Starting phenix.real_space_refine on Fri Aug 2 23:05:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh9_12187/08_2024/7bh9_12187.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh9_12187/08_2024/7bh9_12187.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/7bh9_12187/08_2024/7bh9_12187.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh9_12187/08_2024/7bh9_12187.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh9_12187/08_2024/7bh9_12187.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh9_12187/08_2024/7bh9_12187.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 ------------------------------------------------------------------------------- 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= 0.037 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 Zn 1 6.06 5 S 34 5.16 5 C 3787 2.51 5 N 970 2.21 5 O 1084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 597": "OD1" <-> "OD2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 5876 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4704 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 560} Chain breaks: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 66 Chain: "E" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1129 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.72, per 1000 atoms: 0.80 Number of scatterers: 5876 At special positions: 0 Unit cell: (68.77, 81.466, 111.09, 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) Zn 1 29.99 S 34 16.00 O 1084 8.00 N 970 7.00 C 3787 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=1.99 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 NAG-ASN " NAG A 902 " - " ASN A 546 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 53 " Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1372 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 58.1% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.676A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 81 removed outlier: 3.596A pdb=" N ASN A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.009A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 129 removed outlier: 3.507A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.622A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 193 Proline residue: A 178 - end of helix removed outlier: 3.708A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 221 through 252 removed outlier: 3.799A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 253 through 256 removed outlier: 4.168A pdb=" N ILE A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.630A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.837A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.639A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.890A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.993A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 413 removed outlier: 4.044A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.910A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 481 removed outlier: 3.667A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.536A pdb=" N SER A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.114A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.838A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.895A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.755A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.630A pdb=" N GLU E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.988A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'E' and resid 376 through 379 Processing sheet with id=AA5, first strand: chain 'E' and resid 448 through 454 removed outlier: 6.095A pdb=" N TYR E 449 " --> pdb=" O PHE E 497 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N PHE E 497 " --> pdb=" O TYR E 449 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR E 451 " --> pdb=" O TYR E 495 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 271 hydrogen bonds defined for protein. 747 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: 1.70 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1248 1.33 - 1.45: 1531 1.45 - 1.57: 3206 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 6041 Sorted by residual: bond pdb=" CA SER A 331 " pdb=" CB SER A 331 " ideal model delta sigma weight residual 1.530 1.472 0.058 1.55e-02 4.16e+03 1.40e+01 bond pdb=" C THR E 478 " pdb=" N PRO E 479 " ideal model delta sigma weight residual 1.330 1.372 -0.042 1.25e-02 6.40e+03 1.14e+01 bond pdb=" N VAL E 483 " pdb=" CA VAL E 483 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.15e-02 7.56e+03 8.70e+00 bond pdb=" N SER A 331 " pdb=" CA SER A 331 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.22e-02 6.72e+03 6.28e+00 bond pdb=" C GLU A 22 " pdb=" O GLU A 22 " ideal model delta sigma weight residual 1.236 1.207 0.029 1.19e-02 7.06e+03 5.92e+00 ... (remaining 6036 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.59: 182 106.59 - 113.46: 3137 113.46 - 120.33: 2409 120.33 - 127.20: 2388 127.20 - 134.07: 93 Bond angle restraints: 8209 Sorted by residual: angle pdb=" N ASN E 481 " pdb=" CA ASN E 481 " pdb=" C ASN E 481 " ideal model delta sigma weight residual 112.97 104.76 8.21 1.06e+00 8.90e-01 6.00e+01 angle pdb=" N GLY E 482 " pdb=" CA GLY E 482 " pdb=" C GLY E 482 " ideal model delta sigma weight residual 115.30 106.84 8.46 1.39e+00 5.18e-01 3.71e+01 angle pdb=" N PRO E 479 " pdb=" CA PRO E 479 " pdb=" C PRO E 479 " ideal model delta sigma weight residual 111.22 118.06 -6.84 1.40e+00 5.10e-01 2.39e+01 angle pdb=" CA CYS E 480 " pdb=" C CYS E 480 " pdb=" N ASN E 481 " ideal model delta sigma weight residual 115.51 120.83 -5.32 1.24e+00 6.50e-01 1.84e+01 angle pdb=" C ASN A 330 " pdb=" CA ASN A 330 " pdb=" CB ASN A 330 " ideal model delta sigma weight residual 111.02 104.86 6.16 1.62e+00 3.81e-01 1.44e+01 ... (remaining 8204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 3210 16.40 - 32.79: 282 32.79 - 49.19: 52 49.19 - 65.58: 16 65.58 - 81.98: 4 Dihedral angle restraints: 3564 sinusoidal: 1426 harmonic: 2138 Sorted by residual: dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual -86.00 -121.93 35.93 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CA TYR A 252 " pdb=" C TYR A 252 " pdb=" N PRO A 253 " pdb=" CA PRO A 253 " ideal model delta harmonic sigma weight residual -180.00 -161.11 -18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA PRO A 389 " pdb=" C PRO A 389 " pdb=" N PHE A 390 " pdb=" CA PHE A 390 " ideal model delta harmonic sigma weight residual -180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 3561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 652 0.053 - 0.105: 187 0.105 - 0.158: 31 0.158 - 0.210: 1 0.210 - 0.263: 2 Chirality restraints: 873 Sorted by residual: chirality pdb=" CA ASN E 481 " pdb=" N ASN E 481 " pdb=" C ASN E 481 " pdb=" CB ASN E 481 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PRO E 479 " pdb=" N PRO E 479 " pdb=" C PRO E 479 " pdb=" CB PRO E 479 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB ILE A 21 " pdb=" CA ILE A 21 " pdb=" CG1 ILE A 21 " pdb=" CG2 ILE A 21 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 870 not shown) Planarity restraints: 1049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 495 " 0.023 2.00e-02 2.50e+03 1.35e-02 3.67e+00 pdb=" CG TYR E 495 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR E 495 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR E 495 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 495 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 495 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 495 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 495 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 21 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C ILE A 21 " -0.033 2.00e-02 2.50e+03 pdb=" O ILE A 21 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU A 22 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " -0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 235 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.026 5.00e-02 4.00e+02 ... (remaining 1046 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 37 2.60 - 3.17: 4671 3.17 - 3.75: 8205 3.75 - 4.32: 12466 4.32 - 4.90: 21205 Nonbonded interactions: 46584 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.021 2.230 nonbonded pdb=" OG SER A 19 " pdb=" OE1 GLU A 23 " model vdw 2.175 3.040 nonbonded pdb=" O SER E 438 " pdb=" OG SER E 438 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.284 3.040 nonbonded pdb=" OE2 GLU A 435 " pdb=" NZ LYS A 541 " model vdw 2.289 3.120 ... (remaining 46579 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: 2.620 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 22.230 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 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 : 0.007 0.058 6041 Z= 0.447 Angle : 0.767 8.974 8209 Z= 0.444 Chirality : 0.050 0.263 873 Planarity : 0.005 0.046 1046 Dihedral : 13.182 81.978 2183 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.33 % Allowed : 3.98 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.27), residues: 718 helix: -1.42 (0.24), residues: 375 sheet: -2.04 (0.69), residues: 41 loop : -2.83 (0.28), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 353 HIS 0.010 0.001 HIS A 241 PHE 0.014 0.002 PHE A 512 TYR 0.030 0.002 TYR E 495 ARG 0.002 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.744 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 67 average time/residue: 1.1442 time to fit residues: 80.9960 Evaluate side-chains 49 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 597 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 374 HIS A 380 GLN E 354 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6041 Z= 0.153 Angle : 0.500 5.255 8209 Z= 0.265 Chirality : 0.040 0.130 873 Planarity : 0.004 0.032 1046 Dihedral : 5.049 45.067 857 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.50 % Allowed : 9.29 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.50 (0.30), residues: 718 helix: -0.02 (0.28), residues: 372 sheet: -1.00 (0.66), residues: 49 loop : -2.25 (0.29), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.003 0.001 HIS A 535 PHE 0.009 0.001 PHE E 377 TYR 0.019 0.001 TYR E 495 ARG 0.002 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 455 MET cc_start: 0.8879 (tmm) cc_final: 0.8633 (tmt) REVERT: E 408 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7285 (ptm160) outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 1.0673 time to fit residues: 66.9812 Evaluate side-chains 53 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain E residue 408 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 54 optimal weight: 0.0040 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 0.0040 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.1408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS E 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6041 Z= 0.163 Angle : 0.479 5.311 8209 Z= 0.251 Chirality : 0.040 0.136 873 Planarity : 0.003 0.031 1046 Dihedral : 4.375 38.303 855 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.16 % Allowed : 10.45 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.68 (0.31), residues: 718 helix: 0.65 (0.28), residues: 374 sheet: -0.48 (0.71), residues: 47 loop : -1.91 (0.31), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 HIS 0.004 0.001 HIS A 374 PHE 0.009 0.001 PHE E 342 TYR 0.022 0.001 TYR E 495 ARG 0.001 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 70 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8435 (m) REVERT: E 408 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7323 (ptm160) outliers start: 7 outliers final: 3 residues processed: 55 average time/residue: 1.1605 time to fit residues: 67.4927 Evaluate side-chains 54 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 6041 Z= 0.127 Angle : 0.446 5.295 8209 Z= 0.232 Chirality : 0.039 0.131 873 Planarity : 0.003 0.030 1046 Dihedral : 3.928 32.226 854 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.16 % Allowed : 11.28 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.20 (0.31), residues: 718 helix: 1.07 (0.28), residues: 374 sheet: 0.06 (0.86), residues: 37 loop : -1.72 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 436 HIS 0.002 0.001 HIS A 378 PHE 0.008 0.001 PHE A 452 TYR 0.016 0.001 TYR E 495 ARG 0.001 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 70 SER cc_start: 0.8887 (OUTLIER) cc_final: 0.8449 (m) REVERT: E 408 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7294 (ptm160) outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 1.1228 time to fit residues: 68.9460 Evaluate side-chains 56 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN A 535 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6041 Z= 0.279 Angle : 0.526 5.516 8209 Z= 0.277 Chirality : 0.042 0.146 873 Planarity : 0.004 0.031 1046 Dihedral : 4.134 23.113 854 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.66 % Allowed : 11.94 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.22 (0.31), residues: 718 helix: 0.93 (0.28), residues: 382 sheet: -0.20 (0.73), residues: 47 loop : -1.62 (0.32), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 PHE 0.009 0.001 PHE A 327 TYR 0.025 0.001 TYR E 495 ARG 0.002 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 70 SER cc_start: 0.8912 (OUTLIER) cc_final: 0.8437 (m) REVERT: A 325 GLN cc_start: 0.7835 (tp40) cc_final: 0.7292 (tm-30) REVERT: E 408 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7377 (ptm160) outliers start: 10 outliers final: 7 residues processed: 57 average time/residue: 1.2076 time to fit residues: 72.6770 Evaluate side-chains 59 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 13 optimal weight: 0.0170 chunk 40 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 overall best weight: 2.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6041 Z= 0.310 Angle : 0.543 5.567 8209 Z= 0.287 Chirality : 0.043 0.148 873 Planarity : 0.004 0.033 1046 Dihedral : 4.260 19.887 854 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.32 % Allowed : 12.77 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.23 (0.31), residues: 718 helix: 0.89 (0.28), residues: 382 sheet: -0.19 (0.74), residues: 47 loop : -1.57 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 PHE 0.010 0.001 PHE A 327 TYR 0.026 0.001 TYR E 495 ARG 0.002 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 49 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 325 GLN cc_start: 0.7883 (tp40) cc_final: 0.7377 (tm-30) REVERT: E 408 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7370 (ptm160) outliers start: 14 outliers final: 8 residues processed: 60 average time/residue: 1.1843 time to fit residues: 74.9043 Evaluate side-chains 58 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6041 Z= 0.137 Angle : 0.462 5.335 8209 Z= 0.242 Chirality : 0.039 0.133 873 Planarity : 0.003 0.030 1046 Dihedral : 3.900 22.847 854 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.82 % Allowed : 13.10 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.19 (0.32), residues: 718 helix: 1.32 (0.29), residues: 375 sheet: 0.32 (0.87), residues: 37 loop : -1.45 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 PHE 0.007 0.001 PHE E 342 TYR 0.016 0.001 TYR E 495 ARG 0.001 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 70 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8445 (m) REVERT: A 325 GLN cc_start: 0.7805 (tp40) cc_final: 0.7315 (tm-30) outliers start: 11 outliers final: 7 residues processed: 58 average time/residue: 1.1548 time to fit residues: 70.7774 Evaluate side-chains 59 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6041 Z= 0.155 Angle : 0.471 5.393 8209 Z= 0.244 Chirality : 0.039 0.133 873 Planarity : 0.003 0.030 1046 Dihedral : 3.755 21.233 854 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.82 % Allowed : 13.43 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.40 (0.32), residues: 718 helix: 1.45 (0.29), residues: 375 sheet: 0.56 (0.90), residues: 37 loop : -1.32 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.003 0.001 HIS A 241 PHE 0.007 0.001 PHE A 452 TYR 0.019 0.001 TYR E 495 ARG 0.001 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 70 SER cc_start: 0.8884 (OUTLIER) cc_final: 0.8460 (m) REVERT: A 325 GLN cc_start: 0.7791 (tp40) cc_final: 0.7322 (tm-30) outliers start: 11 outliers final: 7 residues processed: 59 average time/residue: 1.1727 time to fit residues: 73.1953 Evaluate side-chains 59 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 61.3876 > 50: distance: 35 - 39: 20.525 distance: 39 - 40: 8.082 distance: 40 - 41: 33.764 distance: 40 - 43: 17.213 distance: 41 - 42: 28.070 distance: 43 - 44: 21.234 distance: 44 - 45: 20.464 distance: 45 - 46: 36.160 distance: 48 - 49: 18.591 distance: 48 - 51: 33.304 distance: 49 - 50: 7.844 distance: 49 - 52: 22.597 distance: 53 - 54: 9.770 distance: 53 - 56: 16.572 distance: 54 - 55: 26.287 distance: 54 - 60: 27.082 distance: 56 - 57: 22.905 distance: 56 - 58: 12.071 distance: 57 - 59: 4.083 distance: 60 - 61: 10.983 distance: 60 - 147: 16.605 distance: 61 - 62: 30.398 distance: 61 - 64: 12.205 distance: 62 - 63: 12.365 distance: 62 - 72: 37.846 distance: 63 - 144: 28.465 distance: 64 - 65: 15.993 distance: 65 - 66: 22.971 distance: 65 - 67: 9.955 distance: 66 - 68: 19.081 distance: 67 - 69: 5.282 distance: 68 - 70: 11.935 distance: 69 - 70: 20.125 distance: 70 - 71: 23.308 distance: 72 - 73: 11.403 distance: 73 - 74: 27.468 distance: 73 - 76: 31.847 distance: 74 - 75: 26.633 distance: 74 - 81: 42.470 distance: 77 - 78: 7.785 distance: 81 - 82: 40.734 distance: 82 - 83: 3.021 distance: 82 - 85: 32.550 distance: 83 - 84: 36.595 distance: 83 - 86: 37.353 distance: 86 - 87: 20.413 distance: 87 - 88: 16.110 distance: 88 - 89: 28.587 distance: 88 - 90: 10.726 distance: 90 - 91: 24.192 distance: 91 - 92: 17.099 distance: 91 - 94: 28.520 distance: 92 - 93: 18.285 distance: 92 - 98: 8.845 distance: 94 - 95: 48.533 distance: 95 - 96: 22.157 distance: 95 - 97: 23.395 distance: 98 - 99: 16.281 distance: 99 - 100: 26.061 distance: 99 - 102: 10.374 distance: 100 - 101: 43.275 distance: 100 - 105: 8.394 distance: 105 - 106: 7.889 distance: 105 - 111: 14.928 distance: 106 - 109: 9.836 distance: 107 - 108: 8.160 distance: 107 - 112: 28.525 distance: 109 - 110: 10.676 distance: 110 - 111: 24.398