Starting phenix.real_space_refine on Tue Feb 13 14:35:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dqa_30816/02_2024/7dqa_30816.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dqa_30816/02_2024/7dqa_30816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dqa_30816/02_2024/7dqa_30816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dqa_30816/02_2024/7dqa_30816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dqa_30816/02_2024/7dqa_30816.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dqa_30816/02_2024/7dqa_30816.pdb" } resolution = 2.8 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= 0.008 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 Cl 1 4.86 5 C 4151 2.51 5 N 1070 2.21 5 O 1316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 37": "OE1" <-> "OE2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" 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 TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 589": "OE1" <-> "OE2" Residue "A ASP 597": "OD1" <-> "OD2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 609": "OD1" <-> "OD2" Residue "A ASP 615": "OD1" <-> "OD2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C GLU 471": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6576 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "C" Number of atoms: 1547 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 194, 1541 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Conformer: "B" Number of residues, atoms: 194, 1541 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} bond proxies already assigned to first conformer: 1577 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 6.61, per 1000 atoms: 1.01 Number of scatterers: 6576 At special positions: 0 Unit cell: (101.362, 96.3937, 102.356, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 37 16.00 O 1316 8.00 N 1070 7.00 C 4151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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 903 " - " ASN A 546 " " NAG A 904 " - " ASN A 90 " " NAG A 905 " - " ASN A 322 " " NAG A 906 " - " ASN A 53 " " NAG C 601 " - " ASN C 343 " Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 56.9% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.847A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.749A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 193 removed outlier: 4.612A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 252 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.601A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.703A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.722A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.772A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.595A 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 431 through 447 Processing helix chain 'A' and resid 449 through 465 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 484 removed outlier: 3.725A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.870A pdb=" N LEU A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.131A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.757A pdb=" N SER A 563 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU A 564 " --> pdb=" O GLY A 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 564' Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 390 removed outlier: 4.034A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.153A 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 'C' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AA6, first strand: chain 'C' and resid 473 through 474 319 hydrogen bonds defined for protein. 905 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: 1.75 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2085 1.35 - 1.47: 1808 1.47 - 1.60: 2726 1.60 - 1.72: 0 1.72 - 1.85: 58 Bond restraints: 6677 Sorted by residual: bond pdb=" N CYS A 498 " pdb=" CA CYS A 498 " ideal model delta sigma weight residual 1.460 1.428 0.031 1.50e-02 4.44e+03 4.37e+00 bond pdb=" C1 NAG A 905 " pdb=" O5 NAG A 905 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" CB VAL A 581 " pdb=" CG1 VAL A 581 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.01e+00 bond pdb=" C1 NAG A 906 " pdb=" O5 NAG A 906 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" CB TRP A 566 " pdb=" CG TRP A 566 " ideal model delta sigma weight residual 1.498 1.451 0.047 3.10e-02 1.04e+03 2.27e+00 ... (remaining 6672 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.44: 201 106.44 - 113.35: 3519 113.35 - 120.25: 2597 120.25 - 127.15: 2665 127.15 - 134.06: 97 Bond angle restraints: 9079 Sorted by residual: angle pdb=" CA CYS A 141 " pdb=" CB CYS A 141 " pdb=" SG CYS A 141 " ideal model delta sigma weight residual 114.40 123.74 -9.34 2.30e+00 1.89e-01 1.65e+01 angle pdb=" C VAL A 581 " pdb=" CA VAL A 581 " pdb=" CB VAL A 581 " ideal model delta sigma weight residual 111.85 106.72 5.13 1.27e+00 6.20e-01 1.63e+01 angle pdb=" CA LEU A 73 " pdb=" CB LEU A 73 " pdb=" CG LEU A 73 " ideal model delta sigma weight residual 116.30 130.21 -13.91 3.50e+00 8.16e-02 1.58e+01 angle pdb=" N CYS A 498 " pdb=" CA CYS A 498 " pdb=" C CYS A 498 " ideal model delta sigma weight residual 110.06 104.49 5.57 1.43e+00 4.89e-01 1.52e+01 angle pdb=" C PHE C 497 " pdb=" N GLN C 498 " pdb=" CA GLN C 498 " ideal model delta sigma weight residual 122.48 116.77 5.71 1.62e+00 3.81e-01 1.24e+01 ... (remaining 9074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 3452 17.91 - 35.83: 402 35.83 - 53.74: 116 53.74 - 71.65: 28 71.65 - 89.56: 11 Dihedral angle restraints: 4009 sinusoidal: 1679 harmonic: 2330 Sorted by residual: dihedral pdb=" CA CYS A 141 " pdb=" C CYS A 141 " pdb=" N LEU A 142 " pdb=" CA LEU A 142 " ideal model delta harmonic sigma weight residual -180.00 -152.75 -27.25 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA LEU C 390 " pdb=" C LEU C 390 " pdb=" N CYS C 391 " pdb=" CA CYS C 391 " ideal model delta harmonic sigma weight residual -180.00 -154.18 -25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA VAL C 524 " pdb=" C VAL C 524 " pdb=" N CYS C 525 " pdb=" CA CYS C 525 " ideal model delta harmonic sigma weight residual -180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 4006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 679 0.052 - 0.104: 244 0.104 - 0.156: 38 0.156 - 0.209: 1 0.209 - 0.261: 2 Chirality restraints: 964 Sorted by residual: chirality pdb=" C1 NAG A 905 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 905 " pdb=" O5 NAG A 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C1 NAG A 906 " pdb=" ND2 ASN A 53 " pdb=" C2 NAG A 906 " pdb=" O5 NAG A 906 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA CYS C 432 " pdb=" N CYS C 432 " pdb=" C CYS C 432 " pdb=" CB CYS C 432 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 961 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 498 " -0.043 5.00e-02 4.00e+02 6.52e-02 6.80e+00 pdb=" N PRO C 499 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 499 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 499 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO A 235 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 498 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C CYS A 498 " 0.029 2.00e-02 2.50e+03 pdb=" O CYS A 498 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP A 499 " -0.010 2.00e-02 2.50e+03 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 102 2.51 - 3.11: 5149 3.11 - 3.71: 10900 3.71 - 4.30: 15977 4.30 - 4.90: 25314 Nonbonded interactions: 57442 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 1.918 2.230 nonbonded pdb=" O PHE A 327 " pdb=" OG SER A 331 " model vdw 2.007 2.440 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.043 2.440 nonbonded pdb=" O HOH A1022 " pdb=" O HOH A1034 " model vdw 2.069 2.440 nonbonded pdb=" O HOH A1011 " pdb=" O HOH A1052 " model vdw 2.100 2.440 ... (remaining 57437 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.190 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 26.930 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 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 0.066 6677 Z= 0.485 Angle : 0.863 13.914 9079 Z= 0.492 Chirality : 0.051 0.261 964 Planarity : 0.005 0.065 1173 Dihedral : 17.506 89.563 2494 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 6.03 % Allowed : 19.80 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.24), residues: 789 helix: -2.34 (0.19), residues: 393 sheet: -1.53 (0.62), residues: 58 loop : -1.91 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 48 HIS 0.006 0.002 HIS A 34 PHE 0.016 0.003 PHE A 285 TYR 0.021 0.002 TYR C 495 ARG 0.008 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 0.739 Fit side-chains REVERT: A 23 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6902 (mm-30) REVERT: A 30 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6469 (t0) REVERT: A 62 MET cc_start: 0.7554 (ttt) cc_final: 0.7204 (ttp) REVERT: A 68 LYS cc_start: 0.6424 (mtpp) cc_final: 0.6189 (tttm) REVERT: A 73 LEU cc_start: 0.5589 (OUTLIER) cc_final: 0.4740 (mt) REVERT: A 131 LYS cc_start: 0.7440 (ptpp) cc_final: 0.7196 (ptmm) REVERT: A 136 ASP cc_start: 0.3336 (OUTLIER) cc_final: 0.2870 (p0) REVERT: A 146 PRO cc_start: 0.6097 (Cg_endo) cc_final: 0.5814 (Cg_exo) REVERT: A 151 ILE cc_start: 0.6579 (mt) cc_final: 0.5640 (mp) REVERT: A 159 ASN cc_start: 0.6007 (m-40) cc_final: 0.5716 (m110) REVERT: A 249 MET cc_start: 0.5732 (ptt) cc_final: 0.5487 (ttp) REVERT: A 313 LYS cc_start: 0.6775 (ttmt) cc_final: 0.6532 (mtpp) REVERT: A 314 PHE cc_start: 0.7063 (t80) cc_final: 0.6496 (t80) REVERT: A 341 LYS cc_start: 0.6040 (tptt) cc_final: 0.5729 (tttm) REVERT: A 368 ASP cc_start: 0.7211 (t0) cc_final: 0.6560 (m-30) REVERT: A 401 HIS cc_start: 0.8637 (OUTLIER) cc_final: 0.8186 (m-70) REVERT: A 429 GLN cc_start: 0.5970 (OUTLIER) cc_final: 0.5184 (tm-30) REVERT: A 540 HIS cc_start: 0.7053 (p-80) cc_final: 0.6777 (p90) REVERT: A 600 LYS cc_start: 0.6515 (mtmt) cc_final: 0.6286 (mtmm) REVERT: C 356 LYS cc_start: 0.6965 (mptt) cc_final: 0.6707 (mtpp) REVERT: C 459 SER cc_start: 0.6597 (OUTLIER) cc_final: 0.6086 (p) REVERT: C 467 ASP cc_start: 0.5688 (t0) cc_final: 0.5427 (t0) REVERT: C 516 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.4887 (pp20) outliers start: 40 outliers final: 6 residues processed: 183 average time/residue: 1.2297 time to fit residues: 238.6783 Evaluate side-chains 106 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 516 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 117 ASN A 194 ASN A 239 HIS A 325 GLN A 442 GLN A 531 GLN A 535 HIS A 580 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6677 Z= 0.216 Angle : 0.629 8.519 9079 Z= 0.329 Chirality : 0.044 0.194 964 Planarity : 0.004 0.035 1173 Dihedral : 7.910 62.595 989 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.44 % Allowed : 25.39 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.01 (0.28), residues: 789 helix: -0.34 (0.24), residues: 398 sheet: -1.32 (0.70), residues: 47 loop : -0.81 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 353 HIS 0.005 0.001 HIS A 374 PHE 0.017 0.002 PHE A 588 TYR 0.014 0.002 TYR A 385 ARG 0.005 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 0.741 Fit side-chains REVERT: A 23 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6993 (mm-30) REVERT: A 131 LYS cc_start: 0.7713 (ptpp) cc_final: 0.7501 (ptmm) REVERT: A 151 ILE cc_start: 0.6126 (mt) cc_final: 0.5774 (mp) REVERT: A 179 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8083 (mt) REVERT: A 341 LYS cc_start: 0.5679 (tptt) cc_final: 0.5422 (tttm) REVERT: A 383 MET cc_start: 0.7619 (mtp) cc_final: 0.7289 (mtm) REVERT: A 476 LYS cc_start: 0.7550 (tppt) cc_final: 0.7279 (tppp) REVERT: A 597 ASP cc_start: 0.6118 (t0) cc_final: 0.5849 (t70) REVERT: C 354 ASN cc_start: 0.7367 (t0) cc_final: 0.7142 (t0) REVERT: C 356 LYS cc_start: 0.7077 (mptt) cc_final: 0.6657 (mtpp) outliers start: 22 outliers final: 4 residues processed: 124 average time/residue: 1.0268 time to fit residues: 134.9840 Evaluate side-chains 97 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 179 LEU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 0.0470 chunk 63 optimal weight: 0.0770 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6677 Z= 0.181 Angle : 0.583 9.977 9079 Z= 0.303 Chirality : 0.043 0.213 964 Planarity : 0.004 0.041 1173 Dihedral : 5.548 41.632 968 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.73 % Allowed : 26.11 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.05 (0.29), residues: 789 helix: 0.45 (0.25), residues: 399 sheet: -1.05 (0.67), residues: 49 loop : -0.31 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 594 HIS 0.012 0.001 HIS A 195 PHE 0.015 0.002 PHE C 486 TYR 0.019 0.002 TYR C 351 ARG 0.004 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.660 Fit side-chains REVERT: A 61 ASN cc_start: 0.7022 (t0) cc_final: 0.6803 (m-40) REVERT: A 82 MET cc_start: 0.5293 (mmt) cc_final: 0.5063 (tpp) REVERT: A 131 LYS cc_start: 0.7787 (ptpp) cc_final: 0.7330 (ptmm) REVERT: A 151 ILE cc_start: 0.6197 (mt) cc_final: 0.5832 (mp) REVERT: A 171 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6483 (mp0) REVERT: A 179 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8058 (mt) REVERT: A 297 MET cc_start: 0.6846 (mtm) cc_final: 0.6056 (mtt) REVERT: A 300 GLN cc_start: 0.5884 (mt0) cc_final: 0.5347 (tt0) REVERT: A 341 LYS cc_start: 0.5706 (tptt) cc_final: 0.5387 (tttm) REVERT: A 383 MET cc_start: 0.7443 (mtp) cc_final: 0.7178 (mtm) REVERT: A 476 LYS cc_start: 0.7543 (tppt) cc_final: 0.7319 (tppp) REVERT: C 354 ASN cc_start: 0.7334 (t0) cc_final: 0.7120 (t0) outliers start: 17 outliers final: 5 residues processed: 107 average time/residue: 1.0251 time to fit residues: 116.2738 Evaluate side-chains 95 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 491 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 37 optimal weight: 0.0170 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6677 Z= 0.179 Angle : 0.576 11.151 9079 Z= 0.298 Chirality : 0.043 0.221 964 Planarity : 0.004 0.039 1173 Dihedral : 4.898 38.364 968 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.73 % Allowed : 24.68 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.47 (0.29), residues: 789 helix: 0.87 (0.26), residues: 399 sheet: -0.46 (0.72), residues: 47 loop : -0.11 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.002 PHE C 486 TYR 0.020 0.001 TYR C 351 ARG 0.002 0.001 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 0.764 Fit side-chains REVERT: A 61 ASN cc_start: 0.7027 (t0) cc_final: 0.6826 (m-40) REVERT: A 82 MET cc_start: 0.5524 (mmt) cc_final: 0.5246 (mmm) REVERT: A 114 LYS cc_start: 0.7111 (ptmm) cc_final: 0.6302 (pttp) REVERT: A 121 ASN cc_start: 0.7115 (m-40) cc_final: 0.6338 (t0) REVERT: A 131 LYS cc_start: 0.7785 (ptpp) cc_final: 0.7379 (ptmm) REVERT: A 151 ILE cc_start: 0.6414 (mt) cc_final: 0.6028 (mp) REVERT: A 179 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8070 (mt) REVERT: A 300 GLN cc_start: 0.5984 (mt0) cc_final: 0.5450 (tt0) REVERT: A 341 LYS cc_start: 0.5839 (tptt) cc_final: 0.5467 (tttm) REVERT: A 383 MET cc_start: 0.7532 (mtp) cc_final: 0.7244 (mtm) REVERT: A 476 LYS cc_start: 0.7615 (tppt) cc_final: 0.7400 (tppp) REVERT: C 487 ASN cc_start: 0.5747 (OUTLIER) cc_final: 0.4985 (t0) outliers start: 24 outliers final: 6 residues processed: 111 average time/residue: 1.1874 time to fit residues: 139.3702 Evaluate side-chains 93 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain C residue 487 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.0040 chunk 64 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 535 HIS ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6677 Z= 0.217 Angle : 0.589 9.957 9079 Z= 0.303 Chirality : 0.044 0.183 964 Planarity : 0.004 0.038 1173 Dihedral : 4.946 37.048 968 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.30 % Allowed : 26.69 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.38 (0.29), residues: 789 helix: 0.81 (0.25), residues: 402 sheet: -0.38 (0.75), residues: 47 loop : -0.19 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 594 HIS 0.005 0.001 HIS A 540 PHE 0.017 0.002 PHE A 285 TYR 0.021 0.002 TYR C 351 ARG 0.003 0.001 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.744 Fit side-chains REVERT: A 61 ASN cc_start: 0.7075 (t0) cc_final: 0.6827 (m-40) REVERT: A 82 MET cc_start: 0.5497 (mmt) cc_final: 0.5243 (mmm) REVERT: A 121 ASN cc_start: 0.7176 (m-40) cc_final: 0.6364 (t0) REVERT: A 128 SER cc_start: 0.7871 (OUTLIER) cc_final: 0.7604 (p) REVERT: A 131 LYS cc_start: 0.7827 (ptpp) cc_final: 0.7416 (ptmm) REVERT: A 146 PRO cc_start: 0.7145 (Cg_endo) cc_final: 0.6648 (Cg_exo) REVERT: A 148 LEU cc_start: 0.6521 (mt) cc_final: 0.6136 (mt) REVERT: A 163 TRP cc_start: 0.7110 (t60) cc_final: 0.6755 (t60) REVERT: A 179 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8056 (mt) REVERT: A 210 ASN cc_start: 0.7817 (m-40) cc_final: 0.7570 (m110) REVERT: A 300 GLN cc_start: 0.6011 (mt0) cc_final: 0.5483 (tt0) REVERT: A 341 LYS cc_start: 0.5969 (tptt) cc_final: 0.5584 (tttm) REVERT: A 383 MET cc_start: 0.7588 (mtp) cc_final: 0.7251 (mtm) REVERT: C 487 ASN cc_start: 0.5836 (OUTLIER) cc_final: 0.5151 (t0) outliers start: 14 outliers final: 5 residues processed: 105 average time/residue: 1.0509 time to fit residues: 117.3340 Evaluate side-chains 93 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain C residue 487 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6677 Z= 0.224 Angle : 0.594 8.771 9079 Z= 0.305 Chirality : 0.043 0.142 964 Planarity : 0.004 0.036 1173 Dihedral : 4.845 36.214 968 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.87 % Allowed : 27.12 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.39 (0.29), residues: 789 helix: 0.84 (0.25), residues: 402 sheet: -0.28 (0.77), residues: 47 loop : -0.24 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 594 HIS 0.005 0.001 HIS A 241 PHE 0.012 0.002 PHE C 486 TYR 0.023 0.002 TYR C 351 ARG 0.003 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.748 Fit side-chains REVERT: A 61 ASN cc_start: 0.7066 (t0) cc_final: 0.6840 (m-40) REVERT: A 82 MET cc_start: 0.5371 (mmt) cc_final: 0.5131 (mmm) REVERT: A 128 SER cc_start: 0.7768 (OUTLIER) cc_final: 0.7522 (p) REVERT: A 131 LYS cc_start: 0.8073 (ptpp) cc_final: 0.7534 (ptmm) REVERT: A 146 PRO cc_start: 0.7199 (Cg_endo) cc_final: 0.6695 (Cg_exo) REVERT: A 159 ASN cc_start: 0.6588 (m-40) cc_final: 0.6084 (t0) REVERT: A 163 TRP cc_start: 0.7020 (t60) cc_final: 0.6757 (t60) REVERT: A 179 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8042 (mt) REVERT: A 249 MET cc_start: 0.6049 (mtp) cc_final: 0.5123 (OUTLIER) REVERT: A 300 GLN cc_start: 0.6099 (mt0) cc_final: 0.5456 (tt0) REVERT: A 341 LYS cc_start: 0.5962 (tptt) cc_final: 0.5596 (tttm) REVERT: A 383 MET cc_start: 0.7641 (mtp) cc_final: 0.7287 (mtm) REVERT: A 474 MET cc_start: 0.7824 (mmp) cc_final: 0.7178 (mmp) REVERT: A 476 LYS cc_start: 0.7614 (tppt) cc_final: 0.7370 (tppp) outliers start: 11 outliers final: 6 residues processed: 104 average time/residue: 1.3256 time to fit residues: 145.8494 Evaluate side-chains 94 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 128 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 491 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 0.0670 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6677 Z= 0.177 Angle : 0.558 7.806 9079 Z= 0.286 Chirality : 0.042 0.131 964 Planarity : 0.004 0.037 1173 Dihedral : 4.647 36.915 968 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.30 % Allowed : 27.26 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.62 (0.30), residues: 789 helix: 1.07 (0.26), residues: 399 sheet: -0.15 (0.79), residues: 46 loop : -0.18 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 594 HIS 0.005 0.001 HIS A 540 PHE 0.015 0.001 PHE A 588 TYR 0.027 0.001 TYR C 351 ARG 0.003 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.736 Fit side-chains REVERT: A 31 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7188 (tppt) REVERT: A 61 ASN cc_start: 0.7053 (t0) cc_final: 0.6845 (m-40) REVERT: A 82 MET cc_start: 0.5387 (mmt) cc_final: 0.5152 (mmm) REVERT: A 121 ASN cc_start: 0.7319 (m-40) cc_final: 0.6510 (t0) REVERT: A 131 LYS cc_start: 0.8015 (ptpp) cc_final: 0.7431 (ptmm) REVERT: A 146 PRO cc_start: 0.7142 (Cg_endo) cc_final: 0.6656 (Cg_exo) REVERT: A 159 ASN cc_start: 0.6692 (m-40) cc_final: 0.6123 (t0) REVERT: A 179 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8021 (mt) REVERT: A 249 MET cc_start: 0.6030 (mtp) cc_final: 0.5074 (ttp) REVERT: A 300 GLN cc_start: 0.6087 (mt0) cc_final: 0.5460 (tt0) REVERT: A 341 LYS cc_start: 0.6017 (tptt) cc_final: 0.5620 (tttm) REVERT: A 383 MET cc_start: 0.7565 (mtp) cc_final: 0.7249 (mtm) REVERT: A 474 MET cc_start: 0.7805 (mmp) cc_final: 0.7077 (mmp) REVERT: A 476 LYS cc_start: 0.7632 (tppt) cc_final: 0.7399 (tppp) REVERT: C 406 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7346 (mp0) outliers start: 14 outliers final: 5 residues processed: 97 average time/residue: 1.1737 time to fit residues: 120.2775 Evaluate side-chains 90 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 415 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.0070 overall best weight: 0.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6677 Z= 0.185 Angle : 0.562 7.471 9079 Z= 0.288 Chirality : 0.042 0.132 964 Planarity : 0.004 0.037 1173 Dihedral : 4.594 36.612 968 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.15 % Allowed : 27.40 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.69 (0.30), residues: 789 helix: 1.14 (0.26), residues: 399 sheet: -0.10 (0.84), residues: 45 loop : -0.15 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 594 HIS 0.005 0.001 HIS A 540 PHE 0.015 0.001 PHE A 588 TYR 0.025 0.002 TYR C 351 ARG 0.003 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.713 Fit side-chains REVERT: A 121 ASN cc_start: 0.7312 (m-40) cc_final: 0.6543 (t0) REVERT: A 131 LYS cc_start: 0.7978 (ptpp) cc_final: 0.7464 (ptmm) REVERT: A 146 PRO cc_start: 0.7253 (Cg_endo) cc_final: 0.6749 (Cg_exo) REVERT: A 159 ASN cc_start: 0.6880 (m-40) cc_final: 0.6371 (t0) REVERT: A 179 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7976 (mt) REVERT: A 249 MET cc_start: 0.6035 (mtp) cc_final: 0.5084 (ttp) REVERT: A 300 GLN cc_start: 0.6145 (mt0) cc_final: 0.5441 (tt0) REVERT: A 341 LYS cc_start: 0.6028 (tptt) cc_final: 0.5645 (tttm) REVERT: A 383 MET cc_start: 0.7583 (mtp) cc_final: 0.7254 (mtm) REVERT: A 470 LYS cc_start: 0.7806 (mtpt) cc_final: 0.7269 (ttmt) REVERT: A 474 MET cc_start: 0.7823 (mmp) cc_final: 0.7511 (mmp) REVERT: A 476 LYS cc_start: 0.7582 (tppt) cc_final: 0.7302 (tppp) REVERT: C 406 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7353 (mp0) outliers start: 13 outliers final: 7 residues processed: 93 average time/residue: 1.0696 time to fit residues: 105.3715 Evaluate side-chains 88 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 179 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain C residue 406 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6677 Z= 0.168 Angle : 0.557 7.635 9079 Z= 0.285 Chirality : 0.041 0.131 964 Planarity : 0.004 0.037 1173 Dihedral : 4.532 36.790 968 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.72 % Allowed : 27.69 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.78 (0.30), residues: 789 helix: 1.19 (0.26), residues: 399 sheet: -0.11 (0.84), residues: 45 loop : -0.09 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 594 HIS 0.005 0.001 HIS A 540 PHE 0.013 0.001 PHE A 588 TYR 0.028 0.001 TYR C 351 ARG 0.003 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.717 Fit side-chains REVERT: A 89 GLN cc_start: 0.6135 (mp10) cc_final: 0.5825 (mp10) REVERT: A 121 ASN cc_start: 0.7304 (m-40) cc_final: 0.6509 (t0) REVERT: A 131 LYS cc_start: 0.7951 (ptpp) cc_final: 0.7231 (ptmm) REVERT: A 146 PRO cc_start: 0.7262 (Cg_endo) cc_final: 0.6773 (Cg_exo) REVERT: A 159 ASN cc_start: 0.6891 (t0) cc_final: 0.6352 (t0) REVERT: A 179 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7984 (mt) REVERT: A 249 MET cc_start: 0.5987 (mtp) cc_final: 0.5065 (ttp) REVERT: A 300 GLN cc_start: 0.6096 (mt0) cc_final: 0.5384 (tt0) REVERT: A 341 LYS cc_start: 0.6060 (tptt) cc_final: 0.5636 (tttm) REVERT: A 383 MET cc_start: 0.7527 (mtp) cc_final: 0.7275 (mtm) REVERT: A 470 LYS cc_start: 0.7763 (mtpt) cc_final: 0.7259 (ttmt) REVERT: A 474 MET cc_start: 0.7679 (mmp) cc_final: 0.7196 (mmp) REVERT: C 406 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7265 (mp0) outliers start: 10 outliers final: 6 residues processed: 94 average time/residue: 1.0856 time to fit residues: 108.2342 Evaluate side-chains 90 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 49 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6677 Z= 0.197 Angle : 0.580 9.211 9079 Z= 0.295 Chirality : 0.042 0.150 964 Planarity : 0.004 0.035 1173 Dihedral : 4.582 36.308 968 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.58 % Allowed : 28.12 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.71 (0.30), residues: 789 helix: 1.10 (0.26), residues: 402 sheet: 0.03 (0.84), residues: 44 loop : -0.10 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 594 HIS 0.005 0.001 HIS A 540 PHE 0.016 0.002 PHE A 588 TYR 0.035 0.002 TYR C 351 ARG 0.003 0.001 ARG A 482 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.730 Fit side-chains REVERT: A 89 GLN cc_start: 0.6148 (mp10) cc_final: 0.5845 (mp10) REVERT: A 121 ASN cc_start: 0.7315 (m-40) cc_final: 0.6520 (t0) REVERT: A 131 LYS cc_start: 0.7957 (ptpp) cc_final: 0.7230 (ptmm) REVERT: A 146 PRO cc_start: 0.7262 (Cg_endo) cc_final: 0.6778 (Cg_exo) REVERT: A 159 ASN cc_start: 0.6951 (t0) cc_final: 0.6405 (t0) REVERT: A 179 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7965 (mt) REVERT: A 249 MET cc_start: 0.6036 (mtp) cc_final: 0.5096 (ttp) REVERT: A 300 GLN cc_start: 0.6212 (mt0) cc_final: 0.5541 (tt0) REVERT: A 341 LYS cc_start: 0.5989 (tptt) cc_final: 0.5602 (tttm) REVERT: A 383 MET cc_start: 0.7587 (mtp) cc_final: 0.7297 (mtm) REVERT: A 470 LYS cc_start: 0.7755 (mtpt) cc_final: 0.7278 (ttmt) REVERT: A 474 MET cc_start: 0.7767 (mmp) cc_final: 0.7327 (mmp) REVERT: C 406 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7299 (mp0) outliers start: 9 outliers final: 5 residues processed: 92 average time/residue: 1.1767 time to fit residues: 114.3505 Evaluate side-chains 89 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 179 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain C residue 406 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 0.0070 chunk 63 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.181200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.152546 restraints weight = 12090.485| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.12 r_work: 0.3587 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6677 Z= 0.163 Angle : 0.545 7.727 9079 Z= 0.280 Chirality : 0.042 0.131 964 Planarity : 0.004 0.037 1173 Dihedral : 4.473 36.320 968 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.72 % Allowed : 28.12 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.84 (0.30), residues: 789 helix: 1.23 (0.26), residues: 399 sheet: -0.16 (0.82), residues: 45 loop : -0.02 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 594 HIS 0.005 0.001 HIS A 540 PHE 0.013 0.001 PHE A 588 TYR 0.033 0.002 TYR C 351 ARG 0.003 0.000 ARG C 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2958.01 seconds wall clock time: 53 minutes 20.85 seconds (3200.85 seconds total)