Starting phenix.real_space_refine on Fri Aug 2 19:39:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgt_43224/08_2024/8vgt_43224.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgt_43224/08_2024/8vgt_43224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgt_43224/08_2024/8vgt_43224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgt_43224/08_2024/8vgt_43224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgt_43224/08_2024/8vgt_43224.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vgt_43224/08_2024/8vgt_43224.cif" } resolution = 2.9 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= 0.126 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 3014 2.51 5 N 823 2.21 5 O 830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 398": "NH1" <-> "NH2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 417": "OD1" <-> "OD2" Residue "A PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B GLU 388": "OE1" <-> "OE2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 491": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4714 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2040 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 7, 'GLU:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2604 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 331} Chain breaks: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'GLU:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 74 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.65, per 1000 atoms: 0.77 Number of scatterers: 4714 At special positions: 0 Unit cell: (78, 83, 120, 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 47 16.00 O 830 8.00 N 823 7.00 C 3014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.02 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.11 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 605 " distance=2.04 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.11 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 567 " distance=2.02 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.02 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.05 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.08 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 569 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 588 " distance=2.02 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 148 " distance=2.02 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 231 " distance=2.00 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 241 " distance=2.04 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 365 " distance=2.05 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 297 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 465 " distance=2.13 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 701 " - " ASN A 454 " " NAG A 702 " - " ASN A 470 " " NAG A 703 " - " ASN A 433 " " NAG C 1 " - " ASN B 213 " Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 906.7 milliseconds 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1168 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 12 sheets defined 16.1% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.582A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 344 removed outlier: 3.740A pdb=" N TRP A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.955A pdb=" N ARG A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N SER A 399 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.525A pdb=" N ASN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.581A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 220 through 223 Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.929A pdb=" N GLU B 299 " --> pdb=" O HIS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 477 through 490 removed outlier: 5.418A pdb=" N ASP B 482 " --> pdb=" O MET B 478 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TRP B 483 " --> pdb=" O VAL B 479 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 337 through 339 removed outlier: 6.737A pdb=" N VAL A 338 " --> pdb=" O ASN A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.578A pdb=" N SER A 422 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N SER A 428 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N THR A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 349 Processing sheet with id=AA4, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AA5, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.251A pdb=" N CYS A 466 " --> pdb=" O SER A 538 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 504 through 507 Processing sheet with id=AA7, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 152 Processing sheet with id=AA9, first strand: chain 'B' and resid 196 through 200 Processing sheet with id=AB1, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AB2, first strand: chain 'B' and resid 260 through 261 removed outlier: 4.170A pdb=" N CYS B 426 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLY B 475 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR B 459 " --> pdb=" O GLY B 475 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU B 445 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER B 382 " --> pdb=" O PRO B 444 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER B 448 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 378 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 270 through 275 removed outlier: 6.110A pdb=" N VAL B 275 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N HIS B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 348 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL B 331 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS B 350 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TRP B 308 " --> pdb=" O VAL B 328 " (cutoff:3.500A) 143 hydrogen bonds defined for protein. 351 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: 1.31 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1202 1.33 - 1.46: 1377 1.46 - 1.59: 2206 1.59 - 1.72: 0 1.72 - 1.85: 56 Bond restraints: 4841 Sorted by residual: bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.473 -0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" N VAL A 509 " pdb=" CA VAL A 509 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.50e+00 bond pdb=" CD GLU A 345 " pdb=" OE2 GLU A 345 " ideal model delta sigma weight residual 1.249 1.199 0.050 1.90e-02 2.77e+03 6.98e+00 bond pdb=" CG ASP B 345 " pdb=" OD2 ASP B 345 " ideal model delta sigma weight residual 1.249 1.200 0.049 1.90e-02 2.77e+03 6.60e+00 bond pdb=" N ALA B 230 " pdb=" CA ALA B 230 " ideal model delta sigma weight residual 1.457 1.487 -0.031 1.20e-02 6.94e+03 6.50e+00 ... (remaining 4836 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.90: 176 106.90 - 113.68: 2532 113.68 - 120.46: 1853 120.46 - 127.24: 1980 127.24 - 134.01: 67 Bond angle restraints: 6608 Sorted by residual: angle pdb=" C GLY B 153 " pdb=" N PRO B 154 " pdb=" CA PRO B 154 " ideal model delta sigma weight residual 119.56 127.94 -8.38 1.02e+00 9.61e-01 6.75e+01 angle pdb=" C TRP B 267 " pdb=" N PRO B 268 " pdb=" CA PRO B 268 " ideal model delta sigma weight residual 119.56 127.72 -8.16 1.02e+00 9.61e-01 6.39e+01 angle pdb=" C ASP A 529 " pdb=" N PRO A 530 " pdb=" CA PRO A 530 " ideal model delta sigma weight residual 119.56 127.37 -7.81 1.02e+00 9.61e-01 5.87e+01 angle pdb=" C ASP A 523 " pdb=" N PRO A 524 " pdb=" CA PRO A 524 " ideal model delta sigma weight residual 119.82 126.98 -7.16 9.80e-01 1.04e+00 5.34e+01 angle pdb=" C PRO A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta sigma weight residual 119.76 127.15 -7.39 1.03e+00 9.43e-01 5.15e+01 ... (remaining 6603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 2777 17.86 - 35.72: 111 35.72 - 53.58: 21 53.58 - 71.44: 9 71.44 - 89.30: 3 Dihedral angle restraints: 2921 sinusoidal: 1103 harmonic: 1818 Sorted by residual: dihedral pdb=" CB CYS B 410 " pdb=" SG CYS B 410 " pdb=" SG CYS B 426 " pdb=" CB CYS B 426 " ideal model delta sinusoidal sigma weight residual -86.00 -162.51 76.51 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS B 437 " pdb=" SG CYS B 437 " pdb=" SG CYS B 465 " pdb=" CB CYS B 465 " ideal model delta sinusoidal sigma weight residual -86.00 -136.59 50.59 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS A 466 " pdb=" SG CYS A 466 " pdb=" SG CYS A 546 " pdb=" CB CYS A 546 " ideal model delta sinusoidal sigma weight residual -86.00 -128.95 42.95 1 1.00e+01 1.00e-02 2.57e+01 ... (remaining 2918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 486 0.064 - 0.128: 183 0.128 - 0.192: 44 0.192 - 0.256: 10 0.256 - 0.320: 5 Chirality restraints: 728 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.34e+01 chirality pdb=" C2 NAG A 702 " pdb=" C1 NAG A 702 " pdb=" C3 NAG A 702 " pdb=" N2 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C2 NAG A 703 " pdb=" C1 NAG A 703 " pdb=" C3 NAG A 703 " pdb=" N2 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.49 -2.79 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 725 not shown) Planarity restraints: 857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 485 " 0.033 2.00e-02 2.50e+03 1.99e-02 7.92e+00 pdb=" CG TYR B 485 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 485 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 485 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 485 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR B 485 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR B 485 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 485 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 582 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C CYS A 582 " 0.045 2.00e-02 2.50e+03 pdb=" O CYS A 582 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL A 583 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 277 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.89e+00 pdb=" C ASN B 277 " -0.034 2.00e-02 2.50e+03 pdb=" O ASN B 277 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL B 278 " 0.011 2.00e-02 2.50e+03 ... (remaining 854 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 1742 2.88 - 3.38: 4019 3.38 - 3.89: 7811 3.89 - 4.39: 9370 4.39 - 4.90: 15390 Nonbonded interactions: 38332 Sorted by model distance: nonbonded pdb=" O SER B 137 " pdb=" N CYS B 139 " model vdw 2.374 3.120 nonbonded pdb=" O TRP B 483 " pdb=" NE2 GLN B 487 " model vdw 2.495 3.120 nonbonded pdb=" OD1 ASP A 417 " pdb=" N THR A 418 " model vdw 2.507 3.120 nonbonded pdb=" N ASP B 144 " pdb=" OD1 ASP B 144 " model vdw 2.522 3.120 nonbonded pdb=" O ASP B 458 " pdb=" OD1 ASP B 458 " model vdw 2.525 3.040 ... (remaining 38327 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.510 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 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 0.060 4841 Z= 0.722 Angle : 1.299 8.377 6608 Z= 0.889 Chirality : 0.074 0.320 728 Planarity : 0.005 0.026 853 Dihedral : 10.509 89.304 1696 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.88 % Favored : 95.64 % Rotamer: Outliers : 0.70 % Allowed : 3.02 % Favored : 96.28 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 6.67 % 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: -0.41 (0.32), residues: 619 helix: -2.23 (0.45), residues: 83 sheet: 0.52 (0.43), residues: 137 loop : -0.04 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP B 267 HIS 0.008 0.002 HIS A 512 PHE 0.021 0.004 PHE A 450 TYR 0.035 0.004 TYR B 485 ARG 0.005 0.001 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.467 Fit side-chains REVERT: A 536 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8020 (mmtp) REVERT: B 350 LYS cc_start: 0.8660 (tttm) cc_final: 0.8453 (tttp) REVERT: B 424 MET cc_start: 0.8786 (mtt) cc_final: 0.8555 (mtt) outliers start: 3 outliers final: 1 residues processed: 101 average time/residue: 1.0816 time to fit residues: 113.7734 Evaluate side-chains 58 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain B residue 212 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 31 optimal weight: 0.0470 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN A 343 ASN A 458 HIS ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS B 334 HIS B 343 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4841 Z= 0.210 Angle : 0.608 6.631 6608 Z= 0.321 Chirality : 0.049 0.315 728 Planarity : 0.005 0.037 853 Dihedral : 5.632 55.948 782 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.40 % Allowed : 11.16 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.29 (0.32), residues: 619 helix: -1.26 (0.56), residues: 76 sheet: 0.70 (0.47), residues: 113 loop : -0.19 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 384 HIS 0.006 0.002 HIS B 334 PHE 0.016 0.002 PHE A 594 TYR 0.010 0.001 TYR A 427 ARG 0.006 0.001 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.507 Fit side-chains REVERT: A 334 ASN cc_start: 0.7594 (m110) cc_final: 0.7311 (m-40) REVERT: A 544 GLU cc_start: 0.7923 (pt0) cc_final: 0.7711 (pt0) REVERT: B 147 ARG cc_start: 0.7704 (mmm160) cc_final: 0.7323 (mmm160) REVERT: B 395 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6454 (tp30) REVERT: B 482 ASP cc_start: 0.7229 (m-30) cc_final: 0.7008 (m-30) outliers start: 6 outliers final: 2 residues processed: 69 average time/residue: 1.0751 time to fit residues: 77.8390 Evaluate side-chains 60 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 395 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 HIS B 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4841 Z= 0.240 Angle : 0.568 6.894 6608 Z= 0.302 Chirality : 0.048 0.313 728 Planarity : 0.005 0.040 853 Dihedral : 4.583 32.489 778 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.26 % Favored : 97.58 % Rotamer: Outliers : 2.33 % Allowed : 11.63 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.21 (0.33), residues: 619 helix: -0.98 (0.57), residues: 76 sheet: 0.01 (0.42), residues: 142 loop : 0.08 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 384 HIS 0.006 0.002 HIS A 488 PHE 0.016 0.002 PHE A 594 TYR 0.010 0.001 TYR B 414 ARG 0.004 0.001 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.502 Fit side-chains REVERT: B 147 ARG cc_start: 0.7644 (mmm160) cc_final: 0.7397 (mmm160) REVERT: B 395 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6497 (tp30) outliers start: 10 outliers final: 5 residues processed: 68 average time/residue: 1.0224 time to fit residues: 72.9855 Evaluate side-chains 65 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 437 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.0060 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4841 Z= 0.233 Angle : 0.558 6.909 6608 Z= 0.296 Chirality : 0.048 0.307 728 Planarity : 0.005 0.042 853 Dihedral : 4.570 33.820 778 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.26 % Favored : 97.58 % Rotamer: Outliers : 2.33 % Allowed : 12.09 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.21 (0.33), residues: 619 helix: -0.84 (0.59), residues: 76 sheet: -0.08 (0.42), residues: 142 loop : 0.09 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 384 HIS 0.005 0.001 HIS A 488 PHE 0.015 0.002 PHE A 594 TYR 0.009 0.001 TYR B 414 ARG 0.005 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.547 Fit side-chains REVERT: A 544 GLU cc_start: 0.8248 (pt0) cc_final: 0.7928 (pt0) REVERT: B 227 HIS cc_start: 0.8157 (OUTLIER) cc_final: 0.7400 (m90) REVERT: B 395 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.6501 (tp30) REVERT: B 424 MET cc_start: 0.8697 (mtt) cc_final: 0.8429 (mtt) outliers start: 10 outliers final: 5 residues processed: 66 average time/residue: 1.0072 time to fit residues: 69.7850 Evaluate side-chains 67 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 437 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7534 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4841 Z= 0.247 Angle : 0.551 7.067 6608 Z= 0.294 Chirality : 0.048 0.334 728 Planarity : 0.005 0.043 853 Dihedral : 4.541 35.624 778 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.79 % Allowed : 12.09 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.28 (0.33), residues: 619 helix: -0.93 (0.59), residues: 77 sheet: -0.14 (0.43), residues: 142 loop : 0.06 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 306 HIS 0.006 0.002 HIS A 488 PHE 0.015 0.002 PHE A 594 TYR 0.010 0.001 TYR B 414 ARG 0.002 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: B 395 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6538 (tp30) outliers start: 12 outliers final: 8 residues processed: 69 average time/residue: 0.9763 time to fit residues: 70.8428 Evaluate side-chains 68 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 437 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 57 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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: 0.7550 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4841 Z= 0.267 Angle : 0.554 6.907 6608 Z= 0.295 Chirality : 0.049 0.334 728 Planarity : 0.005 0.044 853 Dihedral : 4.565 36.727 778 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.26 % Allowed : 13.02 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.32 (0.34), residues: 619 helix: -1.09 (0.58), residues: 77 sheet: -0.17 (0.43), residues: 142 loop : 0.06 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 306 HIS 0.005 0.002 HIS A 488 PHE 0.014 0.002 PHE A 594 TYR 0.010 0.001 TYR B 414 ARG 0.006 0.001 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 589 ASN cc_start: 0.7250 (OUTLIER) cc_final: 0.6607 (m-40) REVERT: B 227 HIS cc_start: 0.8152 (OUTLIER) cc_final: 0.7373 (m90) REVERT: B 395 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.6576 (tp30) REVERT: B 424 MET cc_start: 0.8704 (mtt) cc_final: 0.8395 (mtt) outliers start: 14 outliers final: 7 residues processed: 66 average time/residue: 0.9577 time to fit residues: 66.7445 Evaluate side-chains 68 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 437 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 73.7147 > 50: distance: 6 - 67: 34.168 distance: 12 - 33: 27.377 distance: 15 - 30: 28.213 distance: 25 - 30: 29.764 distance: 30 - 31: 41.806 distance: 31 - 32: 55.528 distance: 31 - 34: 40.010 distance: 32 - 33: 43.292 distance: 32 - 37: 39.138 distance: 34 - 36: 39.370 distance: 37 - 38: 41.287 distance: 37 - 167: 35.300 distance: 38 - 39: 55.735 distance: 39 - 40: 57.594 distance: 39 - 42: 39.328 distance: 40 - 164: 32.106 distance: 42 - 43: 57.084 distance: 43 - 46: 40.070 distance: 44 - 45: 40.424 distance: 44 - 47: 40.171 distance: 47 - 48: 56.663 distance: 48 - 49: 25.573 distance: 49 - 50: 26.545 distance: 49 - 52: 47.540 distance: 50 - 68: 59.161 distance: 52 - 53: 41.155 distance: 53 - 54: 56.363 distance: 53 - 56: 40.434 distance: 54 - 62: 56.977 distance: 56 - 57: 55.827 distance: 57 - 58: 55.716 distance: 57 - 59: 40.995 distance: 58 - 60: 40.034 distance: 59 - 61: 39.221 distance: 60 - 61: 40.350 distance: 63 - 64: 56.844 distance: 64 - 65: 41.131 distance: 64 - 68: 55.953 distance: 66 - 67: 39.413 distance: 69 - 70: 40.414 distance: 69 - 72: 69.477 distance: 70 - 75: 38.892 distance: 72 - 74: 42.103 distance: 75 - 76: 40.573 distance: 76 - 77: 38.497 distance: 76 - 79: 55.763 distance: 77 - 78: 56.182 distance: 77 - 84: 40.569 distance: 79 - 80: 40.210 distance: 81 - 82: 49.675 distance: 81 - 83: 39.019 distance: 85 - 86: 57.431 distance: 85 - 88: 40.121 distance: 86 - 93: 7.406 distance: 88 - 89: 41.178 distance: 89 - 90: 40.180 distance: 90 - 91: 41.175 distance: 91 - 92: 56.520 distance: 93 - 94: 50.352 distance: 93 - 99: 40.028 distance: 95 - 100: 34.656 distance: 98 - 99: 40.048