341 " pdb=" H BSER A 341 " ideal model delta sigma weight residual 123.65 25.10 98.55 3.00e+00 1.11e-01 1.08e+03 angle pdb=" C LYS D 340 " pdb=" N SER D 341 " pdb=" H BSER D 341 " ideal model delta sigma weight residual 123.65 25.59 98.06 3.00e+00 1.11e-01 1.07e+03 angle pdb=" C LYS C 340 " pdb=" N SER C 341 " pdb=" H BSER C 341 " ideal model delta sigma weight residual 123.65 30.04 93.61 3.00e+00 1.11e-01 9.74e+02 angle pdb=" C LYS E 340 " pdb=" N SER E 341 " pdb=" H BSER E 341 " ideal model delta sigma weight residual 123.65 32.01 91.64 3.00e+00 1.11e-01 9.33e+02 angle pdb=" C LYS B 340 " pdb=" N SER B 341 " pdb=" H BSER B 341 " ideal model delta sigma weight residual 123.65 35.85 87.80 3.00e+00 1.11e-01 8.57e+02 ... (remaining 12217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 2745 16.64 - 33.29: 192 33.29 - 49.93: 70 49.93 - 66.57: 71 66.57 - 83.21: 18 Dihedral angle restraints: 3096 sinusoidal: 1770 harmonic: 1326 Sorted by residual: dihedral pdb=" CA LYS E 347 " pdb=" C LYS E 347 " pdb=" N ASP E 348 " pdb=" CA ASP E 348 " ideal model delta harmonic sigma weight residual -180.00 -153.94 -26.06 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ASP A 358 " pdb=" C ASP A 358 " pdb=" N ASN A 359 " pdb=" CA ASN A 359 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ASP D 358 " pdb=" C ASP D 358 " pdb=" N ASN D 359 " pdb=" CA ASN D 359 " ideal model delta harmonic sigma weight residual 180.00 155.24 24.76 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 3093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 267 0.066 - 0.132: 165 0.132 - 0.198: 38 0.198 - 0.263: 17 0.263 - 0.329: 11 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA LEU B 325 " pdb=" N LEU B 325 " pdb=" C LEU B 325 " pdb=" CB LEU B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA GLN A 351 " pdb=" N GLN A 351 " pdb=" C GLN A 351 " pdb=" CB GLN A 351 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA LEU A 325 " pdb=" N LEU A 325 " pdb=" C LEU A 325 " pdb=" CB LEU A 325 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 495 not shown) Planarity restraints: 978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 338 " -0.240 2.00e-02 2.50e+03 2.69e-01 7.23e+02 pdb=" N VAL A 339 " 0.436 2.00e-02 2.50e+03 pdb=" CA VAL A 339 " -0.204 2.00e-02 2.50e+03 pdb=" H BVAL A 339 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 338 " -0.237 2.00e-02 2.50e+03 2.68e-01 7.16e+02 pdb=" N VAL C 339 " 0.434 2.00e-02 2.50e+03 pdb=" CA VAL C 339 " -0.203 2.00e-02 2.50e+03 pdb=" H BVAL C 339 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 338 " -0.222 2.00e-02 2.50e+03 2.65e-01 7.04e+02 pdb=" N VAL D 339 " 0.437 2.00e-02 2.50e+03 pdb=" CA VAL D 339 " -0.201 2.00e-02 2.50e+03 pdb=" H BVAL D 339 " -0.014 2.00e-02 2.50e+03 ... (remaining 975 not shown) Histogram of nonbonded interaction distances: 0.89 - 1.63: 17 1.63 - 2.38: 1491 2.38 - 3.12: 20164 3.12 - 3.86: 24635 3.86 - 4.60: 38145 Warning: very small nonbonded interaction distances. Nonbonded interactions: 84452 Sorted by model distance: nonbonded pdb=" H BSER B 341 " pdb=" C LYS E 340 " model vdw 0.892 2.750 nonbonded pdb=" C LYS B 340 " pdb=" H BSER F 341 " model vdw 1.115 2.750 nonbonded pdb=" H BSER B 341 " pdb=" CA LYS E 340 " model vdw 1.168 2.750 nonbonded pdb=" HB2 LYS A 340 " pdb=" H BSER A 341 " model vdw 1.431 2.270 nonbonded pdb=" H BLYS B 343 " pdb=" HB2 GLU E 342 " model vdw 1.443 2.270 ... (remaining 84447 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' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'B' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'C' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'D' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'E' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'F' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.810 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: 0.180 Extract box with map and model: 11.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 27.960 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 : 0.011 0.033 3300 Z= 0.734 Angle : 1.825 7.507 4416 Z= 1.206 Chirality : 0.096 0.329 498 Planarity : 0.010 0.067 558 Dihedral : 11.757 83.213 1260 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.33), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 374 PHE 0.037 0.011 PHE B 346 TYR 0.123 0.037 TYR F 310 ARG 0.004 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 349 ARG cc_start: 0.8031 (mtp180) cc_final: 0.6840 (pmt-80) REVERT: C 349 ARG cc_start: 0.8267 (mtp180) cc_final: 0.7038 (mmp-170) REVERT: F 311 LYS cc_start: 0.7624 (mttt) cc_final: 0.7217 (mmpt) REVERT: F 349 ARG cc_start: 0.8506 (mtp180) cc_final: 0.7319 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 2.3489 time to fit residues: 255.8290 Evaluate side-chains 70 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN C 336 GLN E 327 ASN E 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3300 Z= 0.260 Angle : 0.744 9.541 4416 Z= 0.402 Chirality : 0.049 0.127 498 Planarity : 0.003 0.018 558 Dihedral : 6.678 20.091 432 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.49 % Allowed : 12.37 % Favored : 84.14 % 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: -1.99 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 374 PHE 0.011 0.001 PHE B 346 TYR 0.016 0.004 TYR F 310 ARG 0.002 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.566 Fit side-chains REVERT: C 349 ARG cc_start: 0.8153 (mtp180) cc_final: 0.6953 (mmp-170) REVERT: F 311 LYS cc_start: 0.7681 (mttt) cc_final: 0.7306 (mmpt) REVERT: F 349 ARG cc_start: 0.8434 (mtp180) cc_final: 0.7201 (mtt-85) REVERT: F 358 ASP cc_start: 0.8545 (m-30) cc_final: 0.8332 (m-30) outliers start: 13 outliers final: 4 residues processed: 77 average time/residue: 2.1889 time to fit residues: 173.9190 Evaluate side-chains 63 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 325 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3300 Z= 0.261 Angle : 0.633 9.176 4416 Z= 0.351 Chirality : 0.049 0.124 498 Planarity : 0.003 0.025 558 Dihedral : 5.813 17.307 432 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.69 % Allowed : 12.37 % Favored : 84.95 % 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: -1.77 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 362 PHE 0.011 0.002 PHE B 346 TYR 0.015 0.003 TYR F 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.569 Fit side-chains REVERT: D 311 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.6720 (pttt) REVERT: D 349 ARG cc_start: 0.8445 (mtt-85) cc_final: 0.6696 (ptt-90) REVERT: C 349 ARG cc_start: 0.8221 (mtp180) cc_final: 0.7010 (mmp-170) REVERT: F 311 LYS cc_start: 0.7689 (mttt) cc_final: 0.7264 (mmpt) REVERT: F 349 ARG cc_start: 0.8461 (mtp180) cc_final: 0.7262 (mtt-85) REVERT: F 358 ASP cc_start: 0.8587 (m-30) cc_final: 0.8373 (m-30) outliers start: 10 outliers final: 5 residues processed: 68 average time/residue: 2.5747 time to fit residues: 180.0329 Evaluate side-chains 60 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 325 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 351 GLN E 336 GLN E 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3300 Z= 0.210 Angle : 0.581 9.594 4416 Z= 0.328 Chirality : 0.049 0.126 498 Planarity : 0.003 0.025 558 Dihedral : 5.296 16.728 432 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.42 % Allowed : 12.37 % Favored : 85.22 % 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: -1.73 (0.38), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 362 PHE 0.008 0.001 PHE B 346 TYR 0.012 0.003 TYR F 310 ARG 0.002 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.564 Fit side-chains REVERT: D 311 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.6361 (pptt) REVERT: D 349 ARG cc_start: 0.8464 (mtt-85) cc_final: 0.6635 (pmt-80) REVERT: C 349 ARG cc_start: 0.8248 (mtp180) cc_final: 0.7085 (mmp-170) REVERT: F 311 LYS cc_start: 0.7702 (mttt) cc_final: 0.7270 (mmpt) REVERT: F 342 GLU cc_start: 0.8241 (tt0) cc_final: 0.8040 (mp0) REVERT: F 345 ASP cc_start: 0.8894 (t70) cc_final: 0.8667 (t0) REVERT: F 349 ARG cc_start: 0.8475 (mtp180) cc_final: 0.7256 (mtt-85) REVERT: F 358 ASP cc_start: 0.8601 (m-30) cc_final: 0.8383 (m-30) outliers start: 9 outliers final: 6 residues processed: 68 average time/residue: 2.2503 time to fit residues: 157.8269 Evaluate side-chains 62 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 325 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3300 Z= 0.183 Angle : 0.559 9.699 4416 Z= 0.317 Chirality : 0.048 0.124 498 Planarity : 0.003 0.027 558 Dihedral : 5.083 16.280 432 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.15 % Allowed : 14.25 % Favored : 83.60 % 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: -1.69 (0.38), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.006 0.001 PHE B 346 TYR 0.010 0.002 TYR F 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.570 Fit side-chains REVERT: D 311 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.6352 (pptt) REVERT: C 349 ARG cc_start: 0.8287 (mtp180) cc_final: 0.7119 (mmp-170) REVERT: F 311 LYS cc_start: 0.7731 (mttt) cc_final: 0.7278 (mmpt) REVERT: F 342 GLU cc_start: 0.8267 (tt0) cc_final: 0.8021 (mp0) REVERT: F 349 ARG cc_start: 0.8474 (mtp180) cc_final: 0.7283 (mtt-85) REVERT: F 358 ASP cc_start: 0.8586 (m-30) cc_final: 0.8368 (m-30) outliers start: 8 outliers final: 3 residues processed: 66 average time/residue: 2.3526 time to fit residues: 159.8405 Evaluate side-chains 59 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3300 Z= 0.149 Angle : 0.538 9.976 4416 Z= 0.308 Chirality : 0.049 0.125 498 Planarity : 0.003 0.026 558 Dihedral : 4.692 15.781 432 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.61 % Allowed : 14.52 % Favored : 83.87 % 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: -1.61 (0.38), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 362 PHE 0.005 0.001 PHE E 346 TYR 0.009 0.002 TYR F 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.599 Fit side-chains REVERT: D 311 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.6337 (pptt) REVERT: C 349 ARG cc_start: 0.8284 (mtp180) cc_final: 0.7097 (mmp-170) REVERT: E 311 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6520 (pttp) REVERT: F 311 LYS cc_start: 0.7739 (mttt) cc_final: 0.7284 (mmpt) REVERT: F 342 GLU cc_start: 0.8274 (tt0) cc_final: 0.8021 (mp0) REVERT: F 349 ARG cc_start: 0.8490 (mtp180) cc_final: 0.7291 (mtt-85) REVERT: F 358 ASP cc_start: 0.8590 (m-30) cc_final: 0.8367 (m-30) outliers start: 6 outliers final: 3 residues processed: 61 average time/residue: 2.4869 time to fit residues: 156.1408 Evaluate side-chains 60 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 311 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 0.0970 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.0770 overall best weight: 1.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3300 Z= 0.175 Angle : 0.539 9.905 4416 Z= 0.308 Chirality : 0.048 0.123 498 Planarity : 0.003 0.027 558 Dihedral : 4.693 15.673 432 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.69 % Allowed : 12.90 % Favored : 84.41 % 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: -1.54 (0.39), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.007 0.001 PHE E 346 TYR 0.011 0.002 TYR F 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.561 Fit side-chains REVERT: D 311 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.6351 (pptt) REVERT: C 349 ARG cc_start: 0.8301 (mtp180) cc_final: 0.7142 (mmp-170) REVERT: E 311 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6618 (pttp) REVERT: F 311 LYS cc_start: 0.7799 (mttt) cc_final: 0.7345 (mmpt) REVERT: F 342 GLU cc_start: 0.8299 (tt0) cc_final: 0.8040 (mp0) REVERT: F 349 ARG cc_start: 0.8523 (mtp180) cc_final: 0.7311 (mtt-85) REVERT: F 358 ASP cc_start: 0.8606 (m-30) cc_final: 0.8380 (m-30) outliers start: 10 outliers final: 4 residues processed: 62 average time/residue: 2.6180 time to fit residues: 167.2008 Evaluate side-chains 63 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.2618 > 50: distance: 59 - 247: 10.238 distance: 62 - 280: 5.195 distance: 168 - 386: 3.199 distance: 225 - 230: 6.165 distance: 230 - 231: 17.198 distance: 230 - 238: 12.901 distance: 231 - 232: 8.331 distance: 231 - 234: 12.887 distance: 231 - 239: 10.260 distance: 232 - 233: 13.586 distance: 232 - 244: 14.147 distance: 234 - 240: 17.906 distance: 234 - 241: 15.606 distance: 235 - 236: 11.728 distance: 235 - 237: 4.950 distance: 237 - 242: 5.360 distance: 237 - 243: 8.593 distance: 244 - 245: 9.886 distance: 244 - 252: 16.408 distance: 245 - 246: 5.120 distance: 245 - 248: 7.843 distance: 245 - 253: 9.305 distance: 246 - 247: 4.399 distance: 246 - 263: 5.406 distance: 248 - 249: 4.174 distance: 248 - 250: 9.481 distance: 249 - 251: 11.057 distance: 249 - 255: 11.563 distance: 249 - 256: 3.499 distance: 250 - 257: 5.823 distance: 250 - 258: 4.770 distance: 250 - 259: 8.769 distance: 251 - 261: 5.794 distance: 251 - 262: 5.342 distance: 263 - 264: 4.935 distance: 263 - 273: 9.447 distance: 264 - 265: 16.984 distance: 264 - 274: 3.029 distance: 267 - 268: 9.145 distance: 267 - 275: 6.974 distance: 267 - 276: 7.242 distance: 268 - 269: 6.346 distance: 268 - 270: 8.087 distance: 269 - 271: 6.553 distance: 269 - 277: 7.240 distance: 270 - 272: 7.447 distance: 270 - 278: 6.539 distance: 271 - 272: 4.967 distance: 271 - 279: 4.879 distance: 280 - 290: 10.320 distance: 281 - 282: 23.255 distance: 281 - 284: 8.776 distance: 281 - 291: 14.104 distance: 282 - 283: 13.271 distance: 282 - 297: 6.042 distance: 284 - 285: 7.507 distance: 284 - 292: 3.715 distance: 284 - 293: 5.986 distance: 285 - 286: 10.921 distance: 285 - 287: 6.705 distance: 286 - 288: 9.271 distance: 286 - 294: 7.578 distance: 287 - 289: 7.567 distance: 287 - 295: 3.089 distance: 288 - 289: 6.507 distance: 288 - 296: 5.330 distance: 297 - 298: 12.954 distance: 297 - 306: 26.309 distance: 298 - 299: 11.871 distance: 298 - 301: 12.751 distance: 298 - 307: 18.746 distance: 299 - 300: 9.764 distance: 299 - 319: 8.683 distance: 301 - 302: 11.186 distance: 301 - 308: 4.385 distance: 301 - 309: 7.312 distance: 302 - 303: 15.595 distance: 302 - 310: 17.662 distance: 302 - 311: 9.200 distance: 303 - 304: 10.671 distance: 303 - 312: 5.684 distance: 303 - 313: 3.632 distance: 304 - 305: 6.936 distance: 304 - 314: 9.106 distance: 304 - 315: 8.324 distance: 305 - 316: 4.010 distance: 305 - 317: 6.151 distance: 305 - 318: 3.493 distance: 319 - 320: 6.756 distance: 319 - 325: 30.364 distance: 320 - 321: 6.392 distance: 320 - 323: 22.491 distance: 320 - 326: 14.158 distance: 321 - 322: 15.197 distance: 321 - 333: 24.287 distance: 323 - 324: 15.364 distance: 323 - 327: 8.044 distance: 323 - 328: 9.581 distance: 324 - 325: 7.718 distance: 324 - 329: 8.038 distance: 324 - 330: 9.320 distance: 325 - 331: 5.711 distance: 325 - 332: 22.358 distance: 333 - 334: 14.447 distance: 333 - 337: 12.677 distance: 334 - 335: 25.489 distance: 334 - 338: 18.827 distance: 334 - 339: 11.376 distance: 335 - 336: 15.674 distance: 335 - 340: 15.351 distance: 340 - 341: 20.939 distance: 340 - 344: 7.174 distance: 341 - 342: 4.748 distance: 341 - 345: 8.260 distance: 341 - 346: 10.277 distance: 342 - 343: 7.038 distance: 342 - 347: 16.496 distance: 347 - 348: 12.347 distance: 347 - 351: 12.990 distance: 348 - 349: 14.770 distance: 348 - 352: 5.999 distance: 348 - 353: 7.582 distance: 349 - 350: 14.724 distance: 349 - 354: 12.331 distance: 354 - 355: 10.376 distance: 354 - 363: 12.826 distance: 355 - 356: 3.523 distance: 355 - 358: 8.394 distance: 355 - 364: 11.589 distance: 356 - 357: 16.931 distance: 356 - 371: 6.662 distance: 358 - 359: 9.127 distance: 358 - 365: 6.270 distance: 358 - 366: 6.627 distance: 359 - 360: 6.560 distance: 359 - 368: 3.874 distance: 360 - 361: 8.009 distance: 360 - 362: 7.682 distance: 362 - 369: 8.711 distance: 362 - 370: 4.284